id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17325	ChimeraX bug report submission	chimerax-bug-report@…		"{{{
The following bug report has been submitted:
Platform:        macOS-14.4-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000000020184bac0 (most recent call first):
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 124)


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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs""

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Log from Thu Mar 27 15:32:10 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/wujingyi/Desktop/figure/figure4/state1_Fo侧视atom+map.cxs

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.083, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Log from Tue Mar 18 21:19:53 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/wujingyi/Desktop/RfxATPase_figure/figure_5/Rfxatp_state1_hollow.cxs

Log from Mon Aug 12 10:58:14 2024 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2hollow.pdb""

> hide #1 models

> show #1 models

> select add #1

4431 atoms, 3493 bonds, 4431 residues, 1 model selected  

> show sel surfaces

> set bgColor white

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/state_1_Fo.pdb""

Chain information for state_1_Fo.pdb #2  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide sel atoms

[Repeated 2 time(s)]

> select add #2

15578 atoms, 14854 bonds, 2 pseudobonds, 5912 residues, 7 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #1

11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 6 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #2.13

10824 atoms, 11031 bonds, 2 pseudobonds, 1443 residues, 18 models selected  

> select add #2.13

11147 atoms, 11031 bonds, 2 pseudobonds, 1481 residues, 17 models selected  

> hide #2.13 models

> show #2.13 models

> select add #2

11147 atoms, 11361 bonds, 2 pseudobonds, 1481 residues, 18 models selected  

> select subtract #2

16 models selected  

> select add #2.13

323 atoms, 38 residues, 1 model selected  

> select add #2.16

629 atoms, 74 residues, 2 models selected  

> select subtract #2.16

323 atoms, 38 residues, 3 models selected  

> select add #2.14

629 atoms, 74 residues, 2 models selected  

> hide sel cartoons

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo.pdb""

Chain information for RfxATP_state_1_Fo.pdb #3  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide sel cartoons

> hide sel atoms

> select add #3

11776 atoms, 11365 bonds, 2 pseudobonds, 1555 residues, 5 models selected  

> select add #2

22294 atoms, 22726 bonds, 4 pseudobonds, 2962 residues, 6 models selected  

> hide sel atoms

> show sel cartoons

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #2

> show sel surfaces

> hide sel surfaces

> select subtract #3

16 models selected  

> select add #3.13

323 atoms, 38 residues, 1 model selected  

> select add #3.15

646 atoms, 76 residues, 2 models selected  

> hide sel cartoons

> select add #3.14

952 atoms, 112 residues, 3 models selected  

> select add #3.16

1258 atoms, 148 residues, 4 models selected  

> hide sel cartoons

> select add #3.2

1808 atoms, 224 residues, 5 models selected  

> select add #3.3

2331 atoms, 297 residues, 6 models selected  

> select add #3.4

2873 atoms, 372 residues, 7 models selected  

> select add #3.5

3415 atoms, 447 residues, 8 models selected  

> select add #3.6

3965 atoms, 523 residues, 9 models selected  

> select add #3.7

4507 atoms, 598 residues, 10 models selected  

> select add #3.8

5049 atoms, 673 residues, 11 models selected  

> select add #3.9

5599 atoms, 749 residues, 12 models selected  

> select add #3.10

6149 atoms, 825 residues, 13 models selected  

> select add #3.11

6683 atoms, 899 residues, 14 models selected  

> hide sel cartoons

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_inlet_hollow.pdb""

> select add #2

13913 atoms, 5473 bonds, 8129 residues, 16 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #3.2

13363 atoms, 5473 bonds, 8053 residues, 16 models selected  

> show sel surfaces

> hide sel surfaces

> select add #3

18377 atoms, 16838 bonds, 2 pseudobonds, 8711 residues, 16 models selected  

> select subtract #3

7230 atoms, 5473 bonds, 7230 residues, 17 models selected  

> show sel surfaces

> select subtract #2

4 models selected  

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> hide sel surfaces

> hide sel atoms

> select subtract #2

4 models selected  

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> show sel atoms

> select subtract #2

4 models selected  

> select add #2.1

1460 atoms, 1460 residues, 1 model selected  

> select add #2.2

5673 atoms, 5673 residues, 2 models selected  

> select add #2.3

7208 atoms, 7208 residues, 3 models selected  

> select add #2.4

7230 atoms, 7230 residues, 4 models selected  

> select subtract #2.4

7208 atoms, 7208 residues, 5 models selected  

> show sel cartoons

> show sel surfaces

> select add #2.4

7230 atoms, 7230 residues, 4 models selected  

> show sel surfaces

[Repeated 1 time(s)]

> hide sel surfaces

> show sel surfaces

> select subtract #2.4

7208 atoms, 7208 residues, 5 models selected  

> show sel surfaces

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 4 models selected  

> select subtract #2.4

7208 atoms, 5454 bonds, 7208 residues, 5 models selected  

> select add #2.4

7230 atoms, 5454 bonds, 7230 residues, 4 models selected  

> hide sel surfaces

> select subtract #2.4

7208 atoms, 5454 bonds, 7208 residues, 5 models selected  

> show sel surfaces

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 4 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #2.4

7208 atoms, 5454 bonds, 7208 residues, 5 models selected  

> show sel surfaces

> color #2.1 #87ceeb90

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 4 models selected  

> hide sel atoms

> color #2.1 #87ceeb82

> color #2.1 #87ceeb80

> color #2.2 #87ceeb80

> color #2.3 #87ceeb82

> color #2.3 #87ceeb80

> select subtract #2.4

7208 atoms, 5454 bonds, 7208 residues, 5 models selected  

> select subtract #2.3

5673 atoms, 4370 bonds, 5673 residues, 4 models selected  

> select subtract #2.2

1460 atoms, 1278 bonds, 1460 residues, 3 models selected  

> select subtract #2.1

1 model selected  

> hide #!3 models

> show #!3 models

> hide #!1 models

> select add #3.2

550 atoms, 76 residues, 1 model selected  

> select add #3.3

1073 atoms, 149 residues, 2 models selected  

> select add #3.4

1615 atoms, 224 residues, 3 models selected  

> select add #3.5

2157 atoms, 299 residues, 4 models selected  

> show sel cartoons

> hide sel cartoons

> select subtract #3.2

1607 atoms, 223 residues, 5 models selected  

> select subtract #3.3

1084 atoms, 150 residues, 4 models selected  

> select subtract #3.4

542 atoms, 75 residues, 3 models selected  

> select subtract #3.5

1 model selected  

> select add #3.6

550 atoms, 76 residues, 1 model selected  

> select add #3.7

1092 atoms, 151 residues, 2 models selected  

> select add #3.8

1634 atoms, 226 residues, 3 models selected  

> select add #3.9

2184 atoms, 302 residues, 4 models selected  

> select add #3.10

2734 atoms, 378 residues, 5 models selected  

> select add #3.11

3268 atoms, 452 residues, 6 models selected  

> select add #3.12

5500 atoms, 743 residues, 7 models selected  

> select subtract #3.12

3268 atoms, 452 residues, 8 models selected  

> show sel cartoons

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa1_outlet_hollow2.pdb""

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_intlet_hollow.pdb""

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/rfxa2_outlet_hollow.pdb""

> select add #1

7699 atoms, 3493 bonds, 4883 residues, 8 models selected  

> select add #3

15578 atoms, 14858 bonds, 2 pseudobonds, 5912 residues, 13 models selected  

> select subtract #3

4431 atoms, 3493 bonds, 4431 residues, 21 models selected  

> close #1

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 1 model selected  

> select add #5

12781 atoms, 9914 bonds, 12781 residues, 2 models selected  

> select add #4

19169 atoms, 14970 bonds, 19169 residues, 3 models selected  

> show sel surfaces

> select subtract #4

12781 atoms, 9914 bonds, 12781 residues, 13 models selected  

> select subtract #5

5690 atoms, 4616 bonds, 5690 residues, 8 models selected  

> select subtract #6

3 models selected  

> select add #5.4

860 atoms, 860 residues, 1 model selected  

> select add #5.3

4775 atoms, 4775 residues, 2 models selected  

> select add #5.2

7013 atoms, 7013 residues, 3 models selected  

> select subtract #5.2

4775 atoms, 4775 residues, 4 models selected  

> select add #5.1

4853 atoms, 4853 residues, 3 models selected  

> select subtract #5.1

4775 atoms, 4775 residues, 4 models selected  

> select subtract #5.3

860 atoms, 860 residues, 3 models selected  

> select subtract #5.4

1 model selected  

> select add #5.2

2238 atoms, 2238 residues, 1 model selected  

> select subtract #5.2

1 model selected  

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> show sel cartoons

> select subtract #3

16 models selected  

> select add #3.13

323 atoms, 38 residues, 1 model selected  

> select add #3.14

629 atoms, 74 residues, 2 models selected  

> select add #3.16

935 atoms, 110 residues, 3 models selected  

> select add #3.15

1258 atoms, 148 residues, 4 models selected  

> hide sel cartoons

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 11147 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> undo

[Repeated 5 time(s)]

> select add #3.16

306 atoms, 36 residues, 1 model selected  

> select add #3.15

629 atoms, 74 residues, 2 models selected  

> select add #3.14

935 atoms, 110 residues, 3 models selected  

> select add #3.13

1258 atoms, 148 residues, 4 models selected  

> hide sel cartoons

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 6 models selected  

> select subtract #3

16 models selected  

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> select add #6

12920 atoms, 10089 bonds, 12920 residues, 6 models selected  

> select add #5

20011 atoms, 15387 bonds, 20011 residues, 10 models selected  

> select add #4

26399 atoms, 20443 bonds, 26399 residues, 15 models selected  

> show sel surfaces

> select subtract #2

19169 atoms, 14970 bonds, 19169 residues, 18 models selected  

> select subtract #4

12781 atoms, 9914 bonds, 12781 residues, 13 models selected  

> select subtract #5

5690 atoms, 4616 bonds, 5690 residues, 8 models selected  

> select subtract #6

3 models selected  

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> cartoon style (#!3 & sel) modeHelix tube sides 20

> select subtract #3.1

11147 atoms, 11365 bonds, 1481 residues, 17 models selected  

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 18 models selected  

> select subtract #3

16 models selected  

> select add #3.2

550 atoms, 76 residues, 1 model selected  

> select add #3.3

1073 atoms, 149 residues, 2 models selected  

> select add #3.4

1615 atoms, 224 residues, 3 models selected  

> select add #3.5

2157 atoms, 299 residues, 4 models selected  

> select add #3.6

2707 atoms, 375 residues, 5 models selected  

> select add #3.7

3249 atoms, 450 residues, 6 models selected  

> select add #3.8

3791 atoms, 525 residues, 7 models selected  

> select add #3.9

4341 atoms, 601 residues, 8 models selected  

> select add #3.10

4891 atoms, 677 residues, 9 models selected  

> select add #3.11

5425 atoms, 751 residues, 10 models selected  

> color (#!3 & sel) #f5ccdcff

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected  

> select subtract #3

16 models selected  

> select add #3.12

2232 atoms, 291 residues, 1 model selected  

> select add #3.14

2538 atoms, 327 residues, 2 models selected  

> color (#!3 & sel) forest green

> select subtract #3.14

2232 atoms, 291 residues, 3 models selected  

> select add #3.17

4464 atoms, 582 residues, 2 models selected  

> color (#!3 & sel) forest green

> select subtract #3.17

2232 atoms, 291 residues, 3 models selected  

> select add #3.10

2782 atoms, 367 residues, 2 models selected  

> select add #3.9

3332 atoms, 443 residues, 3 models selected  

> select add #3.8

3874 atoms, 518 residues, 4 models selected  

> select add #3.7

4416 atoms, 593 residues, 5 models selected  

> select add #3.6

4966 atoms, 669 residues, 6 models selected  

> select add #3.5

5508 atoms, 744 residues, 7 models selected  

> select add #3.4

6050 atoms, 819 residues, 8 models selected  

> select add #3.3

6573 atoms, 892 residues, 9 models selected  

> select add #3.2

7123 atoms, 968 residues, 10 models selected  

> hide sel cartoons

> select add #3.11

7657 atoms, 1042 residues, 11 models selected  

> select subtract #3.12

5425 atoms, 751 residues, 12 models selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> select add #3.17

7657 atoms, 1042 residues, 11 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> hide sel cartoons

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 13 models selected  

> select subtract #3

16 models selected  

> select add #3.14

306 atoms, 36 residues, 1 model selected  

> select add #3.12

2538 atoms, 327 residues, 2 models selected  

> show sel cartoons

> select subtract #3.14

2232 atoms, 291 residues, 3 models selected  

> select add #3.17

4464 atoms, 582 residues, 2 models selected  

> show sel cartoons

> select add #3.14

4770 atoms, 618 residues, 3 models selected  

> select subtract #3.12

2538 atoms, 327 residues, 4 models selected  

> select subtract #3.17

306 atoms, 36 residues, 3 models selected  

> hide sel cartoons

> color #3.14 #917297ff

> select subtract #3.14

1 model selected  

> lighting soft

> select add #3.2

550 atoms, 76 residues, 1 model selected  

> select add #3.3

1073 atoms, 149 residues, 2 models selected  

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/H #3/L #3/O #3/P

Alignment identifier is 1  

> sequence chain #3/I

Alignment identifier is 3/I  

> sequence chain #3/J #3/K #3/M #3/N

Alignment identifier is 2  

> sequence chain #3/Q

Alignment identifier is 3/Q  

> select #3/Q:3-39,41-74

508 atoms, 515 bonds, 71 residues, 1 model selected  

> select #3/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color (#!3 & sel) byhetero

> select #3/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #3/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> color (#!3 & sel) byhetero

> select #3/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #3/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> color (#!3 & sel) byhetero

> select #3/H,L,O-P:3-39,41-74

2032 atoms, 2060 bonds, 284 residues, 1 model selected  

> ui mousemode right select

> select clear

Drag select of 6 residues  

> select clear

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/T #3/Z

Alignment identifier is 3  

> select #3/T,Z:259

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #3/T,Z:259

22 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 22 atom styles  

> color (#!3 & sel) byhetero

> select clear

Drag select of 9 atoms, 8 bonds  

> select clear

[Repeated 1 time(s)]

> select add #3.11

534 atoms, 74 residues, 1 model selected  

> select add #3.10

1084 atoms, 150 residues, 2 models selected  

> select subtract #3.11

550 atoms, 76 residues, 3 models selected  

> select subtract #3.10

1 model selected  

> select #3/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color (#!3 & sel) byhetero

> select clear

> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc

Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95,
shown at level 0.101, step 2, values float32  
Drag select of rfxa2_intlet_hollow.pdb_E SES surface, 208 of 3672 triangles,
rfxa2_intlet_hollow.pdb_F SES surface, 464 of 25208 triangles, 8 atoms, 8
bonds, 1 J276_003_volume_map_sharp.mrc  

> volume #1 step 1

> volume #1 level 0.2498

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 7 models selected  

> hide #!3 models

> hide #3.1 models

> hide #3.2 models

> show #3.1 models

> hide #!2 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> select clear

[Repeated 1 time(s)]

> close #1

> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc

Opened J276_003_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 0.95,
shown at level 0.101, step 2, values float32  

> volume zlip #1

Expected a density maps specifier or a keyword  

> volume #1 step 1

> volume #1 level 0.224

> volume zlip #1

Expected a density maps specifier or a keyword  

> volume zflip #1

Expected a density maps specifier or a keyword  

> volume flip #1

Opened J276_003_volume_map_sharp.mrc z flip as #7, grid size 400,400,400,
pixel 0.95, shown at step 1, values float32  

> save /Users/wujingyi/Downloads/RfxATP_state1_withoutADP_F1.mrc models #7

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb""

Chain information for RFXATPase_state1_2.98A-1.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
R | No description available  
S | No description available  
T Z | No description available  
U X | No description available  
V | No description available  
W | No description available  
Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select clear

> hide #!8 atoms

> show #!8 cartoons

> select add #7

2 models selected  
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 15 residues  

> ui mousemode right ""translate selected models""

> view matrix models
> #7,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591,#8,1,0,0,-1.2628,0,1,0,0.47837,0,0,1,-1.2591

> view matrix models
> #7,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779,#8,1,0,0,-1.7005,0,1,0,0.32181,0,0,1,0.34779

> view matrix models
> #7,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748,#8,1,0,0,-1.3832,0,1,0,1.3436,0,0,1,-6.5748

> ui mousemode right select

Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 9 residues  

> select subtract #7

69 atoms, 9 residues, 1 model selected  

> select add #7

69 atoms, 9 residues, 3 models selected  

> select subtract #7

69 atoms, 9 residues, 1 model selected  

> select add #8

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 3 residues  
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 24 residues  

> select #8/X:110

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #8

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  

> ui mousemode right ""rotate selected models""

> ui mousemode right ""translate selected models""

> view matrix models #8,1,0,0,-1.6308,0,1,0,1.9901,0,0,1,-10.325

> view matrix models #8,1,0,0,17.812,0,1,0,-0.57249,0,0,1,-3.5122

> view matrix models #8,1,0,0,8.9735,0,1,0,15.372,0,0,1,-18.231

> view matrix models #8,1,0,0,6.1384,0,1,0,40.464,0,0,1,-18.769

> view matrix models #8,1,0,0,0.28461,0,1,0,11.462,0,0,1,-11.994

> ui mousemode right select

> select clear

> volume #7 level 0.1787

Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 18 residues  

> select clear

> select add #8

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.90579,0.37073,-0.20519,328.38,-0.30373,-0.90572,-0.29566,478.69,-0.29545,-0.20548,0.933,94.403

> view matrix models
> #8,-0.96264,0.27066,0.0076537,318.46,-0.26006,-0.91632,-0.3045,474.07,-0.075404,-0.29512,0.95248,66.029

> view matrix models
> #8,-0.92958,-0.23864,0.28095,356.73,0.29128,-0.94264,0.16308,288.68,0.22591,0.23343,0.94577,-88.104

> view matrix models
> #8,-0.84595,0.16919,0.50571,223.41,-0.021766,-0.9585,0.28426,328.28,0.53282,0.22946,0.81452,-121

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.84595,0.16919,0.50571,235.2,-0.021766,-0.9585,0.28426,367.87,0.53282,0.22946,0.81452,-65.315

> view matrix models
> #8,-0.84595,0.16919,0.50571,220.58,-0.021766,-0.9585,0.28426,321.34,0.53282,0.22946,0.81452,-116.96

> view matrix models
> #8,-0.84595,0.16919,0.50571,221.54,-0.021766,-0.9585,0.28426,322.24,0.53282,0.22946,0.81452,-114.19

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.83579,0.078648,0.54339,229.55,-0.07592,-0.99673,0.027491,386.99,0.54378,-0.018278,0.83903,-74.584

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.83579,0.078648,0.54339,222.57,-0.07592,-0.99673,0.027491,390.28,0.54378,-0.018278,0.83903,-87.165

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,-0.91118,0.13459,0.38941,254.79,-0.039499,-0.96932,0.2426,338.58,0.41011,0.20567,0.88854,-112.87

> view matrix models
> #8,-0.97717,-0.025638,0.21089,330.07,0.044447,-0.99539,0.084934,356.72,0.20775,0.092368,0.97381,-69.326

> ui mousemode right ""translate selected models""

> view matrix models
> #8,-0.97717,-0.025638,0.21089,338.54,0.044447,-0.99539,0.084934,351.74,0.20775,0.092368,0.97381,-56.344

> ui mousemode right ""rotate selected models""

> view matrix models
> #8,0.87329,0.37091,0.31591,-103.7,-0.46999,0.81218,0.34565,63.53,-0.12837,-0.45033,0.88359,124.89

> view matrix models
> #8,0.87251,0.34682,0.34414,-104.27,-0.46902,0.79188,0.39108,58.745,-0.13689,-0.50263,0.85359,141.79

> ui mousemode right ""translate selected models""

> view matrix models
> #8,0.87251,0.34682,0.34414,-88.442,-0.46902,0.79188,0.39108,76.727,-0.13689,-0.50263,0.85359,134.61

> select add #7

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected  

> view matrix models
> #7,1,0,0,-6.297,0,1,0,-4.732,0,0,1,-10.051,#8,0.87251,0.34682,0.34414,-93.356,-0.46902,0.79188,0.39108,70.651,-0.13689,-0.50263,0.85359,131.13

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.99677,-0.0017702,0.080268,-20.213,-0.0060842,0.99522,0.097502,-20.723,-0.080056,-0.097676,0.99199,25.283,#8,0.85954,0.30395,0.41086,-95.792,-0.48544,0.73697,0.47034,68.595,-0.15983,-0.60372,0.78101,164.94

> select subtract #8

2 models selected  

> view matrix models
> #7,0.95476,-0.047178,0.29362,-43.084,-0.0629,0.93296,0.35444,-45.638,-0.29066,-0.35687,0.88778,134.06

> view matrix models
> #7,-0.88421,-0.21366,0.41537,319.19,0.41454,-0.76875,0.48701,159.82,0.21526,0.60281,0.7683,-122.46

> ui mousemode right ""translate selected models""

> view matrix models
> #7,-0.88421,-0.21366,0.41537,329.35,0.41454,-0.76875,0.48701,172.07,0.21526,0.60281,0.7683,-126.96

> view matrix models
> #7,-0.88421,-0.21366,0.41537,332.67,0.41454,-0.76875,0.48701,178.44,0.21526,0.60281,0.7683,-131.73

> view matrix models
> #7,-0.88421,-0.21366,0.41537,331.46,0.41454,-0.76875,0.48701,179.89,0.21526,0.60281,0.7683,-135.36

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.94832,0.25093,0.19421,-67.519,-0.30926,0.86791,0.38872,27.724,-0.071014,-0.42869,0.90066,90.153

> view matrix models
> #7,0.70521,0.58704,0.39757,-122.03,-0.69527,0.68242,0.22562,167.18,-0.13886,-0.43553,0.8894,106.57

> view matrix models
> #7,0.82451,0.45778,0.33259,-108.48,-0.56304,0.72221,0.40175,101.62,-0.056283,-0.51851,0.85322,113.1

> view matrix models
> #7,0.82328,0.52176,0.22356,-100.14,-0.5672,0.77161,0.28794,114.17,-0.022268,-0.36385,0.93119,62.872

> view matrix models
> #7,0.67235,0.54008,0.50622,-126.97,-0.70093,0.68439,0.20079,172.5,-0.23801,-0.48982,0.83871,145.28

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.67235,0.54008,0.50622,-119.87,-0.70093,0.68439,0.20079,159.37,-0.23801,-0.48982,0.83871,140.99

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.69879,0.54006,0.46907,-118.06,-0.69186,0.67684,0.25141,149.67,-0.18171,-0.50022,0.84662,130.67

> view matrix models
> #7,0.83451,0.45787,0.30652,-98.483,-0.50917,0.85342,0.11141,107.12,-0.21058,-0.24905,0.94532,70.441

> view matrix models
> #7,0.89321,0.41571,0.17135,-76.748,-0.44856,0.85022,0.27554,65.671,-0.031139,-0.32297,0.9459,49.832

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.85265,0.28815,0.43585,-93.839,-0.38349,0.91169,0.14749,65.269,-0.35486,-0.2929,0.88785,117.1

> ui tool show ""Fit in Map""

> fitmap #8 inMap #7

Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms  
average map value = 0.0361, steps = 248  
shifted from previous position = 3.32  
rotated from previous position = 3.59 degrees  
atoms outside contour = 36794, contour level = 0.17874  
  
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:  
Matrix rotation and translation  
0.97702481 0.20658623 -0.05238958 -29.62036884  
-0.18232674 0.93747643 0.29647078 -1.24036171  
0.11036078 -0.28010728 0.95360391 47.42560830  
Axis -0.80722577 -0.22785516 -0.54448928  
Axis point 0.00000000 159.66635676 39.10884363  
Rotation angle (degrees) 20.92438479  
Shift along axis -1.62978743  
  

> volume #7 level 0.3325

> volume #7 level 0.191

> surface dust #7 size 9.5

> volume #7 level 0.08035

> surface dust #7 size 9.5

[Repeated 1 time(s)]

> volume #7 level 0.0503

> volume #7 level 0.103

> ui mousemode right select

> select clear

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> surface dust #7 size 9.5

> show #!8 models

> select add #8

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  
Drag select of 7 RfxATP_state1_withoutADP_F1.mrc , 60 residues  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.81858,0.56012,0.12724,-82.604,-0.57128,0.81694,0.079034,132.39,-0.059679,-0.13738,0.98872,13.357,#8,0.7117,0.65856,0.24451,-101.51,-0.69838,0.62571,0.3475,152.04,0.075857,-0.41807,0.90524,62.186

> select subtract #7

471 atoms, 60 residues, 1 model selected  

> view matrix models
> #8,-0.66704,-0.73627,0.11385,442.68,0.72058,-0.6764,-0.15248,219.63,0.18927,-0.019677,0.98173,-47.612

> select add #8

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  

> select add #7

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 4 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.81858,0.56012,0.12724,-107.08,-0.57128,0.81694,0.079034,119.88,-0.059679,-0.13738,0.98872,13.446,#8,-0.66704,-0.73627,0.11385,418.2,0.72058,-0.6764,-0.15248,207.12,0.18927,-0.019677,0.98173,-47.523

> select subtract #8

2 models selected  

> select subtract #7

Nothing selected  

> select add #8

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  

> view matrix models
> #8,-0.66704,-0.73627,0.11385,415.23,0.72058,-0.6764,-0.15248,205.72,0.18927,-0.019677,0.98173,-48.196

> view matrix models
> #8,-0.66704,-0.73627,0.11385,414.92,0.72058,-0.6764,-0.15248,206.56,0.18927,-0.019677,0.98173,-49.48

> view matrix models
> #8,-0.66704,-0.73627,0.11385,413.85,0.72058,-0.6764,-0.15248,208.31,0.18927,-0.019677,0.98173,-47.84

> select subtract #8

Nothing selected  

> select add #7

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.82946,0.54181,0.1358,-107.14,-0.55482,0.8273,0.088006,113.07,-0.064669,-0.14834,0.98682,16.887

> view matrix models
> #7,0.82794,0.53632,0.16394,-110.95,-0.54873,0.83508,0.03928,119.35,-0.11584,-0.12248,0.98569,21.764

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.82794,0.53632,0.16394,-116.9,-0.54873,0.83508,0.03928,129.66,-0.11584,-0.12248,0.98569,21.897

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.80067,0.55879,0.21605,-125.69,-0.57153,0.82057,-0.0042587,144.83,-0.17966,-0.12007,0.97637,35.272

> view matrix models
> #7,0.81894,0.56477,0.1019,-109.35,-0.54936,0.82283,-0.14542,166.11,-0.16597,0.063107,0.98411,-4.5857

> select subtract #7

Nothing selected  

> hide #!7 models

> show #!7 models

> fitmap #8 inMap #7

Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms  
average map value = 0.04304, steps = 80  
shifted from previous position = 1.27  
rotated from previous position = 1.72 degrees  
atoms outside contour = 33294, contour level = 0.103  
  
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:  
Matrix rotation and translation  
-0.97766050 -0.21015754 0.00371096 411.17643737  
0.21004182 -0.97748108 -0.02032708 335.92463186  
0.00789929 -0.01909353 0.99978651 8.97038534  
Axis 0.00293548 -0.00996693 0.99994602  
Axis point 187.72593879 189.84909480 0.00000000  
Rotation angle (degrees) 167.87114146  
Shift along axis 6.82876360  
  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/Rfx ATPase ADP map/Rfx ATPase overall
> map/J68_10.48w_2.89A_volumeZ_map.mrc.mrc""

Opened J68_10.48w_2.89A_volumeZ_map.mrc.mrc as #9, grid size 400,400,400,
pixel 0.93, shown at level 0.0643, step 2, values float32  

> select add #9

2 models selected  

> view matrix models
> #9,0.94781,0.29555,0.11964,-65.963,-0.30155,0.9528,0.035199,59.073,-0.10359,-0.069439,0.99219,33.644

> view matrix models
> #9,-0.16235,-0.98146,-0.10184,417.29,0.97581,-0.14439,-0.16413,56.511,0.14638,-0.12602,0.98117,-0.95683

> view matrix models
> #9,-0.64648,-0.75883,0.079063,434.97,0.74348,-0.64985,-0.15787,192.08,0.17118,-0.04328,0.98429,-21.402

> hide #!7 models

> view matrix models
> #9,-0.63471,-0.72188,0.27572,390.81,0.71277,-0.68474,-0.15195,203.21,0.29849,0.10008,0.94915,-65.43

> ui mousemode right ""translate selected models""

> view matrix models
> #9,-0.63471,-0.72188,0.27572,444.16,0.71277,-0.68474,-0.15195,299.14,0.29849,0.10008,0.94915,-102.44

> view matrix models
> #9,-0.63471,-0.72188,0.27572,377.16,0.71277,-0.68474,-0.15195,204.9,0.29849,0.10008,0.94915,-87.29

> view matrix models
> #9,-0.63471,-0.72188,0.27572,380.26,0.71277,-0.68474,-0.15195,209.91,0.29849,0.10008,0.94915,-89.722

> ui mousemode right ""rotate selected models""

> view matrix models
> #9,-0.81475,-0.54434,0.19968,395.03,0.53788,-0.83818,-0.09021,259.98,0.21648,0.033908,0.9757,-66.876

> view matrix models
> #9,-0.81553,-0.55997,0.14609,407.63,0.53884,-0.82683,-0.16124,270.41,0.21109,-0.052776,0.97604,-49.973

> view matrix models
> #9,-0.72178,-0.67644,0.14653,411.36,0.64266,-0.7336,-0.22095,244.41,0.25695,-0.065305,0.96421,-54.174

> view matrix models
> #9,-0.70922,-0.70009,0.082935,424.72,0.68767,-0.71291,-0.1374,217.21,0.15532,-0.040416,0.98704,-43.731

> ui mousemode right ""translate selected models""

> view matrix models
> #9,-0.70922,-0.70009,0.082935,420.42,0.68767,-0.71291,-0.1374,222.59,0.15532,-0.040416,0.98704,-41.757

> show #!7 models

> select subtract #9

Nothing selected  

> select add #7

2 models selected  

> view matrix models
> #7,0.81894,0.56477,0.1019,-109.07,-0.54936,0.82283,-0.14542,166.67,-0.16597,0.063107,0.98411,-8.6208

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.82136,0.57001,0.021207,-95.736,-0.56458,0.81772,-0.11217,164.45,-0.081282,0.080162,0.99346,-29.777

> view matrix models
> #7,-0.8497,-0.52724,0.0058055,439.44,0.52217,-0.84296,-0.12945,285.87,0.073144,-0.10696,0.99157,-22.184

> select subtract #7

Nothing selected  

> hide #!9 models

> select add #7

2 models selected  

> view matrix models
> #7,-0.83572,-0.53982,0.10088,421.78,0.53709,-0.84174,-0.054778,269.08,0.11449,0.0084053,0.99339,-52.947

> ui mousemode right ""translate selected models""

> view matrix models
> #7,-0.83572,-0.53982,0.10088,417.08,0.53709,-0.84174,-0.054778,262.64,0.11449,0.0084053,0.99339,-42.059

> select subtract #7

Nothing selected  

> fitmap #8 inMap #7

Fit molecule RFXATPase_state1_2.98A-1.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#7) using 41723 atoms  
average map value = 0.04408, steps = 112  
shifted from previous position = 3.13  
rotated from previous position = 2.25 degrees  
atoms outside contour = 33470, contour level = 0.103  
  
Position of RFXATPase_state1_2.98A-1.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#7) coordinates:  
Matrix rotation and translation  
0.97622445 0.21492117 -0.02819088 -26.72514574  
-0.21024437 0.97048116 0.11816781 32.35392173  
0.05275548 -0.10943133 0.99259340 14.03890220  
Axis -0.46543944 -0.16553502 -0.86946207  
Axis point 128.83594929 149.69566655 0.00000000  
Rotation angle (degrees) 14.15223914  
Shift along axis -5.12306287  
  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase
> 相关/RfxATPaseRefine/RealSpaceRefine_17/RealSpaceRefine_3/RFXATP_state3_2.98A.pdb""

Chain information for RFXATP_state3_2.98A.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J K L M N O P | No description available  
I | No description available  
Q | No description available  
R | No description available  
S | No description available  
T Z | No description available  
U X | No description available  
V | No description available  
W | No description available  
Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!8,10 atoms

> show #!8,10 cartoons

> select add #10

41664 atoms, 42310 bonds, 2 pseudobonds, 5415 residues, 2 models selected  

> view matrix models #10,1,0,0,-10.589,0,1,0,-7.4647,0,0,1,-9.3559

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,0.76052,0.64884,0.024792,-93.638,-0.62796,0.74469,-0.22605,199.08,-0.16514,0.15635,0.9738,-3.506

> ui mousemode right ""translate selected models""

> view matrix models
> #10,0.76052,0.64884,0.024792,-86.508,-0.62796,0.74469,-0.22605,209.64,-0.16514,0.15635,0.9738,-11.296

> close #10

> select add #7

2 models selected  

> view matrix models
> #7,-0.83572,-0.53982,0.10088,415.05,0.53709,-0.84174,-0.054778,260.68,0.11449,0.0084053,0.99339,-39.287

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.95714,0.16723,0.23649,-89.037,-0.1543,0.98537,-0.072306,37.936,-0.24512,0.032717,0.96894,28.818

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.95714,0.16723,0.23649,-87.29,-0.1543,0.98537,-0.072306,40.751,-0.24512,0.032717,0.96894,27.221

> view matrix models
> #7,0.95714,0.16723,0.23649,-86.543,-0.1543,0.98537,-0.072306,42.25,-0.24512,0.032717,0.96894,24.956

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.92321,0.37982,0.058404,-88.959,-0.38192,0.92371,0.029897,78.808,-0.042593,-0.049907,0.99785,-2.6972

> view matrix models
> #7,0.91969,0.39205,-0.021748,-75.952,-0.39242,0.91582,-0.085316,103.52,-0.01353,0.086998,0.99612,-34.686

> view matrix models
> #7,0.92247,0.38437,0.036047,-85.6,-0.38453,0.92311,-0.0026085,85.396,-0.034278,-0.011455,0.99935,-12.076

> view matrix models
> #7,0.76202,0.644,0.067666,-111.69,-0.64537,0.76387,-0.002207,166.06,-0.053109,-0.041988,0.99771,-2.2214

> view matrix models
> #7,0.65427,0.75569,0.029352,-106.02,-0.75604,0.65266,0.049297,199.4,0.018097,-0.054445,0.99835,-13.441

> view matrix models
> #7,0.95204,-0.28314,-0.11602,67.299,0.24823,0.93635,-0.24825,7.6394,0.17892,0.20754,0.96172,-88.537

> view matrix models
> #7,0.94298,-0.2658,-0.20036,81.127,0.22255,0.95108,-0.21431,3.4041,0.24752,0.1575,0.956,-90.737

> view matrix models
> #7,0.96073,-0.23679,-0.14467,61.843,0.22866,0.97094,-0.070685,-28.033,0.1572,0.034829,0.98695,-55.257

> view matrix models
> #7,0.9619,0.21075,-0.17416,-20.507,-0.22712,0.97058,-0.079934,60.391,0.15219,0.11644,0.98147,-69.263

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.9619,0.21075,-0.17416,-18.141,-0.22712,0.97058,-0.079934,65.506,0.15219,0.11644,0.98147,-70.438

> view matrix models
> #7,0.9619,0.21075,-0.17416,-9.0196,-0.22712,0.97058,-0.079934,60.113,0.15219,0.11644,0.98147,-77.849

> view matrix models
> #7,0.9619,0.21075,-0.17416,-3.0965,-0.22712,0.97058,-0.079934,65.362,0.15219,0.11644,0.98147,-75.215

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.93248,0.31906,-0.16934,-19.577,-0.3338,0.9403,-0.066405,89.08,0.13804,0.11845,0.98332,-73.257

> view matrix models
> #7,0.9156,0.31072,-0.2552,1.0399,-0.34905,0.92927,-0.1209,104.15,0.19958,0.19978,0.9593,-96.453

> view matrix models
> #7,0.91676,0.39096,-0.081908,-46.718,-0.38877,0.92039,0.041794,83.547,0.091726,-0.0064719,0.99576,-42.301

> view matrix models
> #7,0.91372,0.37945,-0.14535,-32.232,-0.35999,0.92185,0.14354,59.093,0.18846,-0.078833,0.97891,-43.441

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.91372,0.37945,-0.14535,-43.381,-0.35999,0.92185,0.14354,51.397,0.18846,-0.078833,0.97891,-38.445

> view matrix models
> #7,0.91372,0.37945,-0.14535,-74.107,-0.35999,0.92185,0.14354,94.41,0.18846,-0.078833,0.97891,-33.917

> view matrix models
> #7,0.91372,0.37945,-0.14535,-48.806,-0.35999,0.92185,0.14354,-0.85681,0.18846,-0.078833,0.97891,-44.749

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.93287,0.35507,-0.060677,-63.236,-0.36003,0.91353,-0.18932,61.939,-0.011792,0.19845,0.98004,-61.127

> view matrix models
> #7,0.59552,0.72577,-0.34442,-19.476,-0.76545,0.64276,0.030941,151.52,0.24383,0.24521,0.93831,-111.2

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.59552,0.72577,-0.34442,-49.852,-0.76545,0.64276,0.030941,124.52,0.24383,0.24521,0.93831,-101.83

> view matrix models
> #7,0.59552,0.72577,-0.34442,-60.128,-0.76545,0.64276,0.030941,116.16,0.24383,0.24521,0.93831,-94.184

> close #9

> close #8

> close #1

> close #7

> open /Users/wujingyi/Downloads/RfxATP_state1_withoutADP_F1.mrc

Opened RfxATP_state1_withoutADP_F1.mrc as #1, grid size 400,400,400, pixel
0.95, shown at level 0.101, step 2, values float32  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb""

Chain information for RFXATPase_state1_2.98A-1.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
R | No description available  
S | No description available  
T Z | No description available  
U X | No description available  
V | No description available  
W | No description available  
Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!7 atoms

> show #!7 cartoons

> surface dust #1 size 9.5

> fitmap #7 inMap #1

Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41723 atoms  
average map value = 0.04077, steps = 136  
shifted from previous position = 4.02  
rotated from previous position = 3.84 degrees  
atoms outside contour = 34651, contour level = 0.10124  
  
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99804835 -0.05934006 -0.01944861 16.74869891  
0.05979253 0.99793245 0.02357275 -13.35557001  
0.01800960 -0.02468963 0.99953293 4.36796433  
Axis -0.36047882 -0.27978089 0.88981890  
Axis point 225.78118362 284.45693547 0.00000000  
Rotation angle (degrees) 3.83836701  
Shift along axis 1.58577930  
  

> volume #1 color #b2b2b24d

> volume #1 color #b2b2b227

> volume #1 color #b22eb227

> volume #1 color #ff80b227

> volume #1 color #ff80b226

> select add #7

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,0.98144,0.18462,0.051915,-38.788,-0.18689,0.98144,0.043017,32.642,-0.04301,-0.051921,0.99772,21.285

> view matrix models
> #7,0.97737,0.20827,-0.037143,-25.986,-0.20456,0.97514,0.085249,29.35,0.053975,-0.075722,0.99567,7.8166

> view matrix models
> #7,0.3135,0.89632,0.31357,-93.877,-0.94688,0.31999,0.032003,301.32,-0.071653,-0.30695,0.94903,83.234

> view matrix models
> #7,0.27847,0.948,0.1541,-67.461,-0.95389,0.25426,0.15953,291.34,0.11206,-0.19141,0.97509,22.238

> view matrix models
> #7,-0.89188,-0.12145,0.43567,300.64,-0.070548,-0.91412,-0.39926,445.84,0.44674,-0.38683,0.80671,26.663

> view matrix models
> #7,-0.97781,-0.1101,0.17823,362.26,0.097028,-0.99202,-0.080488,369.91,0.18567,-0.061408,0.98069,-16.918

> ui mousemode right ""translate selected models""

> view matrix models
> #7,-0.97781,-0.1101,0.17823,369.79,0.097028,-0.99202,-0.080488,367.47,0.18567,-0.061408,0.98069,-16.517

> ui mousemode right ""rotate selected models""

> view matrix models
> #7,-0.95046,-0.2701,0.15386,398.97,0.25491,-0.96051,-0.11154,337.56,0.17791,-0.066792,0.98178,-14.251

> ui mousemode right ""translate selected models""

> view matrix models
> #7,-0.95046,-0.2701,0.15386,397.21,0.25491,-0.96051,-0.11154,335.28,0.17791,-0.066792,0.98178,-14.171

> select subtract #7

Nothing selected  

> fitmap #7 inMap #1

Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41723 atoms  
average map value = 0.04023, steps = 80  
shifted from previous position = 2.74  
rotated from previous position = 1.81 degrees  
atoms outside contour = 34774, contour level = 0.10124  
  
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.94648353 -0.29356976 0.13411086 404.06536557  
0.27833502 -0.95279058 -0.12132491 329.83743239  
0.16339689 -0.07750428 0.98351133 -12.14291093  
Axis 0.07629892 -0.05099179 0.99578025  
Axis point 178.19941142 194.35490456 0.00000000  
Rotation angle (degrees) 163.31174632  
Shift along axis 1.91907946  
  

> select add #1

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.99784,0.031519,-0.057702,3.7445,-0.041622,0.98218,-0.18327,41.551,0.050897,0.18527,0.98137,-42.827

> view matrix models
> #1,0.99784,0.031523,-0.057713,3.7455,-0.04163,0.98218,-0.1833,41.559,0.050906,0.18531,0.98136,-42.834

> view matrix models
> #1,0.99858,0.026368,-0.046311,2.7359,-0.033003,0.9883,-0.14892,33.065,0.041843,0.15024,0.98776,-35.309

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.99858,0.026368,-0.046311,26.097,-0.033003,0.9883,-0.14892,38.648,0.041843,0.15024,0.98776,-34.996

> view matrix models
> #1,0.99858,0.026368,-0.046311,25.542,-0.033003,0.9883,-0.14892,29.187,0.041843,0.15024,0.98776,-37.84

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.99824,0.026046,-0.053332,26.825,-0.033706,0.98839,-0.14818,29.182,0.048853,0.14972,0.98752,-39.032

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.99824,0.026046,-0.053332,8.1344,-0.033706,0.98839,-0.14818,30.937,0.048853,0.14972,0.98752,-37.661

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.97824,0.040182,0.20356,-33.084,-0.0047157,0.98512,-0.17179,29.942,-0.20744,0.16709,0.96387,11.601

> fitmap #7 inMap #1

Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41723 atoms  
average map value = 0.04286, steps = 136  
shifted from previous position = 3.45  
rotated from previous position = 1.82 degrees  
atoms outside contour = 34360, contour level = 0.10124  
  
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96674099 -0.23994963 -0.08852139 428.37710337  
0.23665701 -0.97049707 0.04613999 318.95845950  
-0.09698103 0.02365621 0.99500506 17.97471156  
Axis -0.04711490 0.01772721 0.99873216  
Axis point 195.28656125 185.29015588 0.00000000  
Rotation angle (degrees) 166.19572999  
Shift along axis 3.42322358  
  

> ui mousemode right select

> select clear

[Repeated 1 time(s)]

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase
> 相关/RfxATPaseRefine/RealSpaceRefine_17/RealSpaceRefine_2/RFXATP_state2_3.02A.pdb""

Chain information for RFXATP_state2_3.02A.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H I | No description available  
J K | No description available  
L | No description available  
M N O P Q | No description available  
R | No description available  
S | No description available  
T Z | No description available  
U X | No description available  
V | No description available  
W | No description available  
Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase
> 相关/RfxATPaseRefine/RealSpaceRefine_17/RealSpaceRefine_3/RFXATP_state3_2.98A.pdb""

Chain information for RFXATP_state3_2.98A.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J K L M N O P | No description available  
I | No description available  
Q | No description available  
R | No description available  
S | No description available  
T Z | No description available  
U X | No description available  
V | No description available  
W | No description available  
Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!7-9 atoms

> show #!7-9 cartoons

> hide #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> select add #1

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.97037,-0.23901,0.035515,419.91,0.23572,-0.96865,-0.078444,350.65,0.053151,-0.067748,0.99629,2.5777

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.97037,-0.23901,0.035515,416.59,0.23572,-0.96865,-0.078444,339.72,0.053151,-0.067748,0.99629,-1.2446

> hide #!9 models

> show #!8 models

> view matrix models
> #1,-0.97037,-0.23901,0.035515,345.96,0.23572,-0.96865,-0.078444,363.39,0.053151,-0.067748,0.99629,-2.3113

> ui mousemode right ""translate selected atoms""

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.92075,-0.19413,0.33842,-72.485,0.27823,0.9348,-0.22076,6.7297,-0.2735,0.29743,0.91473,1.8952

> view matrix models
> #1,0.13093,0.98898,0.069111,-109.1,-0.90483,0.1477,-0.39932,415.04,-0.40513,-0.010249,0.9142,87.158

> view matrix models
> #1,-0.23986,0.9708,0.004384,-24.349,-0.96326,-0.23743,-0.12553,456.38,-0.12082,-0.034331,0.99208,24.953

> view matrix models
> #1,-0.21234,0.97717,-0.0064039,-29.056,-0.96114,-0.21003,-0.17918,459.45,-0.17643,-0.031892,0.9838,36.422

> view matrix models
> #1,-0.1936,0.97382,-0.11911,-13.426,-0.96727,-0.20976,-0.14277,454.57,-0.16402,0.087575,0.98256,10.915

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.1936,0.97382,-0.11911,56.039,-0.96727,-0.20976,-0.14277,432.09,-0.16402,0.087575,0.98256,17.749

> fitmap #8 inMap #1

Fit molecule RFXATP_state2_3.02A.pdb (#8) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41693 atoms  
average map value = 0.03895, steps = 312  
shifted from previous position = 2.45  
rotated from previous position = 3.63 degrees  
atoms outside contour = 35104, contour level = 0.10124  
  
Position of RFXATP_state2_3.02A.pdb (#8) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.19496911 -0.96149331 -0.19369476 435.88456688  
0.96437624 -0.22392600 0.14083899 31.70371768  
-0.17878904 -0.15933537 0.97089996 67.54728992  
Axis -0.15400038 -0.00764718 0.98804120  
Axis point 210.43375572 191.70784699 0.00000000  
Rotation angle (degrees) 102.94393921  
Shift along axis -0.62932566  
  

> hide #!8 models

> show #!9 models

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.20069,-0.93673,-0.28682,458.35,0.97475,-0.22019,0.037087,35.013,-0.097896,-0.27213,0.95727,79.624

> view matrix models
> #1,-0.54665,-0.8357,0.052654,448.59,0.78016,-0.53115,-0.3305,193.28,0.30416,-0.13959,0.94234,-20.326

> view matrix models
> #1,-0.98194,0.18213,0.051307,332.73,-0.18307,-0.983,-0.014229,412.84,0.047843,-0.023365,0.99858,-3.5188

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.98194,0.18213,0.051307,336.15,-0.18307,-0.983,-0.014229,410.41,0.047843,-0.023365,0.99858,-14.129

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.21156,-0.97496,0.068448,412.87,0.88946,-0.22109,-0.39997,120.89,0.40509,-0.023736,0.91397,-68.114

> view matrix models
> #1,-0.23443,-0.96721,-0.097748,443.04,0.90288,-0.17935,-0.39069,108.66,0.36035,-0.17984,0.91532,-29.315

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.23443,-0.96721,-0.097748,435.3,0.90288,-0.17935,-0.39069,108.91,0.36035,-0.17984,0.91532,-28.573

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.30949,-0.92218,0.23194,386.54,0.80312,-0.38409,-0.4555,178.56,0.50914,0.0453,0.85949,-91.7

> view matrix models
> #1,-0.29078,-0.93136,0.21914,386.88,0.95319,-0.30183,-0.017985,61.954,0.082893,0.20365,0.97553,-60.629

> view matrix models
> #1,-0.34211,-0.91713,0.20453,396.27,0.933,-0.35741,-0.042049,80.618,0.11166,0.17644,0.97796,-61.185

> view matrix models
> #1,-0.32848,-0.9432,-0.049801,440.61,0.93446,-0.3322,0.12814,47.414,-0.13741,-0.0044456,0.9905,19.494

> view matrix models
> #1,-0.63985,-0.75621,0.13691,432.6,0.76725,-0.61842,0.16997,128.29,-0.043868,0.2138,0.97589,-38.552

> view matrix models
> #1,-0.55479,-0.79218,0.25428,404.14,0.81426,-0.57975,-0.029596,144.61,0.17086,0.19063,0.96668,-73.367

> fitmap #9 inMap #1

Fit molecule RFXATP_state3_2.98A.pdb (#9) to map
RfxATP_state1_withoutADP_F1.mrc (#1) using 41664 atoms  
average map value = 0.04065, steps = 84  
shifted from previous position = 1.73  
rotated from previous position = 2.42 degrees  
atoms outside contour = 34719, contour level = 0.10124  
  
Position of RFXATP_state3_2.98A.pdb (#9) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.52344947 0.82977819 0.19356862 107.43103314  
-0.80993669 -0.55510715 0.18936369 416.56043578  
0.26458118 -0.05765600 0.96263834 -22.37825674  
Axis -0.14883064 -0.04278544 -0.98793666  
Axis point 167.56416462 180.27267990 0.00000000  
Rotation angle (degrees) 123.91477585  
Shift along axis -11.70344924  
  

> hide #!9 models

> show #!7 models

> view matrix models
> #1,0.90249,0.36148,0.23419,-95.305,-0.32338,0.92782,-0.18593,92.182,-0.2845,0.092068,0.95425,34.586

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.90249,0.36148,0.23419,-92.259,-0.32338,0.92782,-0.18593,106.85,-0.2845,0.092068,0.95425,39.176

> view matrix models
> #1,0.90249,0.36148,0.23419,-87.379,-0.32338,0.92782,-0.18593,104.13,-0.2845,0.092068,0.95425,40.688

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.90519,0.41617,-0.086184,-45.877,-0.42093,0.90589,-0.046645,104.06,0.058661,0.0785,0.99519,-28.692

> view matrix models
> #1,0.8977,0.43274,-0.082866,-48.236,-0.43682,0.8987,-0.039055,107.25,0.057571,0.071257,0.9958,-27.17

> view matrix models
> #1,0.90611,0.39509,0.15124,-80.989,-0.38925,0.91864,-0.067724,99.013,-0.16569,0.0024974,0.98617,30.333

> view matrix models
> #1,0.91513,0.39842,0.061622,-68.615,-0.39628,0.91706,-0.044261,96.8,-0.074145,0.016085,0.99712,8.4582

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> view matrix models
> #1,-0.52084,0.83782,-0.16368,155.82,-0.6798,-0.52304,-0.51411,509.47,-0.51634,-0.1565,0.84196,151.85

> view matrix models
> #1,-0.74213,-0.64735,-0.17371,489.82,0.66907,-0.73089,-0.13472,231.02,-0.039753,-0.2162,0.97554,50.859

> view matrix models
> #1,-0.7533,-0.58651,0.29758,402.52,0.52674,-0.80896,-0.26102,294.14,0.39382,-0.039881,0.91832,-56.687

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.7533,-0.58651,0.29758,415.76,0.52674,-0.80896,-0.26102,290.08,0.39382,-0.039881,0.91832,-56.792

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!1 models

> color #1 #ff80b2ff models

> select add #1

2 models selected  

> view matrix models
> #1,-0.7533,-0.58651,0.29758,442.79,0.52674,-0.80896,-0.26102,380.85,0.39382,-0.039881,0.91832,-55.44

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.7533,-0.58651,0.29758,446.69,0.52674,-0.80896,-0.26102,388.45,0.39382,-0.039881,0.91832,-48.116

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.81746,-0.57568,0.018822,502.64,0.57225,-0.81545,-0.087036,352.43,0.065453,-0.060377,0.99603,5.5883

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.81746,-0.57568,0.018822,510.94,0.57225,-0.81545,-0.087036,371.17,0.065453,-0.060377,0.99603,-4.0051

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.9404,-0.30666,-0.14699,151.16,0.31054,0.95055,0.0036449,60.933,0.1386,-0.049073,0.98913,-18.999

> view matrix models
> #1,0.94258,0.27118,0.19494,-18.434,-0.26437,0.96251,-0.060662,178.57,-0.20408,0.0056438,0.97894,37.191

> view matrix models
> #1,0.97155,0.18858,-0.14329,47.837,-0.17573,0.97958,0.09769,132.32,0.15878,-0.06973,0.98485,-18.097

> view matrix models
> #1,0.98671,0.15401,0.051892,19.6,-0.15475,0.9879,0.010558,141.03,-0.049638,-0.018449,0.9986,9.2778

> view matrix models
> #1,0.99318,0.11653,-0.0048243,35.025,-0.11623,0.99236,0.041337,127.77,0.0096042,-0.040494,0.99913,2.2251

> view matrix models
> #1,0.99089,0.11403,-0.071604,46.933,-0.12143,0.98656,-0.1093,154.67,0.058179,0.11699,0.99143,-36.527

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.98298,0.1349,0.12469,12.068,-0.11416,0.98038,-0.16069,162.95,-0.14392,0.14372,0.9791,-1.2664

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.98298,0.1349,0.12469,-19.664,-0.11416,0.98038,-0.16069,157.99,-0.14392,0.14372,0.9791,-0.011895

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.99106,0.12059,0.057146,-7.2929,-0.11296,0.98609,-0.12195,150.27,-0.071058,0.11441,0.99089,-10.087

> view matrix models
> #1,0.99366,0.11208,0.0085199,1.8747,-0.11123,0.9914,-0.069006,140.2,-0.016181,0.067621,0.99758,-12.487

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.99366,0.11208,0.0085199,-8.3383,-0.11123,0.9914,-0.069006,179.3,-0.016181,0.067621,0.99758,-13.796

> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc

Opened J276_003_volume_map_sharp.mrc as #10, grid size 400,400,400, pixel
0.95, shown at level 0.101, step 2, values float32  

> volume flip #10

Opened J276_003_volume_map_sharp.mrc z flip as #11, grid size 400,400,400,
pixel 0.95, shown at step 1, values float32  

> surface dust #1 size 9.5

[Repeated 2 time(s)]

> volume #11 level 0.1898

> view matrix models
> #1,0.99366,0.11208,0.0085199,-8.5676,-0.11123,0.9914,-0.069006,175.82,-0.016181,0.067621,0.99758,-8.4965

> select add #11

4 models selected  

> close #10

> view matrix models
> #1,0.99366,0.11208,0.0085199,-9.271,-0.11123,0.9914,-0.069006,174.67,-0.016181,0.067621,0.99758,-8.5799,#11,1,0,0,-0.70339,0,1,0,-1.151,0,0,1,-0.083462

> select subtract #1

2 models selected  

> view matrix models #11,1,0,0,-24.883,0,1,0,-115.17,0,0,1,-3.4578

> view matrix models #11,1,0,0,-14.96,0,1,0,-8.1909,0,0,1,-4.9614

> view matrix models #11,1,0,0,-12.667,0,1,0,-129.71,0,0,1,-22.609

> select add #1

4 models selected  

> view matrix models
> #1,0.99366,0.11208,0.0085199,-7.888,-0.11123,0.9914,-0.069006,154.52,-0.016181,0.067621,0.99758,-11.139,#11,1,0,0,-11.284,0,1,0,-149.87,0,0,1,-25.167

> select subtract #11

2 models selected  

> view matrix models
> #1,0.99366,0.11208,0.0085199,-6.4335,-0.11123,0.9914,-0.069006,158.49,-0.016181,0.067621,0.99758,-0.46871

> view matrix models
> #1,0.99366,0.11208,0.0085199,-7.6761,-0.11123,0.9914,-0.069006,152,-0.016181,0.067621,0.99758,0.52332

> open /Users/wujingyi/Downloads/J276_003_volume_map_sharp.mrc

Opened J276_003_volume_map_sharp.mrc as #10, grid size 400,400,400, pixel
0.95, shown at level 0.101, step 2, values float32  

> close #11

> volume #10 step 1

> surface dust #1 size 9.5

> volume #10 level 0.1812

> surface dust #1 size 9.5

> fitmap #10 inMap #1

Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 188089 points  
correlation = -0.006151, correlation about mean = 0.01165, overlap = -25.22  
steps = 124, shift = 3.02, angle = 1.44 degrees  
  
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99219120 -0.11872377 -0.03822681 33.00709102  
0.12081950 0.99096707 0.05819723 -151.45253231  
0.03097211 -0.06236133 0.99757295 3.22774595  
Axis -0.43530083 -0.24985658 0.86491900  
Axis point 1221.20725162 293.99472165 0.00000000  
Rotation angle (degrees) 7.95974301  
Shift along axis 26.26513589  
  

> select add #10

4 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.97091,0.099541,-0.21778,40.434,-0.10837,0.99369,-0.028932,143.66,0.21353,0.05169,0.97557,-37.684,#10,0.96861,-0.0030468,-0.24857,56.703,0.011641,0.99938,0.033111,-10.51,0.24832,-0.034965,0.96805,-35.316

> select subtract #1

2 models selected  

> view matrix models
> #10,-0.9324,0.29299,-0.21165,358.89,0.29835,0.95443,0.0068452,-52.02,0.20401,-0.056764,-0.97732,354.17

> view matrix models
> #10,-0.93215,0.31812,-0.17292,346.59,0.28997,0.94188,0.16965,-79.574,0.21684,0.108,-0.97021,319.18

> view matrix models
> #10,-0.95209,0.30384,-0.034637,326.33,0.29532,0.94293,0.15383,-77.736,0.079399,0.13623,-0.98749,343.6

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.95209,0.30384,-0.034637,325.96,0.29532,0.94293,0.15383,-75.425,0.079399,0.13623,-0.98749,332.17

> fitmap #10 inMap #1

Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 188089 points  
correlation = -0.007304, correlation about mean = 0.01435, overlap = -29.43  
steps = 128, shift = 0.762, angle = 2.55 degrees  
  
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.94519797 0.18352083 -0.27003869 390.20153472  
0.17116532 0.98283540 0.06882591 -159.08409996  
0.27803458 0.01883286 -0.96038643 307.90980210  
Axis -0.09081601 -0.99561473 -0.02244469  
Axis point 180.47276345 0.00000000 183.99021934  
Rotation angle (degrees) 164.02346511  
Shift along axis 116.03898949  
  

> surface dust #10 size 9.5

> hide #!1 models

> volume #10 level 0.1163

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.96121,0.27191,-0.046177,336.43,0.26447,0.9562,0.12544,-67.366,0.078264,0.10836,-0.99103,338.37

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.95945,0.26317,-0.10101,349.53,0.24157,0.95229,0.1865,-75.323,0.14527,0.15454,-0.97725,313.7

> view matrix models
> #10,-0.941,0.32028,-0.10925,336.66,0.2949,0.93447,0.19949,-84.745,0.16598,0.1555,-0.97379,308.85

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.941,0.32028,-0.10925,336.51,0.2949,0.93447,0.19949,-85.007,0.16598,0.1555,-0.97379,311.62

> view matrix models
> #10,-0.941,0.32028,-0.10925,335.02,0.2949,0.93447,0.19949,-82.234,0.16598,0.1555,-0.97379,307.58

> view matrix models
> #10,-0.941,0.32028,-0.10925,337.07,0.2949,0.93447,0.19949,-81.211,0.16598,0.1555,-0.97379,307.08

> fitmap #10 inMap #1

Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 412809 points  
correlation = 0.003388, correlation about mean = -0.01098, overlap = 26.25  
steps = 188, shift = 2.96, angle = 3.45 degrees  
  
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.88776004 0.24481426 -0.38980519 394.83049540  
0.20167323 0.96809819 0.14870711 -177.87661799  
0.41377531 0.05340296 -0.90881137 261.15290888  
Axis -0.11760697 -0.99163221 -0.05323677  
Axis point 179.43195104 0.00000000 178.94673905  
Rotation angle (degrees) 156.09754779  
Shift along axis 116.05042942  
  

> select subtract #10

Nothing selected  

> select add #10

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.93304,0.31032,-0.18203,355.25,0.28502,0.94634,0.15235,-72.252,0.21954,0.090268,-0.97142,307.64

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.93304,0.31032,-0.18203,353.2,0.28502,0.94634,0.15235,-85.848,0.21954,0.090268,-0.97142,311.78

> view matrix models
> #10,-0.93304,0.31032,-0.18203,353.31,0.28502,0.94634,0.15235,-85.037,0.21954,0.090268,-0.97142,312.82

> ui mousemode right ""rotate selected models""

> view matrix models
> #10,-0.9315,0.30464,-0.19874,357.71,0.31409,0.94924,-0.017144,-54.858,0.18343,-0.078393,-0.9799,354.37

> fitmap #10 inMap #1

Fit map J276_003_volume_map_sharp.mrc in map RfxATP_state1_withoutADP_F1.mrc
using 412809 points  
correlation = 0.003971, correlation about mean = -0.01138, overlap = 29.2  
steps = 76, shift = 1.45, angle = 1.05 degrees  
  
Position of J276_003_volume_map_sharp.mrc (#10) relative to
RfxATP_state1_withoutADP_F1.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.89202044 0.17867377 -0.41518095 415.57480664  
0.23668091 0.96719546 -0.09227724 -144.51510345  
0.38507361 -0.18057859 -0.90504679 317.47235545  
Axis -0.10939237 -0.99139756 0.07186231  
Axis point 182.93569343 0.00000000 199.07523474  
Rotation angle (degrees) 156.19662314  
Shift along axis 120.62550380  
  

> select subtract #10

Nothing selected  

> fitmap #7 inMap #10

Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
J276_003_volume_map_sharp.mrc (#10) using 41723 atoms  
average map value = 0.03999, steps = 92  
shifted from previous position = 2.94  
rotated from previous position = 3.89 degrees  
atoms outside contour = 34568, contour level = 0.11631  
  
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
J276_003_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99939912 -0.03433994 -0.00470912 14.18609868  
-0.03465788 -0.98811995 -0.14972575 409.89756479  
0.00048839 0.14979899 -0.98871635 348.63431455  
Axis 0.99984892 -0.01734993 -0.00106133  
Axis point 0.00000000 191.94050757 189.76759693  
Rotation angle (degrees) 171.38553254  
Shift along axis 6.70224576  
  

> select add #10

2 models selected  

> view matrix models
> #10,-0.96568,0.16527,-0.20039,392.73,0.18193,0.98098,-0.067662,-24.382,0.1854,-0.1018,-0.97738,358.48

> ui mousemode right ""translate selected models""

> view matrix models
> #10,-0.96568,0.16527,-0.20039,389.82,0.18193,0.98098,-0.067662,-22.699,0.1854,-0.1018,-0.97738,359.38

> select subtract #10

Nothing selected  

> fitmap #7 inMap #10

Fit molecule RFXATPase_state1_2.98A-1.pdb (#7) to map
J276_003_volume_map_sharp.mrc (#10) using 41723 atoms  
average map value = 0.1675, steps = 388  
shifted from previous position = 5.7  
rotated from previous position = 10.9 degrees  
atoms outside contour = 26445, contour level = 0.11631  
  
Position of RFXATPase_state1_2.98A-1.pdb (#7) relative to
J276_003_volume_map_sharp.mrc (#10) coordinates:  
Matrix rotation and translation  
0.98574956 0.16765026 0.01382779 -27.67300286  
0.16781986 -0.98574247 -0.01217687 343.80660039  
0.01158918 0.01432392 -0.99983025 368.53685588  
Axis 0.99643086 0.08417165 0.00637725  
Axis point 0.00000000 171.84256163 185.50305705  
Rotation angle (degrees) 179.23806648  
Shift along axis 3.71478754  
  

> save /Users/wujingyi/Downloads/rfxATPase_withoutADP_F1.mrc models #10

> color #10 #b2b2ff53 models

> color #10 #b2b2ff54 models

> select add #7

41723 atoms, 42367 bonds, 9 pseudobonds, 5426 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 41723 atom styles  

> ui mousemode right select

> select clear

Drag select of 18 atoms, 10 residues, 18 bonds, 10
J276_003_volume_map_sharp.mrc  

> volume #10 color #b2b2ff

> select clear

> close #10

> close #9

> close #8

> close #1

> hide #!7 models

> show #!6 models

> show #!5 models

> show #!4 models

> show #!3 models

> show #!2 models

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo-1.pdb""

Chain information for RfxATP_state_1_Fo-1.pdb #1  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!1-6 atoms

> show #!1-6 cartoons

> select add #3

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> hide target m

> select subtract #3

16 models selected  

> select add #1

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> show #!1 models

> show sel surfaces

> hide sel surfaces

> select subtract #1.2

10597 atoms, 10807 bonds, 2 pseudobonds, 1405 residues, 18 models selected  

> select subtract #1.3

10074 atoms, 10276 bonds, 2 pseudobonds, 1332 residues, 17 models selected  

> select subtract #1.4

9532 atoms, 9726 bonds, 2 pseudobonds, 1257 residues, 16 models selected  

> select subtract #1.5

8990 atoms, 9176 bonds, 2 pseudobonds, 1182 residues, 15 models selected  

> select subtract #1.6

8440 atoms, 8618 bonds, 2 pseudobonds, 1106 residues, 14 models selected  

> select subtract #1.7

7898 atoms, 8068 bonds, 2 pseudobonds, 1031 residues, 13 models selected  

> select subtract #1.8

7356 atoms, 7518 bonds, 2 pseudobonds, 956 residues, 12 models selected  

> select subtract #1.9

6806 atoms, 6960 bonds, 2 pseudobonds, 880 residues, 11 models selected  

> select add #1

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 10 models selected  

> select subtract #1.1

11147 atoms, 11365 bonds, 1481 residues, 17 models selected  

> select subtract #1.12

8915 atoms, 9078 bonds, 1190 residues, 17 models selected  

> select subtract #1.13

8592 atoms, 8748 bonds, 1152 residues, 16 models selected  

> select subtract #1.14

8286 atoms, 8435 bonds, 1116 residues, 15 models selected  

> select subtract #1.15

7963 atoms, 8105 bonds, 1078 residues, 14 models selected  

> select subtract #1.16

7657 atoms, 7792 bonds, 1042 residues, 13 models selected  

> select subtract #1.17

5425 atoms, 5505 bonds, 751 residues, 12 models selected  

> hide sel cartoons

> ui tool show ""Show Sequence Viewer""

[Repeated 1 time(s)]

> close #3

> ui tool show ""Show Sequence Viewer""

> close #7

> ui tool show ""Show Sequence Viewer""

Cell requested for row 0 is out of bounds for table with 22 rows! Resizing
table model.  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/H #1/L #1/O #1/P

Alignment identifier is 1  

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #1/J #1/K #1/M #1/N

Alignment identifier is 2  

> sequence chain #1/Q

Alignment identifier is 1/Q  

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> color (#!1 & sel) byhetero

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) byhetero

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> color (#!1 & sel) byhetero

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) byhetero

> show #!4 models

> show #!5 models

> show #!6 models

> show #!2 models

> select add #4

6397 atoms, 5064 bonds, 6389 residues, 3 models selected  

> select add #2

13627 atoms, 10537 bonds, 13619 residues, 8 models selected  

> select add #5

20718 atoms, 15835 bonds, 20710 residues, 13 models selected  

> select add #6

26408 atoms, 20451 bonds, 26400 residues, 18 models selected  

> show sel surfaces

> select clear

Drag select of RfxATP_state_1_Fo-1.pdb_Q SES surface, 934 of 83818 triangles,
9 atoms, 8 bonds  

> hide sel surfaces

> close #1

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo-2.pdb""

Chain information for RfxATP_state_1_Fo-2.pdb #1  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> select add #1

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #1.1

11147 atoms, 11365 bonds, 1481 residues, 17 models selected  

> select subtract #1.17

8915 atoms, 9078 bonds, 1190 residues, 17 models selected  

> select subtract #1.16

8609 atoms, 8765 bonds, 1154 residues, 16 models selected  

> select subtract #1.15

8286 atoms, 8435 bonds, 1116 residues, 15 models selected  

> select subtract #1.14

7980 atoms, 8122 bonds, 1080 residues, 14 models selected  

> select subtract #1.13

7657 atoms, 7792 bonds, 1042 residues, 13 models selected  

> hide sel cartoons

> select subtract #1.12

5425 atoms, 5505 bonds, 751 residues, 12 models selected  

> hide sel cartoons

> select add #1.12

7657 atoms, 5505 bonds, 1042 residues, 11 models selected  

> select subtract #1.12

5425 atoms, 5505 bonds, 751 residues, 12 models selected  

> select add #1

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected  

> select subtract #1

16 models selected  

> select add #1.12

2232 atoms, 291 residues, 1 model selected  

> select add #1.17

4464 atoms, 582 residues, 2 models selected  

> show sel cartoons

> select subtract #1.12

2232 atoms, 291 residues, 3 models selected  

> select subtract #1.17

1 model selected  

> select add #1.16

306 atoms, 36 residues, 1 model selected  

> select add #1.15

629 atoms, 74 residues, 2 models selected  

> select add #1.13

952 atoms, 112 residues, 3 models selected  

> select add #1.14

1258 atoms, 148 residues, 4 models selected  

> hide sel cartoons

> select add #1

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 6 models selected  

> select subtract #1

16 models selected  

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/H #1/L #1/O #1/P

Alignment identifier is 1  

> sequence chain #1/I

Alignment identifier is 1/I  

> sequence chain #1/J #1/K #1/M #1/N

Alignment identifier is 2  

> sequence chain #1/Q

Alignment identifier is 1/Q  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color (#!1 & sel) byelement

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> color (#!1 & sel) byhetero

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color (#!1 & sel) byhetero

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> color (#!1 & sel) byhetero

> show sel atoms

> style sel stick

Changed 36 atom styles  

> select clear

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RFXATPase_state1_2.98A-1.pdb""

Chain information for RFXATPase_state1_2.98A-1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
R | No description available  
S | No description available  
T Z | No description available  
U X | No description available  
V | No description available  
W | No description available  
Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide atoms

> show cartoons

> hide #!3 models

> select add #1.2

550 atoms, 76 residues, 1 model selected  

> select add #1.3

1073 atoms, 149 residues, 2 models selected  

> select add #1.4

1615 atoms, 224 residues, 3 models selected  

> select add #1.5

2157 atoms, 299 residues, 4 models selected  

> select add #1.6

2707 atoms, 375 residues, 5 models selected  

> select add #1.7

3249 atoms, 450 residues, 6 models selected  

> select add #1.8

3791 atoms, 525 residues, 7 models selected  

> select add #1.9

4341 atoms, 601 residues, 8 models selected  

> select add #1.10

4891 atoms, 677 residues, 9 models selected  

> select add #1.11

5425 atoms, 751 residues, 10 models selected  

> hide sel cartoons

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> hide sel cartoons

> show sel atoms

> select clear

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase 结构/RfxATP_state_1_Fo-3.pdb""

Chain information for RfxATP_state_1_Fo-3.pdb #7  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!1-2,4-7 atoms

> show #!1-2,4-7 cartoons

> show #!1-2,4-7 surfaces

> hide #!1-2,4-7 surfaces

> select add #7.2

550 atoms, 76 residues, 1 model selected  

> select add #7.3

1073 atoms, 149 residues, 2 models selected  

> select add #7.4

1615 atoms, 224 residues, 3 models selected  

> select add #7.5

2157 atoms, 299 residues, 4 models selected  

> select add #7.6

2707 atoms, 375 residues, 5 models selected  

> select add #7.7

3249 atoms, 450 residues, 6 models selected  

> select add #7.8

3791 atoms, 525 residues, 7 models selected  

> select add #7.9

4341 atoms, 601 residues, 8 models selected  

> select add #7.10

4891 atoms, 677 residues, 9 models selected  

> select add #7.11

5425 atoms, 751 residues, 10 models selected  

> hide sel cartoons

[Repeated 1 time(s)]

> hide #!1 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/H #1/L #1/O #1/P #3/H #3/L #3/O #3/P #7/H #7/L #7/O #7/P

Alignment identifier is 3  

> sequence chain #1/I #3/I #7/I

Alignment identifier is 4  

> sequence chain #1/J #1/K #1/M #1/N #3/J #3/K #3/M #3/N #7/J #7/K #7/M #7/N

Alignment identifier is 5  

> sequence chain #1/Q #3/Q #7/Q

Alignment identifier is 6  

> select #1/Q:59 #3/Q:59 #7/Q:59

27 atoms, 24 bonds, 3 residues, 3 models selected  

> select #1/Q:59 #3/Q:59 #7/Q:59

27 atoms, 24 bonds, 3 residues, 3 models selected  
6 [ID: 6] region 3 chains [58] RMSD: 0.294  
  

> show sel & #!7 atoms

> style sel & #!7 stick

Changed 9 atom styles  

> color (#!7 & sel) byhetero

> select #1/J-K,M-N:59 #3/J-K,M-N:59 #7/J-K,M-N:59

108 atoms, 96 bonds, 12 residues, 3 models selected  

> select #1/J-K,M-N:59-60 #3/J-K,M-N:59-60 #7/J-K,M-N:59-60

168 atoms, 156 bonds, 24 residues, 3 models selected  
5 [ID: 5] region 12 chains [58-59] RMSD: 0.425  
  

> select #1/J-K,M-N:59 #3/J-K,M-N:59 #7/J-K,M-N:59

108 atoms, 96 bonds, 12 residues, 3 models selected  

> select #1/J-K,M-N:59 #3/J-K,M-N:59 #7/J-K,M-N:59

108 atoms, 96 bonds, 12 residues, 3 models selected  
5 [ID: 5] region 12 chains [58] RMSD: 0.411  
  

> color (#!7 & sel) byelement

> color (#!7 & sel) byhetero

> show sel & #!7 atoms

> style sel & #!7 stick

Changed 36 atom styles  

> select #1/I:59 #3/I:59 #7/I:59

27 atoms, 24 bonds, 3 residues, 3 models selected  

> color (#!7 & sel) byhetero

> select #1/H,L,O-P:59 #3/H,L,O-P:59 #7/H,L,O-P:59

108 atoms, 96 bonds, 12 residues, 3 models selected  

> select #1/H,L,O-P:59 #3/H,L,O-P:59 #7/H,L,O-P:59

108 atoms, 96 bonds, 12 residues, 3 models selected  
3 [ID: 3] region 12 chains [58] RMSD: 0.353  
  

> color (#!7 & sel) byhetero

> show sel & #!7 atoms

> style sel & #!7 stick

Changed 36 atom styles  

> select clear

> select #1/I:59 #3/I:59 #7/I:59

27 atoms, 24 bonds, 3 residues, 3 models selected  

> select #1/I:59 #3/I:59 #7/I:59

27 atoms, 24 bonds, 3 residues, 3 models selected  
4 [ID: 4] region 3 chains [58] RMSD: 0.292  
  

> show sel & #!7 atoms

> style sel & #!7 stick

Changed 9 atom styles  

> color (#!7 & sel) byhetero

> select clear

> select add #7.12

2232 atoms, 291 residues, 1 model selected  

> select add #7.17

4464 atoms, 582 residues, 2 models selected  

> color (#!7 & sel) forest green

> select add #7

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 4 models selected  

> select subtract #7.13

10824 atoms, 11035 bonds, 2 pseudobonds, 1443 residues, 18 models selected  

> select subtract #7.15

10501 atoms, 10705 bonds, 2 pseudobonds, 1405 residues, 17 models selected  

> select subtract #7.14

10195 atoms, 10392 bonds, 2 pseudobonds, 1369 residues, 16 models selected  

> select subtract #7.16

9889 atoms, 10079 bonds, 2 pseudobonds, 1333 residues, 15 models selected  

> select subtract #7.17

7657 atoms, 7792 bonds, 1 pseudobond, 1042 residues, 14 models selected  

> select subtract #7.12

5425 atoms, 5505 bonds, 751 residues, 12 models selected  

> color (#!7 & sel) #f5ccdcff

> color (#!7 & sel) byhetero

> select clear

> hide #7.15 models

> hide #7.12 models

> select add #7.15

323 atoms, 38 residues, 1 model selected  

> select add #7.13

646 atoms, 76 residues, 2 models selected  

> hide sel cartoons

> select add #7.16

952 atoms, 112 residues, 3 models selected  

> select add #7.14

1258 atoms, 148 residues, 4 models selected  

> hide sel cartoons

> select clear

> volume flip #10

> view

> cartoon style #2,4-6#7.1-11,13-14,16-17#!7 modeHelix tube sides 20

> view

> show #!1 models

> hide #!1 models

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> select add #4

13618 atoms, 10529 bonds, 13618 residues, 6 models selected  

> select add #5

20709 atoms, 15827 bonds, 20709 residues, 11 models selected  

> select add #6

26399 atoms, 20443 bonds, 26399 residues, 16 models selected  

> show sel surfaces

> select subtract #6

20709 atoms, 15827 bonds, 20709 residues, 18 models selected  

> select subtract #4

14321 atoms, 10771 bonds, 14321 residues, 14 models selected  

> color (#!2,5 & sel) #f2d6d7ff

> color (#!2,5 & sel) #f2d2d3ff

> color (#!2,5 & sel) #f2cbcdff

> color (#!2,5 & sel) #f2c3c8ff

> color (#!2,5 & sel) #f2b8c5ff

> color (#!2,5 & sel) #f2b2c6ff

> color (#!2,5 & sel) #f2aec7ff

> color (#!2,5 & sel) #f2a9c7ff

> color (#!2,5 & sel) #f2a5c7ff

> color (#!2,5 & sel) #f2a2c9ff

> color (#!2,5 & sel) #f2a0caff

> color (#!2,5 & sel) #f29fc9ff

> color (#!2,5 & sel) #f2a0caff

> color (#!2,5 & sel) #f2a0cbff

> color (#!2,5 & sel) #f2a0ccff

> color (#!2,5 & sel) #f2a1ccff

> color (#!2,5 & sel) #f2a2cdff

> color (#!2,5 & sel) #f2a5d2ff

> color (#!2,5 & sel) #f2a6d5ff

> color (#!2,5 & sel) #f2a9d9ff

> color (#!2,5 & sel) #f2abddff

> color (#!2,5 & sel) #f2aee3ff

> color (#!2,5 & sel) #f2b2edff

> color (#!2,5 & sel) #efb4f2ff

> color (#!2,5 & sel) #e5b3f2ff

> color (#!2,5 & sel) #dcb1f2ff

> color (#!2,5 & sel) #d6aff2ff

> color (#!2,5 & sel) #d4aff2ff

> color (#!2,5 & sel) #d5aff2ff

> color (#!2,5 & sel) #dea2f2ff

> color (#!2,5 & sel) #e29cf2ff

> color (#!2,5 & sel) #e29bf2ff

> color (#!2,5 & sel) #e39bf2ff

> color (#!2,5 & sel) #e49bf2ff

> color (#!2,5 & sel) #e59bf2ff

> color (#!2,5 & sel) #e89bf2ff

> color (#!2,5 & sel) #ea9cf2ff

> color (#!2,5 & sel) #ed9cf2ff

> color (#!2,5 & sel) #f09cf2ff

> color (#!2,5 & sel) #f29cf2ff

> color (#!2,5 & sel) #f29cf0ff

> color (#!2,5 & sel) #f29cefff

[Repeated 1 time(s)]

> color (#!2,5 & sel) #f29ceeff

> color (#!2,5 & sel) #f29cebff

> color (#!2,5 & sel) #f29ce5ff

> color (#!2,5 & sel) #f299dbff

> color (#!2,5 & sel) #f295d2ff

> color (#!2,5 & sel) #f290caff

> color (#!2,5 & sel) #f286bcff

> color (#!2,5 & sel) #f284b8ff

> color (#!2,5 & sel) #f284b7ff

> color (#!2,5 & sel) #f283b7ff

> color (#!2,5 & sel) #f27fb0ff

> color (#!2,5 & sel) #f27eadff

[Repeated 1 time(s)]

> color (#!2,5 & sel) #f27ca9ff

> color (#!2,5 & sel) #f2779dff

> color (#!2,5 & sel) #f27498ff

[Repeated 1 time(s)]

> color (#!2,5 & sel) #f26e91ff

> color (#!2,5 & sel) #f26a8eff

> color (#!2,5 & sel) #f2678bff

> color (#!2,5 & sel) #f26489ff

> color (#!2,5 & sel) #f26388ff

> color (#!2,5 & sel) #f26287ff

> color (#!2,5 & sel) #f26388ff

> color (#!2,5 & sel) #f26589ff

> color (#!2,5 & sel) #f2708bff

> color (#!2,5 & sel) #f27a8eff

> color (#!2,5 & sel) #f28091ff

> color (#!2,5 & sel) #f28494ff

> color (#!2,5 & sel) #f28796ff

> color (#!2,5 & sel) #f28795ff

> color (#!2,5 & sel) #f28796ff

> color (#!2,5 & sel) #f28596ff

> color (#!2,5 & sel) #f28497ff

> color (#!2,5 & sel) #f2819bff

> color (#!2,5 & sel) #f27c9fff

> color (#!2,5 & sel) #f27ba1ff

> color (#!2,5 & sel) #f27ca2ff

> color (#!2,5 & sel) #f27da3ff

> color (#!2,5 & sel) #f27ca3ff

> color (#!2,5 & sel) #f27da4ff

> color (#!2,5 & sel) #f27ea5ff

> color (#!2,5 & sel) #f27da5ff

> select clear

> select add #1

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> select subtract #1

16 models selected  

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 1 model selected  

> select add #4

12078 atoms, 9672 bonds, 12078 residues, 5 models selected  

> color (#!4,6 & sel) cornflower blue

> select subtract #6

6388 atoms, 5056 bonds, 6388 residues, 8 models selected  

> select subtract #4

4 models selected  

> select add #5

7091 atoms, 5298 bonds, 7091 residues, 1 model selected  

> select add #2

14321 atoms, 10771 bonds, 14321 residues, 6 models selected  

> select subtract #5

7230 atoms, 5473 bonds, 7230 residues, 9 models selected  

> select subtract #2

4 models selected  

> color #2 #f27da581

> color #2 #f27da580

> color #5 #f27da580

> color #6 #6495ed80

> color #4 #6495ed7b

> color #4 #6495ed7d

> color #4 #6495ed80

> lighting simple

> lighting soft

> lighting full

> lighting flat

> view

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> graphics silhouettes false

> lighting soft

> graphics silhouettes true

> lighting flat

> ui tool show ""Show Sequence Viewer""

> sequence chain #1/T #1/Z #3/T #3/Z #7/T #7/Z

Alignment identifier is 1  

> select #1/T,Z:259 #3/T,Z:259 #7/T,Z:259

66 atoms, 60 bonds, 6 residues, 3 models selected  

> select #1/T,Z:259 #3/T,Z:259 #7/T,Z:259

66 atoms, 60 bonds, 6 residues, 3 models selected  
1 [ID: 1] region 6 chains [235] RMSD: 0.547  
  

> show sel & #!7 atoms

> style sel & #!7 stick

Changed 22 atom styles  

> color (#!7 & sel) byhetero

> select clear

> save /Users/wujingyi/1.cxs

> view

[Repeated 1 time(s)]

> save
> /Users/wujingyi/Desktop/RfxATPase_figure/figure_4/Rfxatp_state1_hollow.cxs

——— End of log from Mon Aug 12 10:58:14 2024 ———

opened ChimeraX session  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-0.pdb""

Chain information for RfxATP_state_1_Fo-4-coot-0.pdb #8  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!2,4-8 atoms

> show #!2,4-8 cartoons

> show #!2,4-8 surfaces

> hide #!2,4-8 surfaces

> hide #!7 models

> select add #8.2

550 atoms, 76 residues, 1 model selected  

> select add #8

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 3 models selected  

> select subtract #8.17

8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected  

> select subtract #8.12

6683 atoms, 6791 bonds, 899 residues, 16 models selected  

> select subtract #8.13

6360 atoms, 6461 bonds, 861 residues, 15 models selected  

> select subtract #8.14

6054 atoms, 6148 bonds, 825 residues, 14 models selected  

> select subtract #8.15

5731 atoms, 5818 bonds, 787 residues, 13 models selected  

> select subtract #8.16

5425 atoms, 5505 bonds, 751 residues, 12 models selected  

> color (#!8 & sel) #f5ccdcff

> lighting soft

> select add #8

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected  

> select subtract #8

16 models selected  

> select add #8.12

2232 atoms, 291 residues, 1 model selected  

> select add #8.17

4464 atoms, 582 residues, 2 models selected  

> color (#!8 & sel) forest green

> select subtract #8.17

2232 atoms, 291 residues, 3 models selected  

> select subtract #8.12

1 model selected  

> select add #8.14

306 atoms, 36 residues, 1 model selected  

> select add #8.16

612 atoms, 72 residues, 2 models selected  

> color (#!8 & sel) #9e7bbaff

> select subtract #8.14

306 atoms, 36 residues, 3 models selected  

> select subtract #8.16

1 model selected  

> select add #8.15

323 atoms, 38 residues, 1 model selected  

> select add #8.13

646 atoms, 76 residues, 2 models selected  

> color (#!8 & sel) #c5c5ecff

> select subtract #8.13

323 atoms, 38 residues, 3 models selected  

> select subtract #8.15

1 model selected  

> select add #8.16

306 atoms, 36 residues, 1 model selected  

> select add #8.15

629 atoms, 74 residues, 2 models selected  

> select add #8.14

935 atoms, 110 residues, 3 models selected  

> select add #8.13

1258 atoms, 148 residues, 4 models selected  

> hide sel cartoons

> select subtract #8.13

935 atoms, 110 residues, 5 models selected  

> select subtract #8.14

629 atoms, 74 residues, 4 models selected  

> select subtract #8.15

306 atoms, 36 residues, 3 models selected  

> select subtract #8.16

1 model selected  

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> select add #4

13618 atoms, 10529 bonds, 13618 residues, 6 models selected  

> select add #5

20709 atoms, 15827 bonds, 20709 residues, 11 models selected  

> select add #6

26399 atoms, 20443 bonds, 26399 residues, 16 models selected  

> show sel surfaces

> select subtract #4

20011 atoms, 15387 bonds, 20011 residues, 18 models selected  

> select subtract #5

12920 atoms, 10089 bonds, 12920 residues, 13 models selected  

> select subtract #6

7230 atoms, 5473 bonds, 7230 residues, 8 models selected  

> select subtract #2

4 models selected  

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> select add #5

14321 atoms, 10771 bonds, 14321 residues, 6 models selected  

> color (#!2,5 & sel) #f2b8aeff

[Repeated 1 time(s)]

> color (#!2,5 & sel) #f2b8aeca

> color (#!2,5 & sel) #f2b8aec5

> color (#!2,5 & sel) #f2b8aea2

> color (#!2,5 & sel) #f2b8ae92

> color (#!2,5 & sel) #f2b8ae8f

> color (#!2,5 & sel) #f2b8ae83

> color (#!2,5 & sel) #f2b8ae80

> color (#!2,5 & sel) #f2b8ae77

> color (#!2,5 & sel) #f2b8ae75

> color (#!2,5 & sel) #f2b8ae76

> color (#!2,5 & sel) #f2b8ae7a

> color (#!2,5 & sel) #f2b8ae7b

> select subtract #5

7230 atoms, 5473 bonds, 7230 residues, 9 models selected  

> select subtract #2

4 models selected  

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 1 model selected  

> select add #4

12078 atoms, 9672 bonds, 12078 residues, 5 models selected  

> color (#!4,6 & sel) #c2e5cf7b

> select subtract #6

6388 atoms, 5056 bonds, 6388 residues, 8 models selected  

> select subtract #4

4 models selected  

> select add #5

7091 atoms, 5298 bonds, 7091 residues, 1 model selected  

> select add #2

14321 atoms, 10771 bonds, 14321 residues, 6 models selected  

> color (#!2,5 & sel) #efd6d17b

[Repeated 1 time(s)]

> color (#!2,5 & sel) #efd6d17c

> color (#!2,5 & sel) #efd6d17f

> select add #4

20709 atoms, 15827 bonds, 20709 residues, 11 models selected  

> select subtract #2

13479 atoms, 10354 bonds, 13479 residues, 14 models selected  

> select subtract #4

7091 atoms, 5298 bonds, 7091 residues, 9 models selected  

> select subtract #5

4 models selected  

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 1 model selected  

> select add #4

12078 atoms, 9672 bonds, 12078 residues, 5 models selected  

> color (#!4,6 & sel) #bcc6dd7f

> select subtract #6

6388 atoms, 5056 bonds, 6388 residues, 8 models selected  

> select subtract #4

4 models selected  

> undo

> select subtract #6

6388 atoms, 5056 bonds, 6388 residues, 8 models selected  

> select subtract #4

4 models selected  

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 1 model selected  

> select add #4

12078 atoms, 9672 bonds, 12078 residues, 5 models selected  

> color (#!4,6 & sel) #d5ebf07f

> select subtract #6

6388 atoms, 5056 bonds, 6388 residues, 8 models selected  

> select subtract #4

4 models selected  

> select add #8.2

550 atoms, 76 residues, 1 model selected  

> select add #8.3

1073 atoms, 149 residues, 2 models selected  

> select add #8.4

1615 atoms, 224 residues, 3 models selected  

> select add #8.5

2157 atoms, 299 residues, 4 models selected  

> select add #8.6

2707 atoms, 375 residues, 5 models selected  

> select add #8.7

3249 atoms, 450 residues, 6 models selected  

> select add #8.8

3791 atoms, 525 residues, 7 models selected  

> select add #8.9

4341 atoms, 601 residues, 8 models selected  

> select add #8.10

4891 atoms, 677 residues, 9 models selected  

> select add #8.11

5425 atoms, 751 residues, 10 models selected  
Alignment identifier is 1  
Alignment identifier is 8/I  
Alignment identifier is 2  
Alignment identifier is 8/Q  

> select #8/Q:2

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #8/Q

534 atoms, 542 bonds, 74 residues, 1 model selected  

> hide sel cartoons

> select #8/Q:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #8/Q:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #8/J-K,M-N:2-3

60 atoms, 56 bonds, 8 residues, 1 model selected  

> select #8/J-K,M-N:2-3

60 atoms, 56 bonds, 8 residues, 1 model selected  

> select #8/J-K,M-N:2-3

60 atoms, 56 bonds, 8 residues, 1 model selected  

> select #8/J-K,M-N

2168 atoms, 2200 bonds, 300 residues, 1 model selected  

> hide sel cartoons

> select #8/J-K,M-N:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #8/J-K,M-N:58-61

116 atoms, 112 bonds, 16 residues, 1 model selected  

> show sel cartoons

> select #8/I:2

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #8/I

523 atoms, 531 bonds, 73 residues, 1 model selected  

> hide sel cartoons

> select #8/I:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #8/I:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #8/I:2

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #8/I

523 atoms, 531 bonds, 73 residues, 1 model selected  

> select #8/H,L,O-P:2

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #8/H,L,O-P

2200 atoms, 2232 bonds, 304 residues, 1 model selected  

> hide sel cartoons

> select #8/H,L,O-P:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #8/H,L,O-P:58-61

116 atoms, 112 bonds, 16 residues, 1 model selected  

> show sel cartoons

> select #8/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #8/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #8/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #8/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #8/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #8/J-K,M-N:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #8/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #8/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> view matrix models #8,1,0,0,0.032442,0,1,0,0.0059412,0,0,1,-0.0014518

> select #8/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #8/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> view matrix models #8,1,0,0,0.097325,0,1,0,0.017824,0,0,1,-0.0043555

> ui mousemode right select

> select clear

> style #2,4-6,8 ball

Changed 37546 atom styles  

> select clear

> select #8/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #4/F:4727@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:4243@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:6033@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:5181@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:4730@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:6455@O

1 atom, 1 residue, 1 model selected  

> select #4/F:6009@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:5165@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #4/F:4724@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 630 of 3926 triangles,
5 atoms, 4 residues, 5 bonds  
Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 139 of 3926 triangles,
rfxa1_outlet_hollow2.pdb_G SES surface, 258 of 7744 triangles,
rfxa1_outlet_hollow2.pdb_H SES surface, 293 of 35632 triangles, 3 residues  

> select #4/F:5592@O

1 atom, 1 residue, 1 model selected  

> select #4/G:548@O

1 atom, 1 residue, 1 model selected  

> select #4/F:4717@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 74 of 3926 triangles  
Drag select of rfxa1_outlet_hollow2.pdb_F SES surface, 27 of 3926 triangles  

> hide #!2,4-6,8 surfaces

> show #!2,4-6,8 surfaces

> hide #!2,4-6,8 surfaces

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 2 models selected  

> show sel surfaces

> select add #4

12078 atoms, 9672 bonds, 12078 residues, 6 models selected  

> select add #5

19169 atoms, 14970 bonds, 19169 residues, 10 models selected  

> select add #2

26399 atoms, 20443 bonds, 26399 residues, 15 models selected  

> show sel surfaces

> select clear

> select add #8.17

2232 atoms, 291 residues, 1 model selected  

> select add #8.12

4464 atoms, 582 residues, 2 models selected  
Alignment identifier is 3  

> select #8/T,Z:1

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #8/T,Z:1-108

1608 atoms, 1628 bonds, 216 residues, 1 model selected  

> hide sel cartoons

> select #8/T,Z:109

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #8/T,Z:109-198

994 atoms, 1026 bonds, 2 pseudobonds, 132 residues, 2 models selected  

> hide sel cartoons

> select #5/F:8194@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 603 of 31532 triangles,
2 residues  

> select clear

> select #8/T:202

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #8/T,Z:199

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #8/T,Z:199-216

286 atoms, 292 bonds, 36 residues, 1 model selected  

> hide sel cartoons

> select #8/T,Z:217

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select #8/T,Z:217-223

98 atoms, 98 bonds, 14 residues, 1 model selected  

> hide sel cartoons

> select #8/T,Z:224-225

32 atoms, 32 bonds, 4 residues, 1 model selected  

> select #8/T,Z:224-235

210 atoms, 216 bonds, 24 residues, 1 model selected  

> hide sel cartoons

> select #4/I:3079@O

1 atom, 1 residue, 1 model selected  

> select #4/I:3089@O

1 atom, 1 residue, 1 model selected  

> select add #4

6388 atoms, 5056 bonds, 6388 residues, 2 models selected  

> select subtract #4

4 models selected  

> hide #!6 models

> show #!6 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!2 models

Cell requested for row 0 is out of bounds for table with 28 rows! Resizing
table model.  

> close #1

> close #3

> open
> /Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb

Summary of feedback from opening
/Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (40 )  
  
Chain information for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
R | No description available  
S W | No description available  
T | No description available  
U | No description available  
V | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!1,8 atoms

> show #!1,8 cartoons

> select add #8

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #8

16 models selected  

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #1.27

36450 atoms, 36947 bonds, 2 pseudobonds, 5094 residues, 28 models selected  

> select subtract #1.25

35708 atoms, 36206 bonds, 2 pseudobonds, 4945 residues, 27 models selected  

> select subtract #1.24

35343 atoms, 35842 bonds, 2 pseudobonds, 4871 residues, 26 models selected  

> select subtract #1.23

34585 atoms, 35085 bonds, 2 pseudobonds, 4720 residues, 25 models selected  

> select subtract #1.22

33838 atoms, 34339 bonds, 2 pseudobonds, 4570 residues, 24 models selected  

> select subtract #1.21

32250 atoms, 32736 bonds, 4305 residues, 22 models selected  

> select subtract #1.19

31170 atoms, 31646 bonds, 4167 residues, 21 models selected  

> select subtract #1.18

30643 atoms, 31111 bonds, 4094 residues, 20 models selected  

> select subtract #1.17

30100 atoms, 30560 bonds, 4019 residues, 19 models selected  

> select subtract #1.16

29557 atoms, 30009 bonds, 3944 residues, 18 models selected  

> select subtract #1.15

29022 atoms, 29466 bonds, 3870 residues, 17 models selected  

> select subtract #1.14

28487 atoms, 28923 bonds, 3796 residues, 16 models selected  

> select subtract #1.13

27944 atoms, 28372 bonds, 3721 residues, 15 models selected  

> select subtract #1.12

27409 atoms, 27829 bonds, 3647 residues, 14 models selected  

> select subtract #1.11

26874 atoms, 27286 bonds, 3573 residues, 13 models selected  

> select subtract #1.10

26358 atoms, 26762 bonds, 3501 residues, 12 models selected  

> hide sel cartoons

> select subtract #1.26

25606 atoms, 26011 bonds, 3350 residues, 11 models selected  

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 11 models selected  

> select subtract #1

26 models selected  

> select add #1.19

1080 atoms, 138 residues, 1 model selected  

> hide sel cartoons

> select add #1.22

1827 atoms, 288 residues, 2 models selected  

> select add #1.23

2585 atoms, 439 residues, 3 models selected  

> select add #1.25

3327 atoms, 588 residues, 4 models selected  

> select add #1.26

4079 atoms, 739 residues, 5 models selected  

> select add #1.24

4444 atoms, 813 residues, 6 models selected  

> hide sel cartoons

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 8 models selected  

> select subtract #1

26 models selected  

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> select add #1.27

3130 atoms, 543 residues, 2 models selected  

> color (#!1 & sel) forest green

> select subtract #1.21

1542 atoms, 278 residues, 3 models selected  

> select subtract #1.27

1 model selected  

> select add #1.9

543 atoms, 75 residues, 1 model selected  

> select add #1.10

1059 atoms, 147 residues, 2 models selected  

> select add #1.11

1594 atoms, 221 residues, 3 models selected  

> select add #1.12

2129 atoms, 295 residues, 4 models selected  

> select add #1.13

2672 atoms, 370 residues, 5 models selected  

> select add #1.14

3207 atoms, 444 residues, 6 models selected  

> select add #1.15

3742 atoms, 518 residues, 7 models selected  

> select add #1.16

4285 atoms, 593 residues, 8 models selected  

> select add #1.17

4828 atoms, 668 residues, 9 models selected  

> select add #1.18

5355 atoms, 741 residues, 10 models selected  

> color (#!1 & sel) #f5ccdc7f

> color (#!1 & sel) #f5ccdc73

> color (#!1 & sel) #f5ccdc76

> color (#!1 & sel) #f5ccdc81

> color (#!1 & sel) #f5ccdca6

> color (#!1 & sel) #f5ccdcbb

> color (#!1 & sel) #f5ccdcff

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 12 models selected  

> select subtract #1

26 models selected  

Cell requested for row 0 is out of bounds for table with 34 rows! Resizing
table model.  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!8 models

> show #!1 models

> select clear

> select add #1.9

543 atoms, 75 residues, 1 model selected  

> select subtract #1.9

1 model selected  

> select add #1.9

543 atoms, 75 residues, 1 model selected  

> show sel cartoons

> select subtract #1.9

1 model selected  

> select #1/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style (#!1 & sel) stick

Changed 11 atom styles  

> select clear

> hide #!1 models

> show #!8 models

> select #8/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select add #8

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 3 models selected  

> show #!1 models

> select subtract #8

16 models selected  

> hide #!8 models

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style (#!1 & sel) stick

Changed 11 atom styles  

> select clear

> open ""/Users/wujingyi/Desktop/RfxATPasePDB+map_new/local
> map/Fo/J546_state1_synthasis_Fo_3.52A_14.82w.mrc""

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc as #3, grid size 400,400,400,
pixel 0.93, shown at level 0.041, step 2, values float32  

> volume #3 step 1

> volume #3 level 0.1262

> volume #3 level 0.1343

> color zone #3 near #1 distance 5.58

> surface dust #3 size 9.3

> volume #3 level 0.1059

> ui tool show ""Color Zone""

> color zone #3 near #1 distance 5.58

> volume splitbyzone #3

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  

> surface dust #9.3 size 9.3

> surface dust #9.4 size 9.3

> surface dust #9.12 size 9.3

> surface dust #9.17 size 9.3

> surface dust #9.18 size 9.3

> surface dust #9.19 size 9.3

> surface dust #9.20 size 9.3

> surface dust #9.21 size 9.3

> surface dust #9.22 size 9.3

> volume #9.17 level 0.08025

> volume #9.12 color #f5ccdc80

> volume #9.17 color #228b2275

> select #8/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #8/H,L,O-P:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show #!1 atoms

> hide #!1 atoms

Drag select of 9.12 J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 , 1283
residues, 3 pseudobonds  
Alignment identifier is 1/I  
Alignment identifier is 1/Q  
Alignment identifier is 1  
Alignment identifier is 2  
Alignment identifier is 1/T  
Alignment identifier is 1/Z  

> select #1/N,M,K,J:3

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #1/N,M,K,J

2140 atoms, 2172 bonds, 296 residues, 1 model selected  

> hide sel cartoons

> select #1/P,O,L,H:3

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #1/P,O,L,H

2172 atoms, 2204 bonds, 300 residues, 1 model selected  

> hide sel cartoons

> select #1/Q:3

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/Q

527 atoms, 535 bonds, 73 residues, 1 model selected  

> hide sel cartoons

> select #1/I:3

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/I

516 atoms, 524 bonds, 72 residues, 1 model selected  

> hide sel cartoons

> select #1/I:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/I:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> style (#!1 & sel) stick

Changed 29 atom styles  

> hide sel atoms

> select #1/Q:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/Q:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #1/P,O,L,H:57

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #1/P,O,L,H:57-60

116 atoms, 112 bonds, 16 residues, 1 model selected  

> select #1/P,O,L,H:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #1/P,O,L,H:58-61

116 atoms, 112 bonds, 16 residues, 1 model selected  

> show sel cartoons

> select #1/N,M,K,J:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #1/N,M,K,J:58-60

84 atoms, 80 bonds, 12 residues, 1 model selected  

> select #1/N,M,K,J:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #1/N,M,K,J:58-61

116 atoms, 112 bonds, 16 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59-60

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/Q:58-59

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/Q:58-59

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/P,O,L,H:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/P,O,L,H:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #1/N,M,K,J:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #1/N,M,K,J:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> style #1#9.12#!9 stick

Changed 37992 atom styles  

> hide #!9.12 models

> show #!9.17 models

> color zone #9.17 near #1 distance 5.58

> volume #9.17 level 0.09308

> volume #9.17 color #228b2233

> select clear

> select #1/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) byhetero

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) byhetero

> select #1/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select clear

> style #1#!9 ball

Changed 37992 atom styles  

> select clear

> select #1/P,O,L,H:3

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #1/P,O,L,H

2172 atoms, 2204 bonds, 300 residues, 1 model selected  

> select #1/T:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:1-219

940 atoms, 945 bonds, 2 pseudobonds, 169 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-197

787 atoms, 785 bonds, 1 pseudobond, 160 residues, 2 models selected  

> hide sel cartoons

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> hide sel cartoons

> select #1/T:220

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:220-240

108 atoms, 107 bonds, 21 residues, 1 model selected  

> hide sel cartoons

> select #1/T:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:1-239

1040 atoms, 1045 bonds, 2 pseudobonds, 189 residues, 2 models selected  

> select #1/T:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:1-240

1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected  

> select clear

> select #1/T:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:1-240

1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected  

> color (#!1 & sel) white

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> color (#!1 & sel) white

> show sel cartoons

> select #1/T:1-2

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/T:1-240

1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected  

> show sel cartoons

> select clear

> color zone #3 near #1 distance 5.58

> volume splitbyzone #3

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #10.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #10.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #10.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #10.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #10.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #10.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #10.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #10.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #10.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #10.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #10.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #10.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #10.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #10.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #10.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #10.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #10.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #10.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #10.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #10.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #10.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #10.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  

> surface dust #10.12 size 9.3

> surface dust #10.18 size 9.3

> select #1/T:1-15

74 atoms, 73 bonds, 15 residues, 1 model selected  

> select #1/T:1-240

1048 atoms, 1053 bonds, 2 pseudobonds, 190 residues, 2 models selected  

> hide sel cartoons

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> hide sel cartoons

> volume #10.18 color #228b222f

> volume #10.18 color #228b2220

> volume #10.18 level 0.1266

> volume #10.18 level -0.04986

> volume #10.18 level 0.1485

> volume #10.18 level 0.1716

> hide #!9 models

> hide #!10 models

> hide #!1 models

> show #!8 models

> hide #!8 models

> show #!1 models

> cartoon style (#!1 & sel) modeHelix tube sides 20

> show #!10 models

> hide #!10 models

> show #!9 models

> volume #10.18 color forestgreen

> volume #10.18 level 0.04628

> volume #10.18

[Repeated 1 time(s)]

> hide #!1 models

> show #!1 models

> cartoon style (#!1 & sel) xsection oval modeHelix default

> close #10

> close #9

> show #!3 models

> color zone #3 near #1 distance 5.58

> volume splitbyzone #3

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  

> hide #!9 models

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 3 models selected  

> select clear

> select #1/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #1/Z:259

22 atoms, 20 bonds, 2 residues, 2 models selected  

> color (#!1 & sel) forest green

> select clear

> close #9

> show #!3 models

> color zone #3 near #1 distance 5.58

[Repeated 3 time(s)]

> volume splitbyzone #3

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  

> volume #9.18 color #228b2236

> volume #9.12 color #f5ccdc10

> select clear

> surface dust #9.6 size 9.3

> surface dust #9.7 size 9.3

> surface dust #9.8 size 9.3

> surface dust #9.9 size 9.3

> surface dust #9.10 size 9.3

> surface dust #9.11 size 9.3

> surface dust #9.18 size 9.3

> surface dust #9.22 size 9.3

> hide #!9 models

> show #!9 models

> close #9

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> select add #1.21

3130 atoms, 543 residues, 2 models selected  

> color (#!1 & sel) forest green

> select subtract #1.27

1588 atoms, 265 residues, 3 models selected  

> select subtract #1.21

1 model selected  

> select add #1.22

747 atoms, 150 residues, 1 model selected  

> select subtract #1.22

1 model selected  

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> select add #1.27

3130 atoms, 543 residues, 2 models selected  

> show sel cartoons

> select subtract #1.27

1588 atoms, 265 residues, 3 models selected  

> select subtract #1.21

1 model selected  

> show #!3 models

> color zone #3 near #1 distance 5.58

> volume splitbyzone #3

Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 0 as #9.1, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 1 as #9.2, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 2 as #9.3, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 3 as #9.4, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 4 as #9.5, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 5 as #9.6, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 6 as #9.7, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 7 as #9.8, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 8 as #9.9, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 9 as #9.10, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 10 as #9.11, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 11 as #9.12, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 12 as #9.13, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 13 as #9.14, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 14 as #9.15, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 15 as #9.16, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 16 as #9.17, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 17 as #9.18, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 18 as #9.19, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 19 as #9.20, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 20 as #9.21, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  
Opened J546_state1_synthasis_Fo_3.52A_14.82w.mrc 21 as #9.22, grid size
400,400,400, pixel 0.93, shown at level 0.106, step 1, values float32  

> volume #9.17 color #228b2226

> ui mousemode right ""map eraser""

> color zone #3 near #1 distance 5.46

> color zone #3 near #1 distance 1.16

Can only have one displayed volume when erasing  

[Repeated 3 time(s)]

> volume erase #9.17 center 152.43,174.17,258.92 radius 19.158

> volume erase #9.17 center 153.75,161.59,282.41 radius 19.158

> volume erase #9.17 center 173.67,140.98,285.93 radius 19.158

> volume erase #9.17 center 214.92,154.35,251.25 radius 19.158

> volume erase #9.17 center 189.54,139.56,230.38 radius 19.158

> volume erase #9.17 center 161.94,132.72,255.5 radius 19.158

> volume erase #9.17 center 165.94,129.39,251.54 radius 19.158

> volume erase #9.17 center 219.48,213.42,266.64 radius 19.158

> volume erase #9.17 center 222.62,211.3,261.28 radius 19.158

> volume erase #9.17 center 201.59,143.68,253.31 radius 19.158

> volume erase #9.17 center 175.09,146.43,234.13 radius 19.158

> volume erase #9.17 center 146.96,145.6,254.29 radius 19.158

> volume erase #9.17 center 152.14,200.47,260.87 radius 19.158

> volume erase #9.17 center 190.15,234.78,248.78 radius 19.158

> volume erase #9.17 center 208.66,210.82,271.16 radius 19.158

> volume erase #9.17 center 184.43,226.41,289.75 radius 19.158

> volume erase #9.17 center 187.4,240.87,276.81 radius 19.158

> volume erase #9.17 center 151.67,225.5,267.55 radius 19.158

> volume erase #9.17 center 187.86,206.62,234.8 radius 19.158

> volume erase #9.17 center 176.45,240.53,245.58 radius 19.158

> volume erase #9.17 center 164.05,207.38,291.8 radius 19.158

> volume erase #9.17 center 174.07,217.65,283.92 radius 19.158

> volume erase #9.17 center 157.44,141.71,273.58 radius 19.158

> volume erase #9.17 center 205.82,146.87,282.2 radius 19.158

> volume erase #9.17 center 210.51,210.58,302.68 radius 19.158

> volume erase #9.17 center 172.25,216.53,237.66 radius 19.158

> volume erase #9.17 center 169.46,209.2,240.77 radius 19.158

> volume erase #9.17 center 173.94,234.22,258.62 radius 19.158

> volume erase #9.17 center 181.73,229.18,264.5 radius 19.158

> volume erase #9.17 center 169.94,155.29,236.77 radius 19.158

> volume erase #9.17 center 155.37,158.7,264.92 radius 19.158

> volume erase #9.17 center 177.66,127.42,250.24 radius 19.158

> volume erase #9.17 center 158.83,130.61,239.24 radius 19.158

> volume erase #9.17 center 212.13,147.59,256.04 radius 19.158

> volume erase #9.17 center 192.4,127.04,250.84 radius 19.158

> volume erase #9.17 center 190.29,130.33,251.54 radius 19.158

> volume erase #9.17 center 204.59,208.99,283.98 radius 19.158

> volume erase #9.17 center 187.77,212.27,256.33 radius 6.882

> volume erase #9.17 center 193.69,215,255.53 radius 6.882

> volume erase #9.17 center 194.62,211.78,255.47 radius 6.882

> volume erase #9.17 center 180.75,209.09,252.83 radius 6.882

> volume erase #9.17 center 170.21,213.47,264.81 radius 6.882

> volume erase #9.17 center 168.33,212.78,263.85 radius 6.882

> volume erase #9.17 center 168.44,204.13,263.27 radius 6.882

> volume erase #9.17 center 172.82,196.61,273.72 radius 6.882

> volume erase #9.17 center 190.83,210.71,259.96 radius 6.882

> volume erase #9.17 center 171.54,201.29,268.16 radius 6.882

> volume erase #9.17 center 174.54,211.12,257.86 radius 6.882

> volume erase #9.17 center 172,211.23,261.44 radius 6.882

> volume erase #9.17 center 182.86,208.02,253.73 radius 6.882

> volume erase #9.17 center 178.01,210.41,254.54 radius 6.882

> volume erase #9.17 center 189.64,203.09,265.12 radius 3.534

> volume erase #9.17 center 189.22,205.57,265.53 radius 3.534

> volume erase #9.17 center 188.71,205.82,265.38 radius 3.534

> volume erase #9.17 center 188.45,204.8,265.02 radius 3.534

> volume erase #9.17 center 189.33,209.68,269.7 radius 3.534

> volume erase #9.17 center 189.57,204.42,269.41 radius 3.534

> volume erase #9.17 center 187.92,203.87,268.41 radius 3.534

> volume erase #9.17 center 188.87,208.36,272.62 radius 3.534

> volume erase #9.17 center 178.66,201.46,269.96 radius 3.534

> volume erase #9.17 center 175.41,205.33,266.51 radius 3.534

> volume erase #9.17 center 175.35,202.29,266.21 radius 3.534

> volume erase #9.17 center 175.21,209.99,266.38 radius 3.534

> volume erase #9.17 center 176.57,208.71,265.3 radius 3.534

> undo

> volume erase #9.17 center 174.1,160.84,260.26 radius 3.534

> volume erase #9.17 center 173.62,150.17,257.32 radius 3.534

> volume erase #9.17 center 178.44,147.87,255.11 radius 3.534

> volume erase #9.17 center 177.46,144.05,262.45 radius 6.138

> volume erase #9.17 center 187.16,144.91,265.74 radius 6.138

> volume erase #9.17 center 178.72,143.64,266.97 radius 6.138

> volume erase #9.17 center 174.72,144.39,267.55 radius 6.138

> volume erase #9.17 center 184.24,143.74,260.01 radius 6.138

> volume erase #9.17 center 178.58,149.45,271.81 radius 6.138

> volume erase #9.17 center 188.85,148.87,268.7 radius 6.138

> volume erase #9.17 center 194.67,148.29,267.3 radius 6.138

> volume erase #9.17 center 185.16,146.15,274.14 radius 6.138

> volume erase #9.17 center 189.87,155.34,246.5 radius 6.138

> volume erase #9.17 center 185.27,153.7,249.93 radius 6.138

> volume erase #9.17 center 180.63,153.4,249.85 radius 6.138

> volume erase #9.17 center 172.1,152.35,253.37 radius 6.138

> volume erase #9.17 center 180.4,149.7,253.14 radius 6.138

> volume erase #9.17 center 182.05,147.51,256.42 radius 6.138

> volume erase #9.17 center 174.18,158.85,280.12 radius 6.138

> volume erase #9.17 center 190.24,152.7,260.54 radius 6.138

> volume erase #9.17 center 183.35,148.58,269.85 radius 6.138

> volume erase #9.17 center 168.89,153.93,268.14 radius 6.138

> volume erase #9.17 center 170.22,163.27,261.84 radius 6.138

> volume erase #9.17 center 172.78,146.62,264.18 radius 6.138

> volume erase #9.17 center 172.3,159.1,268.25 radius 6.138

> volume erase #9.17 center 176.79,165.54,279.84 radius 6.138

> volume erase #9.17 center 168.04,159.46,256.93 radius 6.138

> volume erase #9.17 center 170.91,155.78,254.37 radius 6.138

> volume erase #9.17 center 194.02,154.01,257.87 radius 6.138

> volume erase #9.17 center 195.18,156.17,260.96 radius 6.138

> volume erase #9.17 center 186.13,148.92,261.48 radius 2.046

> ui tool show ""Side View""

> view

> volume erase #9.17 center 185.47,151.71,264.21 radius 2.046

> volume erase #9.17 center 184.33,153.52,266.53 radius 2.046

> volume erase #9.17 center 185.22,151.18,263.04 radius 2.046

> volume erase #9.17 center 183.72,151.59,262.72 radius 2.046

> volume erase #9.17 center 185.28,153.23,262.99 radius 2.046

> volume erase #9.17 center 184.9,155.85,263.52 radius 2.046

> volume erase #9.17 center 184.9,155.85,263.52 radius 2.604

> volume erase #9.17 center 183.67,152.73,263.6 radius 2.604

> view

> style #1#9.17#!9 stick

Changed 37992 atom styles  

> open
> /Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb

Summary of feedback from opening
/Users/wujingyi/Desktop/RfxATPasePDB+map_new/RfxATPase_PDB/J436_state1_synthasis_2.82A_14.82w-coot-3.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (40 )  
  
Chain information for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
R | No description available  
S W | No description available  
T | No description available  
U | No description available  
V | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!1,11 atoms

> show #!1,11 cartoons

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #1.26

37240 atoms, 37746 bonds, 3 pseudobonds, 5221 residues, 28 models selected  

> select subtract #1.25

36498 atoms, 37005 bonds, 3 pseudobonds, 5072 residues, 27 models selected  

> select subtract #1.24

36133 atoms, 36641 bonds, 3 pseudobonds, 4998 residues, 26 models selected  

> select subtract #1.23

35375 atoms, 35884 bonds, 3 pseudobonds, 4847 residues, 25 models selected  

> select subtract #1.22

34628 atoms, 35138 bonds, 3 pseudobonds, 4697 residues, 24 models selected  

> select subtract #1.20

34263 atoms, 34774 bonds, 3 pseudobonds, 4623 residues, 23 models selected  

> select subtract #1.19

33183 atoms, 33684 bonds, 3 pseudobonds, 4485 residues, 22 models selected  

> select subtract #1.2

29378 atoms, 29821 bonds, 3 pseudobonds, 3987 residues, 21 models selected  

> select subtract #1.3

25585 atoms, 25970 bonds, 3 pseudobonds, 3491 residues, 20 models selected  

> select subtract #1.4

21763 atoms, 22090 bonds, 3 pseudobonds, 2991 residues, 19 models selected  

> select subtract #1.5

18169 atoms, 18433 bonds, 3 pseudobonds, 2522 residues, 18 models selected  

> select subtract #1.6

14564 atoms, 14765 bonds, 3 pseudobonds, 2052 residues, 17 models selected  

> select subtract #1.7

10978 atoms, 11116 bonds, 3 pseudobonds, 1584 residues, 16 models selected  

> select subtract #1.8

8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 15 models selected  

> hide sel cartoons

Cell requested for row 10 is out of bounds for table with 38 rows! Resizing
table model.  

> hide #!11 models

> show #!11 models

> hide #!1 models

> select add #11

46688 atoms, 47303 bonds, 6 pseudobonds, 6667 residues, 16 models selected  

> show sel & #!11 surfaces

> hide sel & #!11 surfaces

> select subtract #11

8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 40 models selected  

> select add #11.2

12501 atoms, 8806 bonds, 3 pseudobonds, 1793 residues, 15 models selected  

> select add #11.3

16294 atoms, 8806 bonds, 3 pseudobonds, 2289 residues, 16 models selected  

> select add #11.4

20116 atoms, 8806 bonds, 3 pseudobonds, 2789 residues, 17 models selected  

> select add #11.6

23721 atoms, 8806 bonds, 3 pseudobonds, 3259 residues, 18 models selected  

> select add #11.5

27315 atoms, 8806 bonds, 3 pseudobonds, 3728 residues, 19 models selected  

> select add #11.7

30901 atoms, 8806 bonds, 3 pseudobonds, 4196 residues, 20 models selected  

> select add #11.8

33183 atoms, 8806 bonds, 3 pseudobonds, 4485 residues, 21 models selected  

> select add #11.19

34263 atoms, 8806 bonds, 3 pseudobonds, 4623 residues, 22 models selected  

> select add #11.20

34628 atoms, 8806 bonds, 3 pseudobonds, 4697 residues, 23 models selected  

> select add #11.24

34993 atoms, 8806 bonds, 3 pseudobonds, 4771 residues, 24 models selected  

> select add #11.26

35745 atoms, 8806 bonds, 3 pseudobonds, 4922 residues, 25 models selected  

> select add #11.25

36487 atoms, 8806 bonds, 3 pseudobonds, 5071 residues, 26 models selected  

> select add #11.22

37234 atoms, 8806 bonds, 3 pseudobonds, 5221 residues, 27 models selected  

> select add #11.23

37992 atoms, 8806 bonds, 3 pseudobonds, 5372 residues, 28 models selected  

> hide sel & #!11 cartoons

> select add #11

46688 atoms, 47303 bonds, 6 pseudobonds, 6667 residues, 30 models selected  

> select subtract #11

8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 40 models selected  

> select add #11.27

10238 atoms, 8806 bonds, 3 pseudobonds, 1573 residues, 15 models selected  

> select add #11.21

11826 atoms, 8806 bonds, 3 pseudobonds, 1838 residues, 16 models selected  

> color (#!11 & sel) forest green

> select subtract #11.21

10238 atoms, 8806 bonds, 3 pseudobonds, 1573 residues, 17 models selected  

> select subtract #11.27

8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 15 models selected  

> select add #11.18

9223 atoms, 8806 bonds, 3 pseudobonds, 1368 residues, 15 models selected  

> select add #11.17

9766 atoms, 8806 bonds, 3 pseudobonds, 1443 residues, 16 models selected  

> select add #11.16

10309 atoms, 8806 bonds, 3 pseudobonds, 1518 residues, 17 models selected  

> select add #11.15

10844 atoms, 8806 bonds, 3 pseudobonds, 1592 residues, 18 models selected  

> select add #11.14

11379 atoms, 8806 bonds, 3 pseudobonds, 1666 residues, 19 models selected  

> select add #11.13

11922 atoms, 8806 bonds, 3 pseudobonds, 1741 residues, 20 models selected  

> select add #11.12

12457 atoms, 8806 bonds, 3 pseudobonds, 1815 residues, 21 models selected  

> select add #11.11

12992 atoms, 8806 bonds, 3 pseudobonds, 1889 residues, 22 models selected  

> select add #11.10

13508 atoms, 8806 bonds, 3 pseudobonds, 1961 residues, 23 models selected  

> select add #11.9

14051 atoms, 8806 bonds, 3 pseudobonds, 2036 residues, 24 models selected  

> color (#!11 & sel) #f5ccdcff

> select add #11

46688 atoms, 47303 bonds, 6 pseudobonds, 6667 residues, 26 models selected  

> select subtract #11

8696 atoms, 8806 bonds, 3 pseudobonds, 1295 residues, 40 models selected  

> view

> color zone #3 near #1 distance 1.06

> color zone #3 near #1 distance 0.96

> color zone #3 near #1 distance 0.95

> ui mousemode right select

> select #11/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #11/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> style #11#!9 stick

Changed 37992 atom styles  
Drag select of 74 residues  
Drag select of 85 residues  
Alignment identifier is 11/I  
Alignment identifier is 11/Q  
Alignment identifier is 1  
Alignment identifier is 2  

> select #11/I:3

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #11/I

516 atoms, 524 bonds, 72 residues, 1 model selected  

> hide sel cartoons

> select #11/N,M,K,J:3

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #11/N,M,K,J

2140 atoms, 2172 bonds, 296 residues, 1 model selected  

> hide sel cartoons

> select #11/P,O,L,H:3

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #11/P,O,L,H

2172 atoms, 2204 bonds, 300 residues, 1 model selected  

> hide sel cartoons

> select #11/Q:3

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #11/Q

527 atoms, 535 bonds, 73 residues, 1 model selected  

> hide sel cartoons

> select #11/N,M,K,J:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #11/N,M,K,J:58-61

116 atoms, 112 bonds, 16 residues, 1 model selected  

> show sel cartoons

> select #11/P,O,L,H:58

28 atoms, 24 bonds, 4 residues, 1 model selected  

> select #11/P,O,L,H:58-61

116 atoms, 112 bonds, 16 residues, 1 model selected  

> show sel cartoons

> select #11/Q:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/Q:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #11/I:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/I:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select clear

> lighting soft

> select #11/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #11/I:4-39,41-73

489 atoms, 495 bonds, 69 residues, 1 model selected  

> select #11/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #11/P,O,L,H:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #11/P,O,L,H:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select #11/N,M,K,J:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #11/N,M,K,J:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

> show #!1 models

> select add #1.2

3805 atoms, 498 residues, 1 model selected  

> select add #1.3

7598 atoms, 994 residues, 2 models selected  

> select add #1.4

11420 atoms, 1494 residues, 3 models selected  

> select add #1.5

15014 atoms, 1963 residues, 4 models selected  

> select add #1.6

18619 atoms, 2433 residues, 5 models selected  

> select add #1.7

22205 atoms, 2901 residues, 6 models selected  

> select add #1.8

24487 atoms, 3190 residues, 7 models selected  

> select add #1.9

25030 atoms, 3265 residues, 8 models selected  

> select add #1.10

25546 atoms, 3337 residues, 9 models selected  

> select subtract #1.10

25030 atoms, 3265 residues, 10 models selected  

> select subtract #1.9

24487 atoms, 3190 residues, 9 models selected  

> hide sel cartoons

> select add #1.19

25567 atoms, 3328 residues, 8 models selected  

> select add #1.20

25932 atoms, 3402 residues, 9 models selected  

> select add #1.24

26297 atoms, 3476 residues, 10 models selected  

> select add #1.22

27044 atoms, 3626 residues, 11 models selected  

> select add #1.23

27802 atoms, 3777 residues, 12 models selected  

> select add #1.25

28544 atoms, 3926 residues, 13 models selected  

> select add #1.26

29296 atoms, 4077 residues, 14 models selected  

> hide sel cartoons

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 16 models selected  

> select subtract #1

26 models selected  

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> show sel cartoons

> select subtract #1.21

1 model selected  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> show sel cartoons

> select subtract #1.27

1 model selected  

> select add #11.21

1588 atoms, 265 residues, 1 model selected  

> select add #11.27

3130 atoms, 543 residues, 2 models selected  

> hide sel cartoons

> select subtract #11.21

1542 atoms, 278 residues, 3 models selected  

> select subtract #11.27

1 model selected  

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> cartoon style (#!1 & sel) modeHelix tube sides 20

> select subtract #1

26 models selected  

> color #1,11#!9 byhetero

> select clear

[Repeated 1 time(s)]

> volume #9.12 color #f5ccdc27

> ui mousemode right ""map eraser""

Can only have one displayed volume when erasing  

> volume erase #9.12 center 184.1,172.1,227.7 radius 15.252

> volume erase #9.12 center 184.32,173.74,226.15 radius 21.39

> volume erase #9.12 center 186.52,200.84,224.47 radius 21.39

> volume erase #9.12 center 185.09,179.62,220.84 radius 21.39

> volume erase #9.12 center 170.15,177.87,222.26 radius 21.39

> volume erase #9.12 center 215.69,164.39,225.17 radius 21.39

> volume erase #9.12 center 216.27,170.95,228.22 radius 21.39

> volume erase #9.12 center 219.37,188.32,232.19 radius 21.39

> volume erase #9.12 center 221.77,198.05,232.67 radius 21.39

> volume erase #9.12 center 199.82,151.87,227.61 radius 21.39

> volume erase #9.12 center 210.63,174.67,229.21 radius 21.39

> volume erase #9.12 center 189.58,200.46,228.62 radius 21.39

> volume erase #9.12 center 201.15,199.61,227.53 radius 21.39

> volume erase #9.12 center 169.94,190.74,229.69 radius 21.39

> volume erase #9.12 center 169.7,163.35,224.36 radius 21.39

> volume erase #9.12 center 169.9,173.13,228.26 radius 21.39

> volume erase #9.12 center 170.12,179.65,296.99 radius 21.39

> volume erase #9.12 center 176.61,190.26,292.89 radius 21.39

> volume erase #9.12 center 185.4,157.68,290.36 radius 21.39

> volume erase #9.12 center 213.28,183.99,298.98 radius 21.39

> volume erase #9.12 center 213.03,159.31,289.71 radius 21.39

> volume erase #9.12 center 208.87,201.17,291.62 radius 21.39

> volume erase #9.12 center 215.87,170.23,292.11 radius 21.39

> volume erase #9.12 center 196.57,176.8,291.69 radius 21.39

> volume erase #9.12 center 191.52,210.19,292.08 radius 21.39

> volume erase #9.12 center 171.81,170.99,288.63 radius 21.39

> volume erase #9.12 center 210.68,175.67,289.23 radius 21.39

> volume erase #9.12 center 206.45,189.34,233.5 radius 21.39

> volume erase #9.12 center 209.93,175.44,233.17 radius 21.39

> volume erase #9.12 center 200.8,206.37,235.59 radius 21.39

> volume erase #9.12 center 183.1,160.4,230.21 radius 21.39

> volume erase #9.12 center 175.47,172.03,232.27 radius 21.39

> volume erase #9.12 center 160.52,176.91,233.03 radius 21.39

> volume erase #9.12 center 166.54,188.87,234.37 radius 21.39

> volume erase #9.12 center 189.24,182.31,255.42 radius 7.812

> volume erase #9.12 center 188.92,183.04,248.3 radius 7.812

> volume erase #9.12 center 187.49,182.01,258.55 radius 7.812

> volume erase #9.12 center 185.79,180.87,262.65 radius 7.812

> volume erase #9.12 center 185.95,179.3,267.44 radius 6.882

> volume erase #9.12 center 185.26,182.54,267.4 radius 6.882

> volume erase #9.12 center 189.69,183.11,267.13 radius 6.882

> volume erase #9.12 center 190.92,180.28,267.14 radius 6.882

> volume erase #9.12 center 215.04,190.21,264.25 radius 6.882

> surface dust #9.12 size 9.3

> volume erase #9.12 center 184.24,174.01,269.49 radius 6.882

> volume erase #9.12 center 191.11,173.89,268.94 radius 9.3

> volume erase #9.12 center 190.48,172.8,268.72 radius 9.3

> volume erase #9.12 center 193.88,181.19,269.01 radius 9.3

> volume erase #9.12 center 187.96,184.06,270.77 radius 9.3

> volume erase #9.12 center 185.52,183.78,269.87 radius 9.3

> volume erase #9.12 center 183.1,182.21,269.56 radius 9.3

> volume erase #9.12 center 184.72,178.47,262.38 radius 9.3

> volume erase #9.12 center 185.13,178.34,260.06 radius 9.3

> volume erase #9.12 center 188.45,179.77,258.99 radius 9.3

> volume erase #9.12 center 189.45,182.63,259.39 radius 9.3

> volume erase #9.12 center 187.75,185.93,259.34 radius 9.3

> volume erase #9.12 center 183.66,183.86,258.44 radius 9.3

> volume erase #9.12 center 184.18,178.26,255.5 radius 9.3

> volume erase #9.12 center 192.37,182.56,255.04 radius 9.3

> volume erase #9.12 center 192.09,179.03,255.86 radius 9.3

> volume erase #9.12 center 184.66,187.36,250.02 radius 9.3

> volume erase #9.12 center 177.46,188.32,248.92 radius 9.3

> volume erase #9.12 center 187.86,175.68,260.08 radius 9.3

> volume erase #9.12 center 184.25,176.71,260.31 radius 9.3

> volume erase #9.12 center 189.78,175.3,251.29 radius 9.3

> volume erase #9.12 center 193.96,181.47,255.43 radius 9.3

> volume erase #9.12 center 193.73,183.07,258.27 radius 9.3

> volume erase #9.12 center 192.98,179.02,257.36 radius 9.3

> volume erase #9.12 center 183.39,200.21,279.43 radius 9.3

> volume erase #9.12 center 172.34,194.09,277.6 radius 9.3

> volume erase #9.12 center 166.7,183.16,275.79 radius 9.3

> volume erase #9.12 center 167.25,189.29,276.18 radius 9.3

> volume erase #9.12 center 175.93,157.41,272.95 radius 9.3

> volume erase #9.12 center 172.21,159.67,272.12 radius 9.3

> volume erase #9.12 center 160.83,175.29,272.1 radius 9.3

> volume erase #9.12 center 197.05,158.92,273.59 radius 9.3

> volume erase #9.12 center 185.44,160.03,273.73 radius 9.3

> volume erase #9.12 center 203.92,166.03,275.21 radius 9.3

> volume erase #9.12 center 206.96,192,276.94 radius 9.3

> volume erase #9.12 center 193.11,199.4,277.69 radius 9.3

> volume erase #9.12 center 181.19,180.13,268.05 radius 9.3

> volume erase #9.12 center 187.06,185.68,265.92 radius 9.3

> volume erase #9.12 center 183.64,184.63,262.57 radius 9.3

> volume erase #9.12 center 154.78,187.08,258.92 radius 9.3

> volume erase #9.12 center 209.28,182.52,275.57 radius 9.3

> volume erase #9.12 center 211.12,177.72,275.43 radius 9.3

> volume erase #9.12 center 211.62,173.18,272.77 radius 9.3

> volume erase #9.12 center 201.18,199.48,275.42 radius 9.3

> volume erase #9.12 center 190.27,185.12,264.27 radius 9.3

> volume erase #9.12 center 190.37,185.81,264.28 radius 9.3

> volume erase #9.12 center 192.76,183.8,261.73 radius 9.3

> volume erase #9.12 center 211.01,157.81,252.3 radius 9.3

> volume erase #9.12 center 197.77,162.56,247.3 radius 6.138

> volume erase #9.12 center 194.95,174.09,254.2 radius 6.138

> volume erase #9.12 center 194.54,175.08,258.85 radius 6.138

> volume erase #9.12 center 198.16,180.12,259.16 radius 6.138

> volume erase #9.12 center 178.51,176.9,258 radius 6.138

> volume erase #9.12 center 186.02,194.42,251.21 radius 6.138

> volume erase #9.12 center 180.91,201.48,247.92 radius 6.138

> volume erase #9.12 center 177.32,202.11,251.5 radius 6.138

> volume erase #9.12 center 189.36,204.86,251.93 radius 6.138

> volume erase #9.12 center 196.64,165.41,246.98 radius 6.138

> volume erase #9.12 center 202.11,164.05,248.42 radius 6.138

> volume erase #9.12 center 188.59,163.81,247.75 radius 6.138

> volume erase #9.12 center 206.74,177.37,271.52 radius 6.138

> volume erase #9.12 center 207.27,177.56,269.78 radius 6.138

> volume erase #9.12 center 212.56,177.76,269.99 radius 6.138

> volume erase #9.12 center 192.22,190.68,265.26 radius 6.138

> volume erase #9.12 center 203.15,185.1,272.41 radius 6.138

> volume erase #9.12 center 209.61,188.74,255.54 radius 3.348

> volume erase #9.12 center 209.12,176.58,253.99 radius 3.348

> volume erase #9.12 center 205.76,167.23,266.32 radius 3.348

> volume erase #9.12 center 182.43,162.7,250.28 radius 3.348

> volume erase #9.12 center 168.7,180.89,253.17 radius 3.348

> volume erase #9.12 center 165.82,183.19,255.02 radius 3.348

> volume erase #9.12 center 165.69,179.65,253.86 radius 3.348

> volume erase #9.12 center 167.47,164.1,254.65 radius 3.348

> volume erase #9.12 center 168.13,173.05,255.06 radius 1.488

> volume erase #9.12 center 166.62,188.47,256.38 radius 2.232

> volume erase #9.12 center 175.28,197.9,257.61 radius 2.232

> volume erase #9.12 center 175.57,201.08,256.18 radius 2.232

> volume erase #9.12 center 181.09,195.37,272.08 radius 2.232

> volume erase #9.12 center 179.61,196.92,272.58 radius 3.534

> volume erase #9.12 center 169.64,185.02,266.02 radius 2.046

> volume erase #9.12 center 169.92,183.65,267.55 radius 2.046

> volume erase #9.12 center 169.14,184.16,265.41 radius 2.046

> volume erase #9.12 center 171.46,184.85,262.93 radius 2.046

> volume erase #9.12 center 172.44,183.01,263.15 radius 2.046

> volume erase #9.12 center 185.11,197.53,267.64 radius 2.976

> volume erase #9.12 center 198.09,194.54,267.16 radius 2.976

> volume erase #9.12 center 197.15,195.09,267.25 radius 2.976

> volume erase #9.12 center 202.82,187.35,263.76 radius 2.418

> volume erase #9.12 center 202.99,187.65,265.52 radius 2.418

> volume erase #9.12 center 205.72,188.36,266.97 radius 2.418

> volume erase #9.12 center 199.49,168.29,264.78 radius 2.418

> volume erase #9.12 center 189.36,162.93,264.17 radius 2.418

> volume erase #9.12 center 179.94,167.12,262.62 radius 2.418

> volume erase #9.12 center 179.73,165.96,264.92 radius 2.418

> volume erase #9.12 center 172.3,172.9,264.8 radius 2.418

> volume erase #9.12 center 175.74,193.26,267.56 radius 2.418

> volume erase #9.12 center 188.92,163.79,260.56 radius 1.302

> volume erase #9.12 center 188.44,166,260.96 radius 1.302

> volume erase #9.12 center 191.97,158.18,263.11 radius 1.302

> volume erase #9.12 center 193.63,158.15,263.19 radius 1.302

> volume erase #9.12 center 192.76,159.15,264 radius 1.302

> volume erase #9.12 center 198.51,168.88,254.85 radius 1.302

> volume erase #9.12 center 199.71,169.88,255.91 radius 1.302

> volume erase #9.12 center 199.71,169.88,255.91 radius 1.86

> volume erase #9.12 center 204.17,175.8,261.63 radius 1.86

> volume erase #9.12 center 172.2,195.24,256.4 radius 1.86

> volume erase #9.12 center 171.3,193.77,255.96 radius 1.86

> volume erase #9.12 center 200.87,163.58,255.5 radius 1.86

> volume #9.12 level 0.083

> volume erase #9.12 center 207.93,193.98,255.12 radius 4.65

> volume erase #9.12 center 209.68,201.98,257.22 radius 4.65

> volume erase #9.12 center 214.6,177.35,254.25 radius 4.65

> volume erase #9.12 center 216.87,182.4,258.95 radius 4.65

> volume erase #9.12 center 215.86,171.68,257.39 radius 6.696

> volume erase #9.12 center 206.05,204.49,262.94 radius 6.696

> volume erase #9.12 center 193.24,191.28,250.88 radius 6.696

> volume erase #9.12 center 157.95,174.2,259.6 radius 6.696

> volume erase #9.12 center 159.18,169.52,259.77 radius 6.696

> volume erase #9.12 center 186.01,189.41,261.1 radius 6.696

> volume erase #9.12 center 178.73,183.27,253.83 radius 6.696

> volume erase #9.12 center 211.88,182.74,252.48 radius 6.696

> volume erase #9.12 center 207.36,194.07,251.61 radius 6.696

> volume erase #9.12 center 206.13,164.9,251.38 radius 6.696

> volume erase #9.12 center 207.78,170.34,248.51 radius 6.696

> volume erase #9.12 center 201.27,202.03,253.51 radius 6.696

> volume erase #9.12 center 195,199.31,250.4 radius 6.696

> volume erase #9.12 center 194.47,204.1,253.32 radius 6.696

> volume erase #9.12 center 182.23,202.2,252.09 radius 6.696

> volume erase #9.12 center 169.22,199.88,254.89 radius 6.696

> volume erase #9.12 center 161.93,196.55,257.12 radius 6.696

> volume erase #9.12 center 176.91,206.8,258.12 radius 6.696

> volume erase #9.12 center 173.29,184.41,255.72 radius 2.79

> volume erase #9.12 center 172.18,184.39,256.72 radius 2.79

> volume erase #9.12 center 171.92,185.05,257.24 radius 2.79

> volume erase #9.12 center 169.01,174.26,254.74 radius 2.79

> volume erase #9.12 center 172.08,175.63,261.58 radius 1.488

> volume erase #9.12 center 171.52,175.58,262.8 radius 1.488

> volume erase #9.12 center 196.67,195.6,258.92 radius 1.488

> volume erase #9.12 center 197.62,194.73,262.63 radius 1.488

> volume erase #9.12 center 188.36,203.39,269.5 radius 1.488

> volume erase #9.12 center 188.66,202.09,268.26 radius 1.488

> volume erase #9.12 center 192.04,201.52,269.55 radius 1.488

> volume erase #9.12 center 192.04,201.52,269.55 radius 2.232

> volume erase #9.12 center 194.45,203.49,268.33 radius 2.232

> volume erase #9.12 center 197.18,202.52,267.91 radius 2.232

> volume erase #9.12 center 191.54,203.42,267.86 radius 2.232

> volume erase #9.12 center 207.73,193.75,268.03 radius 2.232

> volume erase #9.12 center 207.6,191.7,266.66 radius 2.232

> volume erase #9.12 center 205.54,195.6,268.01 radius 2.232

> volume erase #9.12 center 209.14,193.95,265.53 radius 2.232

> volume erase #9.12 center 196.62,194.57,264.82 radius 2.232

> volume erase #9.12 center 196.85,191.74,263.62 radius 2.232

> volume erase #9.12 center 186.31,196.72,263.71 radius 2.232

> volume erase #9.12 center 185.88,198.13,264.72 radius 2.232

> volume erase #9.12 center 184.84,195.57,265.65 radius 2.232

> volume erase #9.12 center 172.16,183.66,264.03 radius 2.232

> volume erase #9.12 center 171.76,182.85,263.81 radius 2.232

> volume erase #9.12 center 170.72,184.39,264.98 radius 2.232

> volume erase #9.12 center 171.49,182.88,266.59 radius 2.232

> volume erase #9.12 center 179.15,166.74,261.29 radius 2.232

> volume erase #9.12 center 178.87,164.06,263.52 radius 2.232

> volume erase #9.12 center 198.17,157.98,262.84 radius 2.232

> volume erase #9.12 center 196.37,157.87,264.09 radius 2.232

> volume erase #9.12 center 194.34,158.92,264.5 radius 2.232

> volume erase #9.12 center 195.72,158.08,263.56 radius 2.232

> volume erase #9.12 center 201.58,168.23,265.11 radius 2.232

> volume erase #9.12 center 204.06,178.3,265.26 radius 2.232

> volume erase #9.12 center 207.2,171.8,253.33 radius 2.232

> volume erase #9.12 center 182.09,156.89,255.37 radius 2.232

> volume erase #9.12 center 179.67,158.49,264.13 radius 2.79

> volume erase #9.12 center 199.48,167.75,261.41 radius 1.302

> volume erase #9.12 center 199.29,166.63,262.29 radius 1.302

> volume erase #9.12 center 197.13,168.94,260.81 radius 1.302

> volume erase #9.12 center 196.97,168.35,255.11 radius 1.302

> volume erase #9.12 center 189.83,160.27,254.03 radius 1.302

> volume erase #9.12 center 176.49,163.63,254.58 radius 1.302

> volume erase #9.12 center 173.91,163.42,253.82 radius 1.302

> volume erase #9.12 center 188.4,164.13,260.27 radius 1.302

> volume erase #9.12 center 188.45,164.32,260.22 radius 1.302

> volume erase #9.12 center 187.98,163.39,260.8 radius 1.302

> volume erase #9.12 center 187.93,163.16,262.27 radius 1.302

> volume erase #9.12 center 203.58,186.48,261.77 radius 1.302

> volume erase #9.12 center 188.6,202.12,258.59 radius 1.302

> volume erase #9.12 center 188.13,201.53,258.4 radius 1.302

> volume erase #9.12 center 187.85,202.17,258.04 radius 1.302

> volume erase #9.12 center 196.63,197.98,266.59 radius 1.302

> volume erase #9.12 center 195,201.99,265.96 radius 1.302

> volume erase #9.12 center 195.26,201.96,266.98 radius 2.046

> volume erase #9.12 center 194.1,202.28,266.88 radius 2.046

> volume erase #9.12 center 195.01,201.77,266.73 radius 2.046

> volume erase #9.12 center 169.05,194.15,266.61 radius 2.046

> volume erase #9.12 center 164.62,180.47,265.09 radius 2.046

> volume erase #9.12 center 168.71,180.39,267.54 radius 2.046

> volume erase #9.12 center 169.25,189.34,267.22 radius 2.046

> volume erase #9.12 center 171.83,193.4,267.25 radius 2.046

> volume erase #9.12 center 174.32,199.59,267.49 radius 2.046

> volume erase #9.12 center 204.58,185.48,263.24 radius 2.046

> volume erase #9.12 center 209.04,174.47,254.29 radius 2.046

> volume erase #9.12 center 208.15,174.41,256.03 radius 2.046

> volume erase #9.12 center 209.2,172.04,254.9 radius 2.046

> volume erase #9.12 center 203.32,171.82,253.03 radius 2.046

> volume erase #9.12 center 197.09,167.61,261.64 radius 2.046

> volume erase #9.12 center 190.05,165.29,260.95 radius 2.046

> volume erase #9.12 center 166.94,175.41,255.61 radius 2.046

> volume erase #9.12 center 164.43,178.66,257.44 radius 2.046

> volume erase #9.12 center 165.27,178.75,256.96 radius 2.046

> volume erase #9.12 center 167.95,178.15,254.46 radius 2.046

> volume erase #9.12 center 168.71,191.92,257.08 radius 2.046

> volume erase #9.12 center 171.92,192.05,255.22 radius 2.046

> volume erase #9.12 center 167.56,193.6,258.06 radius 2.046

> volume erase #9.12 center 168.48,192.7,259.22 radius 2.046

> volume erase #9.12 center 167.16,189.2,259.01 radius 2.046

> volume erase #9.12 center 177.73,189.97,265.54 radius 2.046

> volume erase #9.12 center 164.83,176.17,256.01 radius 2.046

> volume erase #9.12 center 187.19,159.39,253.32 radius 2.046

> volume erase #9.12 center 187.76,160.93,254.39 radius 2.046

> volume erase #9.12 center 200.75,161.43,255.11 radius 2.046

> volume erase #9.12 center 199.8,173.83,256.52 radius 2.046

> volume erase #9.12 center 199.88,169.15,256.4 radius 2.046

> volume erase #9.12 center 177.57,193.36,263.08 radius 2.046

> volume erase #9.12 center 177.52,194.14,264.2 radius 2.046

> volume erase #9.12 center 176.39,198.61,270.06 radius 2.046

> volume erase #9.12 center 177.48,199.24,269.15 radius 2.046

> volume erase #9.12 center 180.56,198.81,269.71 radius 2.046

> volume erase #9.12 center 181.64,201.92,267.75 radius 2.046

> volume erase #9.12 center 178.32,201.57,267.94 radius 2.046

> volume erase #9.12 center 179.92,199.74,268.99 radius 2.046

> volume erase #9.12 center 177.91,198.42,268.97 radius 2.046

> volume erase #9.12 center 182.72,200.9,268.03 radius 2.046

> volume erase #9.12 center 168.77,192.56,267.85 radius 2.046

> volume erase #9.12 center 169.88,167,266.26 radius 2.046

> volume erase #9.12 center 168.87,166.02,263.63 radius 2.046

> volume erase #9.12 center 174.56,164.55,254.84 radius 2.046

> volume erase #9.12 center 170.27,169.04,253.83 radius 2.046

> volume erase #9.12 center 171.39,171.99,254.18 radius 2.046

> volume erase #9.12 center 169.11,170.84,254.99 radius 2.046

> volume erase #9.12 center 198.75,191.53,258.17 radius 2.046

> volume erase #9.12 center 200.35,189.69,258.05 radius 2.046

> volume erase #9.12 center 175.1,200.1,259.4 radius 2.046

> volume erase #9.12 center 169.59,167,255.02 radius 2.046

> volume erase #9.12 center 172.21,166.28,254.44 radius 2.046

> volume erase #9.12 center 173.12,169.18,253.77 radius 2.046

> volume erase #9.12 center 175.59,165.3,256.26 radius 1.116

> volume erase #9.12 center 210.55,180.34,264.99 radius 1.116

> volume erase #9.12 center 209.31,182.15,266.22 radius 1.116

> volume erase #9.12 center 174.21,188.44,257.58 radius 1.116

> volume erase #9.12 center 175.04,189.6,257.47 radius 1.116

> volume erase #9.12 center 174.68,188.31,258.97 radius 1.116

> volume erase #9.12 center 182.49,194.98,257.93 radius 1.302

> volume erase #9.12 center 180.89,194.59,257.99 radius 1.302

> volume erase #9.12 center 172.82,189.41,255.87 radius 1.302

> volume erase #9.12 center 179.86,200.18,258.51 radius 1.302

> volume erase #9.12 center 203.52,198.12,258.69 radius 2.604

> volume erase #9.12 center 205.7,196.86,257.2 radius 2.604

> volume erase #9.12 center 199.73,199.1,257.84 radius 2.604

> volume erase #9.12 center 202.23,196.65,254.86 radius 2.604

> volume erase #9.12 center 214.39,181.65,261.94 radius 2.604

> volume erase #9.12 center 201.63,169.64,266.87 radius 2.604

> volume erase #9.12 center 203.44,176.56,264.28 radius 2.604

> volume erase #9.12 center 199.65,173.13,256.57 radius 2.604

> volume erase #9.12 center 207.41,195.15,266.81 radius 2.604

> volume erase #9.12 center 197.6,194.56,263.23 radius 2.046

> volume erase #9.12 center 196.63,192.06,264.06 radius 2.046

> volume erase #9.12 center 208.53,168.55,255.65 radius 2.046

> volume erase #9.12 center 199.24,167.43,264.15 radius 2.046

> volume erase #9.12 center 202.29,179.83,262.7 radius 2.046

> volume erase #9.12 center 202.59,180.06,265.14 radius 2.046

> volume erase #9.12 center 204.66,164.48,264.21 radius 2.046

> volume erase #9.12 center 207.54,188.07,257.39 radius 2.046

> volume erase #9.12 center 190.2,164.16,264.62 radius 2.046

> volume erase #9.12 center 190.78,162.66,264.21 radius 2.046

> volume erase #9.12 center 191.04,164.57,264.48 radius 2.046

> volume erase #9.12 center 191.74,162.88,264.01 radius 2.046

> volume erase #9.12 center 169.31,168.78,265.58 radius 2.046

> volume erase #9.12 center 178.43,165.86,264.01 radius 2.046

> volume erase #9.12 center 168.09,175.4,256.5 radius 2.046

> volume erase #9.12 center 187.52,197.18,263.46 radius 2.046

> volume erase #9.12 center 195.2,196.96,266.89 radius 2.046

> volume erase #9.12 center 173.38,180.8,256.98 radius 2.046

> volume erase #9.12 center 173.04,177,262.32 radius 2.046

> volume erase #9.12 center 202.13,183.82,257.15 radius 2.046

> volume erase #9.12 center 202.59,183.01,257.41 radius 2.046

> volume erase #9.12 center 201.81,183.26,259.26 radius 2.046

> volume erase #9.12 center 202.47,188.32,266.44 radius 2.046

> volume erase #9.12 center 202.54,188.53,264.11 radius 2.046

> volume erase #9.12 center 199.27,197.29,257.92 radius 2.046

> volume erase #9.12 center 199.08,196.93,257.18 radius 2.046

> volume erase #9.12 center 198.56,194.64,257.17 radius 2.046

> volume erase #9.12 center 200.41,197.94,258.49 radius 2.046

> volume erase #9.12 center 200.78,197.63,257.26 radius 2.046

> volume erase #9.12 center 171.11,186.58,262.63 radius 1.302

> volume erase #9.12 center 172.53,186.62,263.26 radius 1.302

> volume erase #9.12 center 167.28,181.59,265.98 radius 1.302

> volume erase #9.12 center 204.71,190.74,266.51 radius 1.302

> volume erase #9.12 center 205.21,192.8,266.78 radius 1.302

> volume erase #9.12 center 175.11,193.67,265.78 radius 1.302

> volume erase #9.12 center 174.65,191.1,268.05 radius 1.302

> volume erase #9.12 center 194.48,167.68,256 radius 1.302

> volume erase #9.12 center 194.93,165.18,252.98 radius 1.302

> volume erase #9.12 center 199.68,169.25,258.87 radius 1.302

> volume erase #9.12 center 199.8,168.54,259.04 radius 1.302

> volume erase #9.12 center 182.85,198.53,265.9 radius 1.302

> volume erase #9.12 center 184.13,197.25,266.1 radius 1.302

> volume erase #9.12 center 183.16,197.67,265.33 radius 1.302

> volume erase #9.12 center 178.4,168.3,263.12 radius 1.302

> volume erase #9.12 center 177.59,167.43,260.27 radius 1.302

> view

[Repeated 1 time(s)]

> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo侧视atom+map.cxs
> includeMaps true

——— End of log from Tue Mar 18 21:19:53 2025 ———

opened ChimeraX session  

> ui tool show ""Model Panel""

> hide #!9 models

> select add #11.27

1542 atoms, 278 residues, 1 model selected  

> select add #11.21

3130 atoms, 543 residues, 2 models selected  
Alignment identifier is 11/T  
Alignment identifier is 11/Z  

> select #11/T:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #11/T:1-108

536 atoms, 535 bonds, 1 pseudobond, 99 residues, 2 models selected  

> hide sel cartoons

> select #11/T:135-136

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #11/T:135-240

323 atoms, 321 bonds, 1 pseudobond, 65 residues, 2 models selected  

> hide sel cartoons

[Repeated 1 time(s)]

> select subtract #11.21

1 model selected  

> select add #11.21

1588 atoms, 265 residues, 1 model selected  

> select subtract #11.21

1 model selected  

> hide #!11 models

> show #!11 models

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> select add #1.21

3130 atoms, 543 residues, 2 models selected  
Alignment identifier is 1/T  
Alignment identifier is 1/Z  

> select #1/T:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:1-88

436 atoms, 435 bonds, 1 pseudobond, 79 residues, 2 models selected  

> hide sel cartoons

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-88

431 atoms, 430 bonds, 88 residues, 1 model selected  

> hide sel cartoons

> select #1/T:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:89-107

95 atoms, 94 bonds, 19 residues, 1 model selected  

> select #1/T:29-109

404 atoms, 403 bonds, 1 pseudobond, 72 residues, 2 models selected  

> select #1/T:29-113

424 atoms, 423 bonds, 1 pseudobond, 76 residues, 2 models selected  

> select #1/T:29-110

409 atoms, 408 bonds, 1 pseudobond, 73 residues, 2 models selected  

> select #1/T:110

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:110-239

499 atoms, 504 bonds, 1 pseudobond, 89 residues, 2 models selected  

> hide sel cartoons

> select add #1.27

2041 atoms, 504 bonds, 1 pseudobond, 367 residues, 3 models selected  

> select subtract #1.21

1542 atoms, 278 residues, 3 models selected  

> hide sel cartoons

> ui mousemode right select

> select clear

> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo俯视atom+mapT细节1.png
> width 1660 height 1243 supersample 3 transparentBackground true

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> show sel cartoons

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-58

284 atoms, 283 bonds, 58 residues, 1 model selected  

> hide sel cartoons

> select #1/Z:79

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:79-238

604 atoms, 602 bonds, 1 pseudobond, 123 residues, 2 models selected  

> hide sel cartoons

> select #1/Z:59

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:59-88

147 atoms, 146 bonds, 30 residues, 1 model selected  

> hide sel cartoons

> select #1/Z:89-90

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/Z:89-111

115 atoms, 114 bonds, 23 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/Z:257

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add #11.27

1553 atoms, 10 bonds, 279 residues, 3 models selected  

> hide sel atoms

> select subtract #11.27

11 atoms, 10 bonds, 1 residue, 3 models selected  

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo俯视atom+mapZ细节1.png
> width 1660 height 1243 supersample 3 transparentBackground true

[Repeated 1 time(s)]

> ui tool show Distances

> select #11/J:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #11/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #11/J:59@CA

1 atom, 1 residue, 1 model selected  

> select add #11/I:59@CA

2 atoms, 2 residues, 2 models selected  

> distance #11/J:59@CA #11/I:59@CA

Distance between J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #11/J GLU 59 CA
and /I GLU 59 CA: 12.159Å  

> save /Users/wujingyi/Desktop/figure/figure4/state1_Fo俯视atom+mapZ细节1.cxs

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!5 models

> show #!6 models

> select add #5

7093 atoms, 5298 bonds, 7093 residues, 4 models selected  

> select subtract #5

2 atoms, 2 residues, 7 models selected  

> select add #5

7093 atoms, 5298 bonds, 7093 residues, 4 models selected  

> color (#!5,11 & sel) #ffa07aff

[Repeated 1 time(s)]

> color (#!5,11 & sel) #ffa07af8

> color (#!5,11 & sel) #ffa07af6

> color (#!5,11 & sel) #ffa07adf

> color (#!5,11 & sel) #ffa07ad2

> color (#!5,11 & sel) #ffa07ab5

> color (#!5,11 & sel) #ffa07aa5

> color (#!5,11 & sel) #ffa07a8b

> color (#!5,11 & sel) #ffa07a84

> color (#!5,11 & sel) #ffa07a7e

[Repeated 3 time(s)]

> color (#!5,11 & sel) #ffa07a80

[Repeated 1 time(s)]

> color (#!5,11 & sel) #ff9f7a80

> color (#!5,11 & sel) #ff9d7a80

> color (#!5,11 & sel) #ff9c7a80

[Repeated 1 time(s)]

> color (#!5,11 & sel) #ff9b7a80

> color (#!5,11 & sel) #ff9a7a80

> color (#!5,11 & sel) #ff9b7a80

> color (#!5,11 & sel) #ff9c7a80

> color (#!5,11 & sel) #ff9d7a80

> color (#!5,11 & sel) #ff9e7a80

[Repeated 1 time(s)]

> color (#!5,11 & sel) #f5bc9780

> color (#!5,11 & sel) #f5bc9680

> color (#!5,11 & sel) #f5bb9680

> color (#!5,11 & sel) #f5b89380

> color (#!5,11 & sel) #f5b59280

> color (#!5,11 & sel) #f5b39180

> color (#!5,11 & sel) #f5b29080

> color (#!5,11 & sel) #f5b19080

> color (#!5,11 & sel) #f5a78c80

> color (#!5,11 & sel) #f5a48c80

> color (#!5,11 & sel) #f5a38c80

> color (#!5,11 & sel) #f59e8f80

> color (#!5,11 & sel) #f5999180

> color (#!5,11 & sel) #f5999280

[Repeated 1 time(s)]

> color (#!5,11 & sel) #f59b9280

> color (#!5,11 & sel) #f59f9180

> color (#!5,11 & sel) #f5a28f80

> color (#!5,11 & sel) #f5a58c80

[Repeated 2 time(s)]

> color (#!5,11 & sel) #f5a98980

> color (#!5,11 & sel) #f5af8680

> color (#!5,11 & sel) #f5b08480

[Repeated 1 time(s)]

> color (#!5,11 & sel) #f5b28580

[Repeated 1 time(s)]

> color (#!5,11 & sel) #f5b58680

> color (#!5,11 & sel) #f5bc8880

> color (#!5,11 & sel) #f5c08880

[Repeated 1 time(s)]

> color (#!5,11 & sel) #f5b77780

> color (#!5,11 & sel) #f5af6680

[Repeated 2 time(s)]

> color (#!5,11 & sel) #f5b46680

> color (#!5,11 & sel) #f5bb6480

> color (#!5,11 & sel) #f5be6380

[Repeated 1 time(s)]

> color (#!5,11 & sel) #f5bf6380

> color (#!5,11 & sel) #f5b95580

> color (#!5,11 & sel) #f5b74d80

> color (#!5,11 & sel) #f5b74c80

> color (#!5,11 & sel) #f5b74d80

> color (#!5,11 & sel) #f5b84e80

> color (#!5,11 & sel) #f5bc4f80

> color (#!5,11 & sel) #f5c24f80

> color (#!5,11 & sel) #f5c34e80

> select subtract #5

2 atoms, 2 residues, 7 models selected  

> select add #5

7093 atoms, 5298 bonds, 7093 residues, 4 models selected  

> select subtract #5

2 atoms, 2 residues, 7 models selected  

> color #5 #f1b56380

> color #5 #f1ab4d80

> color #5 #f1bf5380

> color #5 #f1bb6480

> color #5 #f1c14b80

> color #5 #f1c94480

> color #5 #f1bf4180

> color #5 #e9b93f80

> color #6 #ff40ffff

> color #6 #00fdffff

> color #6 #00fdff88

[Repeated 1 time(s)]

> color #6 #00fdff87

> color #6 #00fdff80

> color #6 #00fdff60

> color #6 #64dade60

> color #6 #62d6da60

> color #6 #64bada60

> color #6 #72dad960

> color #6 #71d4da60

> color #6 #6cc7da60

> color #6 #66bccd60

> color #6 #6aafcd60

> color #6 #639ecd60

> color #6 #63a1cd60

> color #6 #3aaccd60

> color #6 #39cdc060

> color #6 #59cdc060

> color #6 #56c0cd60

> color #6 #50b3bf60

> select add #1.21

1590 atoms, 267 residues, 4 models selected  

> hide sel cartoons

> hide sel atoms

> show sel atoms

> hide sel atoms

> undo

[Repeated 2 time(s)]

> select clear

Drag select of 11 atoms, 10 bonds  

> hide sel atoms

> select #11/J:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> select #11/J:61

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #11/J:60

5 atoms, 4 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #11/I:61

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add #11/I:60

13 atoms, 11 bonds, 2 residues, 2 models selected  

> select add #11/I:58

20 atoms, 17 bonds, 3 residues, 2 models selected  

> hide sel cartoons

> select #11/H:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #11/H:61

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #11/H:60

20 atoms, 17 bonds, 3 residues, 2 models selected  

> select add #11/H:59

29 atoms, 25 bonds, 4 residues, 2 models selected  

> select subtract #11/H:59

20 atoms, 17 bonds, 3 residues, 2 models selected  

> hide sel cartoons

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #11/Q:60

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #11/Q:61

20 atoms, 17 bonds, 3 residues, 2 models selected  

> hide sel cartoons

> show sel cartoons

> select clear

> show sel cartoons

> select clear

[Repeated 1 time(s)]

> select #11/I:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #11/J:59

18 atoms, 16 bonds, 2 residues, 2 models selected  

> color (#!11 & sel) #50b3bf61

[Repeated 1 time(s)]

> color (#!11 & sel) #f5ccdc61

> color (#!11 & sel) #f5ccdc63

> color (#!11 & sel) #f5ccdcf9

> color (#!11 & sel) #f5ccdcff

> select clear

Drag select of 1 residues  

> select add #11/I:59

18 atoms, 8 bonds, 2 residues, 2 models selected  

> select clear

> ~distance #11/J:59@CA #11/I:59@CA

> select clear

> select #11/J:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #11/I:59

18 atoms, 16 bonds, 2 residues, 2 models selected  

> color (#!11 & sel) byhetero

> select clear

Drag select of 24 atoms, 16 residues, 20 bonds  

> hide sel cartoons

> hide sel atoms

Drag select of 9 atoms, 8 residues, 8 bonds  

> hide sel atoms

> hide sel cartoons

> select #1/Z:111

5 atoms, 4 bonds, 1 residue, 1 model selected  
Destroying pre-existing alignment with identifier 1/Z  
Alignment identifier is 1/Z  

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> show sel cartoons

> ui tool show ""Side View""

> select clear

[Repeated 1 time(s)]

> color #5 #f6b93f80

> color #5 #f6a33f80

> color #5 #f6a73f80

> select #6/B:9615@O

1 atom, 1 residue, 1 model selected  

> select subtract #6.2

1 model selected  

> select add #6.2

2066 atoms, 2066 residues, 1 model selected  

> select subtract #6.2

1 model selected  

> color #6.3 #50b3bf73

> select #1/Z:33

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:32

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:32-33

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/Z:31

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:31-39

45 atoms, 44 bonds, 9 residues, 1 model selected  

> select #1/Z:23

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/Z:23-45

112 atoms, 111 bonds, 23 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #1/Z:228

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:228

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #6/A:291@O

1 atom, 1 residue, 1 model selected  

> select add #6.3

386 atoms, 386 residues, 2 models selected  

> select subtract #6.3

1 atom, 1 residue, 3 models selected  

> select add #6.2

2067 atoms, 2067 residues, 2 models selected  

> select subtract #6.2

1 atom, 1 residue, 3 models selected  

> select add #6.1

3239 atoms, 3239 residues, 3 models selected  

> select subtract #6.1

1 model selected  

> select #6/A:2100@O

1 atom, 1 residue, 1 model selected  

> select add #6.1.1

1 atom, 1 residue, 3 models selected  

> select subtract #6.1.1

1 atom, 1 residue, 2 models selected  
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 8730 of 31532 triangles  
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 7934 of 31532 triangles  

> select #6/A:279@O

1 atom, 1 residue, 1 model selected  
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2470 of 31532 triangles  

> select #6/A:189@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:279@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:382@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:286@O

1 atom, 1 residue, 1 model selected  
Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2328 of 31532 triangles  

> hide #!1,5-6,11 surfaces

> show #!1,5-6,11 surfaces

> hide #!1,5-6,11 surfaces

> select add #6

5690 atoms, 4616 bonds, 5690 residues, 3 models selected  

> select subtract #6

3 models selected  

> select add #6.1

3239 atoms, 3239 residues, 3 models selected  

> select add #6.2

5305 atoms, 5305 residues, 4 models selected  

> select add #6.3

5690 atoms, 5690 residues, 5 models selected  

> show sel surfaces

> select clear

Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2577 of 31532 triangles  

> select #6/A:279@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:210@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:189@O

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> select add #6.3

386 atoms, 386 residues, 2 models selected  

> select add #6.1.1

386 atoms, 386 residues, 4 models selected  

> select subtract #6.3

1 atom, 1 residue, 4 models selected  

> select subtract #6.1.1

1 atom, 1 residue, 2 models selected  

> select add #6.1.1

1 atom, 1 residue, 3 models selected  

> select subtract #6.1.1

1 atom, 1 residue, 2 models selected  

> select add #6.1.1

1 atom, 1 residue, 3 models selected  

> hide sel surfaces

> select subtract #6.1.1

1 atom, 1 residue, 2 models selected  

> select add #6.1.1

1 atom, 1 residue, 3 models selected  

> select #6/A:662@O

1 atom, 1 residue, 1 model selected  

> select add #6.2

2067 atoms, 2067 residues, 2 models selected  

> select subtract #6.2

1 atom, 1 residue, 3 models selected  

> select add #6.3

386 atoms, 386 residues, 2 models selected  

> select subtract #6.3

1 atom, 1 residue, 3 models selected  

> select #6/A:521@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:191@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 1148 of 31532 triangles  

> select #6/A:537@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:286@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:190@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 2809 of 31532 triangles  

> select #6/A:417@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:321@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:382@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:282@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:193@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:662@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:280@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:291@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:241@O

1 atom, 1 residue, 1 model selected  

> select #6/A:295@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:386@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:202@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:194@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:199@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:281@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:664@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:474@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:424@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:445@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:555@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:729@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:547@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:133@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:131@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:128@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:206@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:129@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:659@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:763@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:737@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

[Repeated 1 time(s)]

> select #6/A:508@O

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> hide sel surfaces

> select #6/A:516@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:349@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:139@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:562@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:648@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:751@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:633@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:660@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:513@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:242@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:365@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:769@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:352@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 30 of 31532 triangles  

> select clear

[Repeated 1 time(s)]

> select #6/A:490@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:241@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:222@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:427@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:468@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:609@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:499@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:224@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:135@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:339@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:207@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:203@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:200@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:196@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:392@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:209@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:213@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:520@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:852@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:519@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

Drag select of rfxa2_outlet_hollow.pdb_A SES surface, 49 of 31532 triangles  

> select clear

[Repeated 2 time(s)]

> select #6/A:854@O

1 atom, 1 residue, 1 model selected  

> select #6/A:197@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:931@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:851@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:932@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:948@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:958@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:782@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:680@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:876@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:663@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:569@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:528@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:538@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:312@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

[Repeated 1 time(s)]

> select #6/A:408@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:303@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:296@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:322@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:130@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:211@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:201@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:216@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:220@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:536@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:527@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:623@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:554@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:443@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:974@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

[Repeated 1 time(s)]

> select #6/A:745@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:761@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:735@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:815@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:967@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

[Repeated 2 time(s)]

> select #6/A:968@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:788@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

> select #6/A:741@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:600@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:384@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:283@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:581@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select clear

[Repeated 1 time(s)]

> select #6/A:829@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:750@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #6/A:2118@O

1 atom, 1 residue, 1 model selected  

> select add #6.1

3239 atoms, 3239 residues, 4 models selected  

> select subtract #6.1

1 model selected  

> select add #6.1.1

1 model selected  

> select subtract #6.1.1

Nothing selected  

> select add #6.1.2

1 model selected  

> select subtract #6.1.2

Nothing selected  

> select add #6.2

2066 atoms, 2066 residues, 2 models selected  

> select subtract #6.2

1 model selected  

> select add #6.2

2066 atoms, 2066 residues, 2 models selected  

> select subtract #6.2

1 model selected  

> select add #6.3

385 atoms, 385 residues, 2 models selected  

> select subtract #6.3

1 model selected  

> hide #!5 models

> show #!5 models

> select add #5

7091 atoms, 5298 bonds, 7091 residues, 1 model selected  

> show sel surfaces

> select clear

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> lighting soft

> select clear

> select #6/A:2013@O

1 atom, 1 residue, 1 model selected  

> select clear

> color #6 #508ebf60

> color #6 #50abbf60

> color #6 #50a7bf60

> color #6 #b9bec860

> color #6 #b8bfc860

> color #6 #b7bfc860

> color #6 #b6bfc860

> color #6 #c89e9d60

> color #6 #8bc8a060

> color #6 #76c8b460

> color #6 #74c0c860

> color #6 #63b2c860

> color #6 #5bb4c860

> color #6 #6cb1c860

> color #6 #76c2c860

> color #6 #6cc0c860

> color #6 #69c2c860

> color #6 #6cc4c860

> color #6 #6cc4c868

> color #6 #65b8bc68

> color #6 #65b8bc69

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.png""
> width 1660 height 1151 supersample 3 transparentBackground true

> color #5 #f6a73fad

> color #5 #f6a73f99

> color #5 #efd85899

> color #5 #efc36299

> color #5 #efbd7799

> color #5 #efb96c99

> ui tool show ""Color Actions""

> color sandy brown

> undo

> color #5 #ecc08499

> color #5 #ecbc8099

> color #6 #65b8bca8

> color #6 #65b8bcb3

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.png""
> width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:89-94

30 atoms, 29 bonds, 6 residues, 1 model selected  

> select #1/Z:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:89-107

95 atoms, 94 bonds, 19 residues, 1 model selected  

> color (#!1 & sel) #008f00ff

[Repeated 1 time(s)]

> color (#!1 & sel) #008f00f2

> color (#!1 & sel) #008f00dd

> color (#!1 & sel) #008f00da

> color (#!1 & sel) #008f00ca

> color (#!1 & sel) #008f00ba

> color (#!1 & sel) #008f00b7

> color (#!1 & sel) #008f00af

> color (#!1 & sel) #008f00a6

> color (#!1 & sel) #008f00c1

> color (#!1 & sel) #008f00d2

> color (#!1 & sel) #008f00d3

> color (#!1 & sel) #008f00de

> color (#!1 & sel) #008f00ff

> select clear

> select #1/Z:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:89-107

95 atoms, 94 bonds, 19 residues, 1 model selected  

> hide sel cartoons

> select #1/Z:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:89-110

110 atoms, 109 bonds, 22 residues, 1 model selected  

> hide sel cartoons

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.png""
> width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:89-108

100 atoms, 99 bonds, 20 residues, 1 model selected  

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs""
> includeMaps true

> select #1/Z:221

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:221-224

18 atoms, 17 bonds, 4 residues, 1 model selected  

> select #1/Z:199

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:199-204

30 atoms, 29 bonds, 6 residues, 1 model selected  

> select #1/Z:239-240

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/Z:239-315

555 atoms, 564 bonds, 77 residues, 1 model selected  

> hide sel cartoons

> hide #!6 models

> hide #!5 models

> hide #!11 models

> hide sel atoms

> select clear

> select #1/Z:89

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:89-111

115 atoms, 114 bonds, 23 residues, 1 model selected  

> show sel cartoons

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA
> exH6H7.png"" width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:239-240

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/Z:239-315

555 atoms, 564 bonds, 77 residues, 1 model selected  

> show sel cartoons

> select clear

> select #1/Z:238

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> hide sel cartoons

> show #!6 models

> show #!5 models

> select
> #1/Z:2-22,46-49,59-78,89-107,112-133,195-197,199-218,221-232,239-274,281-314

1117 atoms, 1117 bonds, 191 residues, 1 model selected  

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> show #!11 models

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA H6H7.png""
> width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:202

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:202

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:187

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:187

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select add #11.12

535 atoms, 74 residues, 1 model selected  

> show sel atoms

> select add #1.21

2123 atoms, 339 residues, 3 models selected  

> select subtract #11.12

1588 atoms, 265 residues, 3 models selected  

> hide sel atoms

> undo

[Repeated 3 time(s)]

> select subtract #11.12

1 model selected  

Cell requested for row 0 is out of bounds for table with 64 rows! Resizing
table model.  

> hide #!1 models

> select add #11.15

535 atoms, 74 residues, 1 model selected  

> select subtract #11.15

1 model selected  

> select add #11.12

535 atoms, 74 residues, 1 model selected  

> show sel atoms

> select subtract #11.12

1 model selected  

> select add #11

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> select subtract #11

26 models selected  

> undo

[Repeated 3 time(s)]

> select subtract #11.12

1 model selected  

> select add #11.12

535 atoms, 74 residues, 1 model selected  

> show sel cartoons

Alignment identifier is 11/K  

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/K:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

[Repeated 1 time(s)]

> show sel atoms

> select #11/K:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/K:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select add #11.12

535 atoms, 74 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/K:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select clear

> select #11/K:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/K:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color (#!11 & sel) byhetero

> select clear

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/K:60

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #11/K:60-61

13 atoms, 12 bonds, 2 residues, 1 model selected  

> hide sel atoms

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> show #!1 models

> select add #5

7091 atoms, 5298 bonds, 7091 residues, 4 models selected  

> select add #6

12781 atoms, 9914 bonds, 12781 residues, 9 models selected  

> select clear

> select #5/F:8194@O

1 atom, 1 residue, 1 model selected  

> hide sel surfaces

> select #1/Z:298

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select clear

> select #11/K:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #11/K:61

8 atoms, 7 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select clear

> color #6 #65b8bcbe

[Repeated 1 time(s)]

> color #6 #65b8bcbf

> color #5 #ecbc80ae

> color #5 #ecbc80bf

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA H6H7.png""
> width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:1-2

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/Z

1542 atoms, 1550 bonds, 1 pseudobond, 278 residues, 2 models selected  

> show sel cartoons

> select clear

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> hide sel cartoons

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA H6H7.png""
> width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:239-241

15 atoms, 14 bonds, 3 residues, 1 model selected  

> select #1/Z:239-315

555 atoms, 564 bonds, 77 residues, 1 model selected  

> select #1/Z:1

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:1-238

987 atoms, 985 bonds, 1 pseudobond, 201 residues, 2 models selected  

> show sel cartoons

> select #1/Z:239

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:239-315

555 atoms, 564 bonds, 77 residues, 1 model selected  

> hide sel cartoons

> hide #!5 models

> hide #!6 models

> hide #!11 models

> hide sel atoms

> select clear

> select #1/Z:35

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:35

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:35-44

48 atoms, 47 bonds, 10 residues, 1 model selected  

> select #1/Z:23

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/Z:23-35

64 atoms, 63 bonds, 13 residues, 1 model selected  

> select #1/Z:24-25

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/Z:24-35

60 atoms, 59 bonds, 12 residues, 1 model selected  

> hide sel cartoons

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA
> exH6H7.png"" width 1660 height 1151 supersample 3 transparentBackground true

> select #1/Z:227

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/Z:228

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select #1/Z:1-7

35 atoms, 34 bonds, 7 residues, 1 model selected  

> select #1/Z

1542 atoms, 1550 bonds, 1 pseudobond, 278 residues, 2 models selected  

> show sel cartoons

> select clear

> show #!5 models

> show #!6 models

> show #!11 models

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a2hollow+AA 整体.cxs""
> includeMaps true

——— End of log from Thu Mar 27 15:32:10 2025 ———

opened ChimeraX session  

> ui tool show ""Model Panel""

> hide #!6 models

> hide #!5 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!1 models

> show #!8 models

> hide #!8 models

> show #!1 models

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> show sel cartoons

> select subtract #1.21

1 model selected  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel cartoons

> ui tool show ""Side View""

> ui mousemode right select

Drag select of 10 atoms, 8 bonds  

> hide sel atoms

Drag select of 30 atoms, 6 residues, 25 bonds  

> hide sel atoms

> hide sel cartoons

> select add #11

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 7 models selected  

> select subtract #11

26 models selected  

> select add #11.9

543 atoms, 75 residues, 1 model selected  

> select add #11.10

1059 atoms, 147 residues, 2 models selected  

> select add #11.11

1594 atoms, 221 residues, 3 models selected  

> select add #11.13

2137 atoms, 296 residues, 4 models selected  

> select add #11.12

2672 atoms, 370 residues, 5 models selected  

> show sel cartoons

> hide sel cartoons

> select subtract #11.9

2129 atoms, 295 residues, 6 models selected  

> select subtract #11.10

1613 atoms, 223 residues, 5 models selected  

> select subtract #11.11

1078 atoms, 149 residues, 4 models selected  

> select subtract #11.12

543 atoms, 75 residues, 3 models selected  

> select subtract #11.13

1 model selected  

> select add #11.14

535 atoms, 74 residues, 1 model selected  

> select add #11.15

1070 atoms, 148 residues, 2 models selected  

> select add #11.16

1613 atoms, 223 residues, 3 models selected  

> select add #11.17

2156 atoms, 298 residues, 4 models selected  

> select add #11.18

2683 atoms, 371 residues, 5 models selected  

> show sel cartoons

Alignment identifier is 11/Q  
Alignment identifier is 1  
Alignment identifier is 2  

> select clear

> select #11/N,M:3

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #11/N,M

1070 atoms, 1086 bonds, 148 residues, 1 model selected  

> hide sel cartoons

> select #11/N,M:58

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #11/N,M:58-61

58 atoms, 56 bonds, 8 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> hide sel atoms

> select #11/P,O:58

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #11/P,O:58-60

42 atoms, 40 bonds, 6 residues, 1 model selected  

> select #11/P,O:3

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select #11/P,O

1086 atoms, 1102 bonds, 150 residues, 1 model selected  

> hide sel cartoons

> select #11/P,O:58

14 atoms, 12 bonds, 2 residues, 1 model selected  

> select #11/P,O:58-61

58 atoms, 56 bonds, 8 residues, 1 model selected  

> show sel cartoons

> select #11/Q:3

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #11/Q

527 atoms, 535 bonds, 73 residues, 1 model selected  

> hide sel cartoons

> select #11/Q:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #11/Q:58-61

29 atoms, 28 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select clear

Drag select of 13 residues  

> hide sel cartoons

Drag select of 9 residues  

> hide sel cartoons

> select clear

Drag select of 7 residues  

> show sel cartoons

> ~hbonds

Alignment identifier is 1/T  

> select #1/T:241

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/T:241-250

78 atoms, 78 bonds, 10 residues, 1 model selected  

> show sel cartoons

> select clear

> show #!4 models

> show #!2 models

> hide #!2 models

> hide #!4 models

> show #!8 models

> hide #!1 models

> hide #!11 models

> show #!2 models

> show #!4 models

> ui tool show Matchmaker

> matchmaker #1/T to #8/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1), sequence
alignment score = 1188.2  
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)  
  

> matchmaker #1/T to #8/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1), sequence
alignment score = 1188.2  
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)  
  

> show #!1 models

> hide #!4 models

> show #!4 models

> hide #!8 models

> select add #1.18

527 atoms, 73 residues, 1 model selected  

> select add #1.17

1070 atoms, 148 residues, 2 models selected  

> select add #1.16

1613 atoms, 223 residues, 3 models selected  

> select add #1.15

2148 atoms, 297 residues, 4 models selected  

> select add #1.14

2683 atoms, 371 residues, 5 models selected  

> show sel cartoons

Alignment identifier is 1/Q  
Alignment identifier is 1  
Alignment identifier is 2  

> hide sel cartoons

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59-60

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select #1/P,O:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/P,O:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel cartoons

> select #1/N,M:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/N,M:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel cartoons

> select clear

> cartoon style #1-2,4 xsection oval modeHelix default

> select clear

> undo

> cartoon style #1-2,4 modeHelix tube sides 20

> select clear

> hide #!4 models

> show #!11 models

> ui tool show Matchmaker

> matchmaker #11/T to #8/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#11), sequence
alignment score = 1188.2  
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)  
  

> matchmaker #11/T to #8/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RfxATP_state_1_Fo-4-coot-0.pdb, chain T (#8) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#11), sequence
alignment score = 1188.2  
RMSD between 144 pruned atom pairs is 1.326 angstroms; (across all 265 pairs:
3.573)  
  

> select add #11

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> select subtract #11.2

34187 atoms, 34634 bonds, 3 pseudobonds, 4874 residues, 28 models selected  

> select subtract #11.3

30394 atoms, 30783 bonds, 3 pseudobonds, 4378 residues, 27 models selected  

> select subtract #11.4

26572 atoms, 26903 bonds, 3 pseudobonds, 3878 residues, 26 models selected  

> select subtract #11.5

22978 atoms, 23246 bonds, 3 pseudobonds, 3409 residues, 25 models selected  

> select subtract #11.7

19392 atoms, 19597 bonds, 3 pseudobonds, 2941 residues, 24 models selected  

> select subtract #11.6

15787 atoms, 15929 bonds, 3 pseudobonds, 2471 residues, 23 models selected  

> select subtract #11.8

13505 atoms, 13619 bonds, 3 pseudobonds, 2182 residues, 22 models selected  

> select subtract #11.19

12425 atoms, 12529 bonds, 3 pseudobonds, 2044 residues, 21 models selected  

> select subtract #11.20

12060 atoms, 12165 bonds, 3 pseudobonds, 1970 residues, 20 models selected  

> select subtract #11.21

10472 atoms, 10562 bonds, 1 pseudobond, 1705 residues, 19 models selected  

> select subtract #11.22

9725 atoms, 9816 bonds, 1 pseudobond, 1555 residues, 18 models selected  

> select subtract #11.23

8967 atoms, 9059 bonds, 1 pseudobond, 1404 residues, 17 models selected  

> select subtract #11.24

8602 atoms, 8695 bonds, 1 pseudobond, 1330 residues, 16 models selected  

> select subtract #11.25

7860 atoms, 7954 bonds, 1 pseudobond, 1181 residues, 15 models selected  

> select subtract #11.27

6318 atoms, 6404 bonds, 903 residues, 13 models selected  

> select subtract #11.26

5566 atoms, 5653 bonds, 752 residues, 12 models selected  

> show sel cartoons

Alignment identifier is 11/I  
Alignment identifier is 11/Q  
Alignment identifier is 1  
Alignment identifier is 2  

> hide sel cartoons

Drag select of 2 residues  

> hide sel cartoons

Drag select of 4 residues  

> select clear

> select #1/N:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #1/O:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #1/P:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> show #!4 models

> select #11/N,M,K,J:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #11/N,M,K,J:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #11/P,O,L,H:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> select #11/P,O,L,H:59

36 atoms, 32 bonds, 4 residues, 1 model selected  

> show sel cartoons

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select clear

Drag select of 5 residues  

> hide sel cartoons

Drag select of 1 residues  

> select clear

> undo

Drag select of 1 residues  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:59-60

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:59-60

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select #4/F:4727@O

1 atom, 1 residue, 1 model selected  

> select add #4.4

1328 atoms, 1328 residues, 2 models selected  

> select subtract #4.4

1 atom, 1 residue, 3 models selected  

> select subtract #4.1

1 model selected  

> select add #4.1

230 atoms, 230 residues, 1 model selected  

> hide sel surfaces

> select clear

> select #1/T:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> select add #1.9

543 atoms, 75 residues, 1 model selected  

> select add #1.10

1059 atoms, 147 residues, 2 models selected  

> select add #1.11

1594 atoms, 221 residues, 3 models selected  

> select add #1.12

2129 atoms, 295 residues, 4 models selected  

> select add #1.13

2672 atoms, 370 residues, 5 models selected  

> select subtract #1.10

2156 atoms, 298 residues, 6 models selected  

> select subtract #1.9

1613 atoms, 223 residues, 5 models selected  

> select subtract #1.11

1078 atoms, 149 residues, 4 models selected  

> select subtract #1.12

543 atoms, 75 residues, 3 models selected  

> select subtract #1.13

1 model selected  

> select add #1.18

527 atoms, 73 residues, 1 model selected  

> select add #1.17

1070 atoms, 148 residues, 2 models selected  

> select add #1.16

1613 atoms, 223 residues, 3 models selected  

> select add #1.15

2148 atoms, 297 residues, 4 models selected  

> select add #1.14

2683 atoms, 371 residues, 5 models selected  

> show sel cartoons

> select clear

> hide #!1-2,4,11 cartoons

> undo

> select add #1.18

527 atoms, 73 residues, 1 model selected  

> select add #1.17

1070 atoms, 148 residues, 2 models selected  

> select add #1.16

1613 atoms, 223 residues, 3 models selected  

> select add #1.15

2148 atoms, 297 residues, 4 models selected  

> select add #1.14

2683 atoms, 371 residues, 5 models selected  

> hide sel cartoons

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 7 models selected  

> select subtract #1

26 models selected  

> select add #2

7230 atoms, 5473 bonds, 7230 residues, 1 model selected  

> select subtract #2

4 models selected  

> color #2 #efd6d180

> color #2 #efd6d1be

> color #2 #ecbc80be

> color #4 #65b8bc7f

> color #4 #65b8bcc4

> color #4 #65b8bcc0

> select clear

> select #11/Q:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #11/P:59

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add #11/O:59

27 atoms, 24 bonds, 3 residues, 3 models selected  

> select add #11/N:59

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select add #11/M:59

45 atoms, 40 bonds, 5 residues, 5 models selected  

> show sel atoms

> select clear

> select #1/T:27

5 atoms, 4 bonds, 1 residue, 1 model selected  
Alignment identifier is 1/T  

> select #1/T:27

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:27-58

133 atoms, 131 bonds, 1 pseudobond, 23 residues, 2 models selected  

> hide sel cartoons

> select clear

> select #1/T:148

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:135-136

10 atoms, 9 bonds, 2 residues, 1 model selected  

> select #1/T:135-190

72 atoms, 70 bonds, 1 pseudobond, 15 residues, 2 models selected  

> hide sel cartoons

> select clear

> select #4/I:483@O

1 atom, 1 residue, 1 model selected  

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a1hollow+AA 整体.png""
> width 1660 height 1174 supersample 3 transparentBackground true

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_Fo_a1hollow+AA 整体.cxs""

> hide #!2 models

> hide #!4 models

> hide #!11 models

> coulombic #!1

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PRO 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 87  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 88  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 91  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 92  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 96  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 98  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PRO 99  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 102  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 104  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LYS 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S TYR 113  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PRO 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 120  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S PHE 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 122  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLU 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 133  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 137  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S VAL 139  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASP 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 142  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S SER 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S LEU 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 146  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S MET 148  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ILE 151  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S GLN 152  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ARG 153  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S ASN 154  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S MET 155  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S MET 156  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/S THR 157  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T MET 1  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 2  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 3  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 4  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 5  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 6  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 7  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 8  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 9  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 11  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 12  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 13  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 15  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 17  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 18  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 19  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 20  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 21  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 22  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 24  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 25  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 26  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 27  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LYS 28  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 29  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T HIS 30  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 31  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 32  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 33  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 55  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 56  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 57  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 58  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 59  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 60  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 61  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 62  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 63  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 64  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 65  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 66  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 67  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 68  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 70  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 71  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 72  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 73  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 75  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 76  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 89  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 91  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 92  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLU 94  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T MET 96  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLU 98  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 102  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASP 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 111  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LYS 114  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 136  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T CYS 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 146  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 190  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 191  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 192  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 193  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 195  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 196  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASP 198  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 199  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 200  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 201  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 202  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 203  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TRP 205  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 207  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 208  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T SER 209  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 210  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 212  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ILE 213  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 214  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 215  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 216  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 218  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLN 219  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 221  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 223  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 225  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 226  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T THR 227  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LYS 228  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 229  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 230  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ASN 231  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 232  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T ARG 233  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T GLU 234  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 236  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 271  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 272  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T VAL 273  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T MET 274  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 276  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 277  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 278  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 279  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 280  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 281  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T LEU 282  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 283  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PRO 285  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T PHE 286  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/T TYR 287  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 11  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 12  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 14  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 15  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 16  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 17  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 18  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 19  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U PHE 20  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 21  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 22  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U TRP 23  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 24  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 25  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 26  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 27  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U PHE 28  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 29  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U TYR 30  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 31  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U PRO 32  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 33  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 34  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 35  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U MET 36  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 37  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 38  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 39  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 40  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 41  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 42  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 43  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 44  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 45  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 46  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 48  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 49  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 50  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 52  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 53  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 54  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 55  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 56  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 57  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 58  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 60  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 62  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 63  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 64  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U TYR 65  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 66  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 68  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 69  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 71  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 73  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 74  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 75  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U SER 78  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 79  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 80  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 82  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 84  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 88  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 94  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U HIS 99  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 104  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U SER 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 114  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLN 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U MET 120  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U MET 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 130  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 133  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U THR 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 137  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U VAL 139  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LYS 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASN 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U HIS 148  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ASP 149  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ARG 150  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 151  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U ILE 152  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 153  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 154  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U SER 155  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 156  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U GLU 158  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/U LEU 159  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TRP 8  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 10  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 11  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 12  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 14  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 15  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 16  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 17  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 18  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 19  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V PHE 20  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 21  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 22  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TRP 23  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 24  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 25  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 26  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 27  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V PHE 28  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 29  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TYR 30  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 31  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V PRO 32  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 33  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 34  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 35  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V MET 36  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 37  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 38  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 39  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 40  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 41  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 42  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 43  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 44  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 45  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 46  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 48  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 49  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 50  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 52  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 53  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 54  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 55  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 56  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 57  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 58  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 60  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 62  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 63  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 64  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V TYR 65  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 66  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 68  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 69  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 71  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 73  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 74  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 75  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V SER 78  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 79  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 80  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 82  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 84  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 88  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 94  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V HIS 99  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 104  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V SER 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 114  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLN 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V MET 120  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V MET 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 130  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 133  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V THR 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 137  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V VAL 139  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LYS 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASN 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V HIS 148  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ASP 149  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ARG 150  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 151  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V ILE 152  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 153  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V GLU 154  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V SER 155  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/V LEU 156  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PRO 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 87  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 88  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 91  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 92  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 96  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 98  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PRO 99  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 102  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 104  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LYS 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W TYR 113  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PRO 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 120  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W PHE 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 122  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLU 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 133  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 137  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W VAL 139  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASP 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 142  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W SER 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W LEU 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 146  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W MET 148  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ILE 151  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W GLN 152  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ARG 153  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W ASN 154  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W MET 155  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W MET 156  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/W THR 157  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 12  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 14  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 15  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 16  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 17  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 18  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 19  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X PHE 20  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 21  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 22  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X TRP 23  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 24  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 25  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 26  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 27  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X PHE 28  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 29  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X TYR 30  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 31  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X PRO 32  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 33  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 34  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 35  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X MET 36  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 37  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 38  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 39  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 40  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 41  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 42  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 43  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 44  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 45  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 46  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 48  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 49  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 50  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 52  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 53  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 54  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 55  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 56  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 57  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 58  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 60  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 62  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 63  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 64  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X TYR 65  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 66  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 68  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 69  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 71  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 73  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 74  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 75  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X SER 78  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 79  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 80  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 82  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 84  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 88  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 94  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X HIS 99  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 104  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X SER 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 114  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLN 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X MET 120  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X MET 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 130  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 133  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X THR 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 137  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X VAL 139  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LYS 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASN 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X HIS 148  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ASP 149  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ARG 150  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 151  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X ILE 152  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 153  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 154  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X SER 155  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 156  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X GLU 158  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/X LEU 159  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TRP 8  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 10  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 11  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 12  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 14  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 15  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 16  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 17  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 18  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 19  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y PHE 20  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 21  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 22  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TRP 23  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 24  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 25  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 26  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 27  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y PHE 28  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 29  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TYR 30  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 31  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y PRO 32  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 33  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 34  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 35  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y MET 36  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 37  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 38  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 39  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 40  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 41  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 42  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 43  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 44  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 45  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 46  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 48  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 49  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 50  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 52  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 53  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 54  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 55  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 56  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 57  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 58  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 60  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 62  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 63  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 64  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y TYR 65  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 66  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 68  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 69  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 71  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 73  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 74  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 75  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y SER 78  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 79  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 80  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 82  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 84  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 88  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 94  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y HIS 99  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 104  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y SER 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 114  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLN 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y MET 120  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y MET 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 130  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 133  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y THR 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 137  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y VAL 139  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LYS 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASN 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y HIS 148  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ASP 149  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ARG 150  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 151  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y ILE 152  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 153  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 154  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y SER 155  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y LEU 156  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Y GLU 158  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 1  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 2  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 3  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 4  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 5  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 6  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 7  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 8  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 9  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 11  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 12  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 13  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 15  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 17  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 18  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 19  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 20  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 21  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 22  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 24  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 25  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 26  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 27  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LYS 28  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 29  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z HIS 30  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 31  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 32  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 33  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 36  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 37  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 38  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 39  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 40  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 41  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 45  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 47  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 48  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 49  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 50  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 51  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 53  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 55  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 56  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 57  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 58  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 59  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 60  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 61  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 62  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 63  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 64  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 65  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 66  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 67  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 68  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 70  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 71  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 72  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 73  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 75  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 76  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 79  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 80  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 82  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 83  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 84  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 85  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 86  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 87  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 89  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 90  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 91  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 92  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 93  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 94  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 95  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 96  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 97  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 98  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 100  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 101  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 102  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 103  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 105  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 106  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 107  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASP 108  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 109  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 110  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 111  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 112  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LYS 114  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 115  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 116  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 117  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 118  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 119  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 121  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 123  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 124  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 125  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 126  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 127  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 128  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 129  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 130  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 131  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 132  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 134  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 135  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 136  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 138  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 140  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 141  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 143  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z CYS 144  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 145  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 146  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 147  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 186  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 187  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 188  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 189  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 190  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 191  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 192  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 193  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 195  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 196  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASP 198  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 199  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 200  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 201  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 202  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 203  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TRP 205  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 207  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 208  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z SER 209  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 210  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 212  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ILE 213  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 214  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 215  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 216  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 218  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLN 219  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 221  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 223  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 225  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 226  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z THR 227  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LYS 228  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 229  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 230  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ASN 231  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 232  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z ARG 233  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z GLU 234  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 236  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 237  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 240  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z VAL 241  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z MET 274  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 276  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 277  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 278  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 279  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 280  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 281  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z LEU 282  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 283  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PRO 285  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z PHE 286  
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb #1/Z TYR 287  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_A SES
surface #1.2: minimum, -18.27, mean -1.83, maximum 13.91  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_B SES
surface #1.3: minimum, -15.47, mean -1.37, maximum 13.82  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_C SES
surface #1.4: minimum, -16.31, mean -1.63, maximum 13.40  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_D SES
surface #1.5: minimum, -28.87, mean -2.68, maximum 10.52  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_E SES
surface #1.6: minimum, -20.09, mean -2.56, maximum 8.70  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_F SES
surface #1.7: minimum, -18.01, mean -2.95, maximum 8.98  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_G SES
surface #1.8: minimum, -16.97, mean 1.81, maximum 17.95  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_H SES
surface #1.9: minimum, -10.11, mean -0.93, maximum 7.53  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_I SES
surface #1.10: minimum, -10.05, mean -0.85, maximum 6.44  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_J SES
surface #1.11: minimum, -12.46, mean -0.37, maximum 8.45  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_K SES
surface #1.12: minimum, -11.92, mean -0.41, maximum 9.98  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_L SES
surface #1.13: minimum, -10.16, mean -0.92, maximum 7.70  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_M SES
surface #1.14: minimum, -9.92, mean -0.18, maximum 9.75  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_N SES
surface #1.15: minimum, -10.12, mean -0.53, maximum 8.00  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_O SES
surface #1.16: minimum, -10.15, mean -0.67, maximum 9.21  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_P SES
surface #1.17: minimum, -11.20, mean -1.02, maximum 7.64  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Q SES
surface #1.18: minimum, -10.56, mean -0.41, maximum 7.82  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_R SES
surface #1.19: minimum, -19.83, mean -2.00, maximum 12.65  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_S SES
surface #1.20: minimum, -13.38, mean -0.26, maximum 7.63  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES
surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_U SES
surface #1.22: minimum, -7.30, mean -1.52, maximum 9.63  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_V SES
surface #1.23: minimum, -9.18, mean -1.53, maximum 10.50  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_W SES
surface #1.24: minimum, -13.86, mean -0.26, maximum 7.70  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_X SES
surface #1.25: minimum, -8.05, mean -1.46, maximum 9.60  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Y SES
surface #1.26: minimum, -8.08, mean -1.63, maximum 9.55  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES
surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> select subtract #1.21

36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected  

> hide sel surfaces

> hide sel cartoons

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 27 models selected  

> select subtract #1

26 models selected  

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> hide sel cartoons

> show sel surfaces

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> lighting flat

> lighting full

> select clear

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:249

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:249

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:245

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:245

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:234

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:234

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:290

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select subtract #1.21

1 model selected  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> show sel surfaces

Alignment identifier is 1/Z  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:265-266

16 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/Z:265-270

44 atoms, 44 bonds, 6 residues, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268-269

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> color #1.21 #65b8bcff

> select add #1.21

1597 atoms, 8 bonds, 266 residues, 2 models selected  

> coulombic sel

Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_T SES
surface #1.21: minimum, -18.46, mean -0.85, maximum 9.62  
Coulombic values for J436_state1_synthasis_2.82A_14.82w-coot-3.pdb_Z SES
surface #1.27: minimum, -13.95, mean -1.49, maximum 9.76  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select subtract #1.21

9 atoms, 8 bonds, 1 residue, 3 models selected  

> select add #1.25

751 atoms, 8 bonds, 150 residues, 2 models selected  

> select subtract #1.25

9 atoms, 8 bonds, 1 residue, 3 models selected  

> select subtract #1.27

1 model selected  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> show sel surfaces

> select clear

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel surfaces

> lighting simple

> lighting soft

> lighting full

> lighting flat

> lighting full

> lighting shadows false

> graphics silhouettes false

> lighting flat

> lighting full

> lighting shadows false

> lighting soft

> view

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select clear

> save /Users/wujingyi/Desktop/figure/figure4/state1_a1电势.png width 1660
> height 1174 supersample 3 transparentBackground true

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> hide sel surfaces

> hide sel atoms

> select clear

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> show sel surfaces

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> hide sel surfaces

> select subtract #1.27

1 model selected  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel surfaces

> show sel cartoons

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> select clear

> hide #!1 atoms

> hide #!1 cartoons

> show #!1 surfaces

> undo

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel surfaces

> select subtract #1.27

1 model selected  

> select add #1.1

3 pseudobonds, 1 model selected  

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> select subtract #1.27

36450 atoms, 36947 bonds, 2 pseudobonds, 5094 residues, 28 models selected  

> hide sel surfaces

> select clear

Drag select of 5 atoms, 12 residues, 5 bonds  

> hide sel atoms

> select clear

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel surfaces

> hide sel cartoons

> show sel surfaces

> select #1/Z:234@CB

1 atom, 1 residue, 1 model selected  

> select clear

> save /Users/wujingyi/Desktop/figure/figure4/state1_a2电势.png width 1660
> height 1174 supersample 3 transparentBackground true

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel surfaces

> select subtract #1.27

1 model selected  

> select add #1.9

543 atoms, 75 residues, 1 model selected  

> select add #1.10

1059 atoms, 147 residues, 2 models selected  

> select add #1.11

1594 atoms, 221 residues, 3 models selected  

> select add #1.12

2129 atoms, 295 residues, 4 models selected  

> select add #1.14

2664 atoms, 369 residues, 5 models selected  

> select add #1.13

3207 atoms, 444 residues, 6 models selected  

> select add #1.15

3742 atoms, 518 residues, 7 models selected  

> select add #1.16

4285 atoms, 593 residues, 8 models selected  

> select add #1.17

4828 atoms, 668 residues, 9 models selected  

> select add #1.18

5355 atoms, 741 residues, 10 models selected  

> show sel surfaces

> select clear

> view

> save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势.png width 1660
> height 1174 supersample 3 transparentBackground true

> save /Users/wujingyi/Desktop/figure/figure4/state1_c-ring电势图.cxs

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> select subtract #1.27

1 model selected  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> show sel surfaces

> select add #1.26

2294 atoms, 429 residues, 2 models selected  

> select subtract #1.27

752 atoms, 151 residues, 3 models selected  

> select subtract #1.26

1 model selected  

> select add #1.20

365 atoms, 74 residues, 1 model selected  

> select add #1.19

1445 atoms, 212 residues, 2 models selected  

> select subtract #1.20

1080 atoms, 138 residues, 3 models selected  

> select subtract #1.19

1 model selected  

> select add #1.19

1080 atoms, 138 residues, 1 model selected  

> select subtract #1.19

1 model selected  

> select add #1.18

527 atoms, 73 residues, 1 model selected  

> select add #1.17

1070 atoms, 148 residues, 2 models selected  

> select add #1.16

1613 atoms, 223 residues, 3 models selected  

> select add #1.15

2148 atoms, 297 residues, 4 models selected  

> select add #1.14

2683 atoms, 371 residues, 5 models selected  

> select add #1.13

3226 atoms, 446 residues, 6 models selected  

> select add #1.12

3761 atoms, 520 residues, 7 models selected  

> select add #1.11

4296 atoms, 594 residues, 8 models selected  

> select add #1.10

4812 atoms, 666 residues, 9 models selected  

> select add #1.9

5355 atoms, 741 residues, 10 models selected  

> hide sel surfaces

> select #1/Z:245

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:245

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/T:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:274@CB

1 atom, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:268

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/Z:274@CB

1 atom, 1 residue, 1 model selected  

> select #1/Z:276@O

1 atom, 1 residue, 1 model selected  

> select #1/Z:263@O

1 atom, 1 residue, 1 model selected  

> select subtract #1.27

1 model selected  

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> show sel surfaces

> select clear

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!8 models

> hide #!8 models

> show #!1 models

> show #!11 models

> hide #!11 models

> hide #!1 models

> show #!1 models

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> hide sel surfaces

> show sel cartoons

> select subtract #1

26 models selected  

> select add #1.21

1588 atoms, 265 residues, 1 model selected  

> select add #1.27

3130 atoms, 543 residues, 2 models selected  

> color (#!1 & sel) forest green

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 4 models selected  

> select subtract #1

26 models selected  

> select add #1

37992 atoms, 38497 bonds, 3 pseudobonds, 5372 residues, 2 models selected  

> select subtract #1.21

36404 atoms, 36894 bonds, 1 pseudobond, 5107 residues, 28 models selected  

> select subtract #1.27

34862 atoms, 35344 bonds, 4829 residues, 26 models selected  

> hide sel cartoons

> select clear

> show #!11 models

> select add #11.21

1588 atoms, 265 residues, 1 model selected  

> select add #11.27

3130 atoms, 543 residues, 2 models selected  

> show sel cartoons

> select clear

> ui tool show Matchmaker

> matchmaker #11/Z to #1/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain T (#1) with
J436_state1_synthasis_2.82A_14.82w-coot-3.pdb, chain Z (#11), sequence
alignment score = 1208.4  
RMSD between 157 pruned atom pairs is 1.357 angstroms; (across all 265 pairs:
3.245)  
  

> select add #1.27

1542 atoms, 278 residues, 1 model selected  

> hide sel cartoons

> select add #11.21

3130 atoms, 543 residues, 3 models selected  

> hide sel cartoons

> ui mousemode right select

Drag select of 30 atoms, 5 residues, 25 bonds  

> hide sel atoms

> hide sel cartoons

> cartoon style (#!11 & sel) modeHelix tube sides 20

> select clear

> select add #11.27

1542 atoms, 278 residues, 1 model selected  

> color (#!11 & sel) light gray

> select clear

> select add #11.21

1588 atoms, 265 residues, 1 model selected  

> select subtract #11.21

1 model selected  

> select add #11.27

1542 atoms, 278 residues, 1 model selected  
Alignment identifier is 11/Z  

> select add #1.21

3130 atoms, 543 residues, 3 models selected  
Alignment identifier is 1/T  
Destroying pre-existing alignment with identifier 11/Z  
Alignment identifier is 11/Z  

> select clear

> select #11/Z:30

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #11/Z:30

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> show sel cartoons

> select #1/T:30

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/T:30

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show sel atoms

> select subtract #1.21

1 model selected  

Cell requested for row 0 is out of bounds for table with 37 rows! Resizing
table model.  

> hide #!1 models

> hide #!11 models

> show #!8 models

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-2.pdb""

Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #10  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> open ""/Volumes/暴躁的喷火龙/Rfx ATPase 相关/RFX ATPase
> 结构/RfxATP_state_1_Fo-4-coot-2.pdb""

Chain information for RfxATP_state_1_Fo-4-coot-2.pdb #12  
---  
Chain | Description  
H L O P | No description available  
I | No description available  
J K M N | No description available  
Q | No description available  
T Z | No description available  
U X | No description available  
V Y | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!8 models

> select add #10

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select add #12

22294 atoms, 22730 bonds, 4 pseudobonds, 2962 residues, 20 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #10

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 34 models selected  

> select add #10.2

11697 atoms, 11365 bonds, 2 pseudobonds, 1557 residues, 19 models selected  

> select add #10.3

12220 atoms, 11365 bonds, 2 pseudobonds, 1630 residues, 20 models selected  

> select add #10.4

12762 atoms, 11365 bonds, 2 pseudobonds, 1705 residues, 21 models selected  

> select add #10.5

13304 atoms, 11365 bonds, 2 pseudobonds, 1780 residues, 22 models selected  

> select add #10.6

13854 atoms, 11365 bonds, 2 pseudobonds, 1856 residues, 23 models selected  

> select add #10.7

14396 atoms, 11365 bonds, 2 pseudobonds, 1931 residues, 24 models selected  

> select add #10.8

14938 atoms, 11365 bonds, 2 pseudobonds, 2006 residues, 25 models selected  

> select add #10.9

15488 atoms, 11365 bonds, 2 pseudobonds, 2082 residues, 26 models selected  

> select add #10.10

16038 atoms, 11365 bonds, 2 pseudobonds, 2158 residues, 27 models selected  

> select add #10.11

16572 atoms, 11365 bonds, 2 pseudobonds, 2232 residues, 28 models selected  

> select subtract #12

5425 atoms, 751 residues, 27 models selected  

> select add #10

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 12 models selected  

> select subtract #10

16 models selected  

> select add #10.12

2232 atoms, 291 residues, 1 model selected  

> select add #10.17

4464 atoms, 582 residues, 2 models selected  

> color (#!10 & sel) forest green

> hide sel atoms

> show sel cartoons

> select add #10

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 4 models selected  

> select subtract #10

16 models selected  

> select add #12.12

2232 atoms, 291 residues, 1 model selected  

> select add #12.17

4464 atoms, 582 residues, 2 models selected  

> color (#!12 & sel) light gray

> hide sel atoms

> show sel cartoons

> select subtract #12.17

2232 atoms, 291 residues, 3 models selected  

> select subtract #12.12

1 model selected  

> select add #12

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> select subtract #12.17

8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected  

> select subtract #12.12

6683 atoms, 6791 bonds, 899 residues, 16 models selected  

> hide sel cartoons

> hide sel atoms

> select add #12

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected  

> select subtract #12

16 models selected  

> select add #10

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> select subtract #10.12

8915 atoms, 9078 bonds, 1 pseudobond, 1190 residues, 18 models selected  

> select subtract #10.17

6683 atoms, 6791 bonds, 899 residues, 16 models selected  

> hide sel atoms

> select add #10

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 16 models selected  

> select subtract #10

16 models selected  

> select add #10.12

2232 atoms, 291 residues, 1 model selected  

> select add #10.17

4464 atoms, 582 residues, 2 models selected  

> show sel cartoons

> select clear

> select add #10.17

2232 atoms, 291 residues, 1 model selected  

> select add #10.12

4464 atoms, 582 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> show sel surfaces

> hide sel surfaces

> select clear

> show #!10,12 cartoons

> select add #10.17

2232 atoms, 291 residues, 1 model selected  

> select clear

> undo

> select add #12.17

2232 atoms, 291 residues, 1 model selected  

> select subtract #12.17

1 model selected  

> select add #12.12

2232 atoms, 291 residues, 1 model selected  

> hide sel cartoons

> select subtract #12.12

1 model selected  

> select add #10.17

2232 atoms, 291 residues, 1 model selected  

> select subtract #10.17

1 model selected  

> select add #10.17

2232 atoms, 291 residues, 1 model selected  

> select subtract #10.17

1 model selected  

> select add #10.17

2232 atoms, 291 residues, 1 model selected  

> hide sel cartoons

> select subtract #10.17

1 model selected  

> ui tool show Matchmaker

> matchmaker #12/Z to #10/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with
RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score =
1380.4  
RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs:
2.932)  
  

> matchmaker #12/Z to #10/T pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker RfxATP_state_1_Fo-4-coot-2.pdb, chain T (#10) with
RfxATP_state_1_Fo-4-coot-2.pdb, chain Z (#12), sequence alignment score =
1380.4  
RMSD between 187 pruned atom pairs is 1.074 angstroms; (across all 291 pairs:
2.932)  
  

> select add #10.12

2232 atoms, 291 residues, 1 model selected  

> select add #12.17

4464 atoms, 582 residues, 3 models selected  
Alignment identifier is 1  

> select #10/T:30 #12/Z:30

20 atoms, 20 bonds, 2 residues, 2 models selected  

> select #10/T:30 #12/Z:30

20 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [30] RMSD: 0.804  
  

> show sel atoms

> select #10/T:130 #12/Z:130

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #10/T:130 #12/Z:130

16 atoms, 14 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [130] RMSD: 0.879  
  

> show sel atoms

> select #10/T:140 #12/Z:140

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #10/T:140 #12/Z:140

12 atoms, 10 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [140] RMSD: 3.423  
  

> show sel atoms

> select #10/T:187 #12/Z:187

14 atoms, 12 bonds, 2 residues, 2 models selected  

> select #10/T:187 #12/Z:187

14 atoms, 12 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [163] RMSD: 2.893  
  

> show sel atoms

> select #10/T:263 #12/Z:263

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #10/T:263 #12/Z:263

16 atoms, 14 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [239] RMSD: 0.744  
  

> select #10/T:263,268 #12/Z:263,268

34 atoms, 30 bonds, 4 residues, 2 models selected  
1 [ID: 1] region chains T,Z [239] + 1 other block RMSD: 0.813  
  

> show sel atoms

> select #10/T:259 #12/Z:259

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #10/T:259 #12/Z:259

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [235] RMSD: 0.890  
  

> show sel atoms

> select #10/T:252 #12/Z:252

22 atoms, 20 bonds, 2 residues, 2 models selected  

> select #10/T:252 #12/Z:252

22 atoms, 20 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [228] RMSD: 0.342  
  

> show sel atoms

> select #10/T:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314
> #12/Z:2-22,59-78,88-108,116-133,199-220,224-230,237-278,282-314

2874 atoms, 2928 bonds, 368 residues, 2 models selected  

> select #10/T:248 #12/Z:248

12 atoms, 10 bonds, 2 residues, 2 models selected  

> select #10/T:248-249 #12/Z:248-249

30 atoms, 28 bonds, 4 residues, 2 models selected  
1 [ID: 1] region chains T,Z [224-225] RMSD: 0.828  
  

> show sel atoms

> select #10/T:245 #12/Z:245

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #10/T:245 #12/Z:245

18 atoms, 16 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [221] RMSD: 1.184  
  

> show sel atoms

> select #10/T:228 #12/Z:228

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #10/T:228 #12/Z:228

18 atoms, 16 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [204] RMSD: 2.971  
  

> show sel atoms

> select clear

> style #10,12 stick

Changed 22294 atom styles  

> select clear

> cartoon style #10,12 modeHelix tube sides 20

> select clear

> select add #12.17

2232 atoms, 291 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel light yellow

> color sel lemon chiffon

> color sel light goldenrod yellow

> color sel old lace

> color sel light yellow

> color sel ivory

> color sel light yellow

> color sel lemon chiffon

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png"" width 1660
> height 1174 supersample 3 transparentBackground true

> select add #12.17

2232 atoms, 291 residues, 1 model selected  

> select clear

> select add #12

11147 atoms, 11365 bonds, 2 pseudobonds, 1481 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> hide #!1 models

> select add #10.12

13379 atoms, 11365 bonds, 2 pseudobonds, 1772 residues, 19 models selected  

> hide sel cartoons

> select clear

> color #10,12 byhetero

> select clear

> ui mousemode right select

> select clear

Drag select of 2 atoms, 1 bonds  
Drag select of 1 atoms, 1 bonds  

> ui tool show ""Color Actions""

> color sel lemon chiffon

> select clear

> select #12/Z:245@O

1 atom, 1 residue, 1 model selected  

> select add #12/Z:245@N

2 atoms, 1 bond, 1 residue, 2 models selected  

> color sel lemon chiffon

> select clear

> select add #12/Z:249@N

1 atom, 1 bond, 1 residue, 1 model selected  

> select subtract #12/Z:249@N

1 model selected  

> select add #12/Z:249@N

1 atom, 1 residue, 1 model selected  

> select add #12/Z:249@O

2 atoms, 1 bond, 1 residue, 2 models selected  

> color sel lemon chiffon

> select clear

> select add #10/T:248@O

1 atom, 1 residue, 1 model selected  

> select add #12/Z:248@O

2 atoms, 2 residues, 3 models selected  

> color sel lemon chiffon

> select clear

> select #12/Z:252@O

1 atom, 1 residue, 1 model selected  

> select subtract #12/Z:252@O

Nothing selected  

> select add #12/Z:252@N

1 atom, 1 residue, 1 model selected  

> select add #12/Z:252@O

2 atoms, 1 residue, 1 model selected  

> color sel lemon chiffon

> select clear

> select #12/Z:259@O

1 atom, 1 residue, 1 model selected  

> select add #12/Z:259@N

2 atoms, 1 bond, 1 residue, 2 models selected  

> color sel lemon chiffon

> select clear

> select #12/Z:263@O

1 atom, 1 residue, 1 model selected  

> select add #12/Z:263@N

2 atoms, 1 bond, 1 residue, 2 models selected  

> color sel lemon chiffon

> select clear

> select #12/Z:130@O

1 atom, 1 residue, 1 model selected  

> select add #10/T:130@O

2 atoms, 1 bond, 2 residues, 2 models selected  

> select subtract #10/T:130@O

1 atom, 1 bond, 1 residue, 2 models selected  

> select add #12/Z:130@N

2 atoms, 1 bond, 1 residue, 1 model selected  

> select subtract #12/Z:130@N

1 atom, 1 bond, 1 residue, 1 model selected  
Drag select of 1 atoms  

> color sel lemon chiffon

> select clear

Drag select of 1 atoms, 1 bonds  
Drag select of 1 atoms  

> color sel lemon chiffon

> select clear

> select add #12/Z:268@O

1 atom, 1 residue, 1 model selected  

> select add #12/Z:268@N

2 atoms, 1 bond, 1 residue, 1 model selected  

> color sel lemon chiffon

> select clear

> select add #10.12

2232 atoms, 291 residues, 1 model selected  

> ui tool show ""Color Actions""

> color sel lemon chiffon

> select subtract #10.12

1 model selected  

> select add #12.17

2232 atoms, 291 residues, 1 model selected  

> color (#!12 & sel) forest green

> select clear

> select add #12.17

2232 atoms, 291 residues, 1 model selected  

> select add #10.12

4464 atoms, 582 residues, 3 models selected  

> show sel cartoons

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png"" width 1660
> height 1174 supersample 3 transparentBackground true

> select add #10.12

2232 atoms, 291 residues, 1 model selected  

> select add #12.17

4464 atoms, 582 residues, 3 models selected  

> hide sel cartoons

> select clear

> ui mousemode right select

> select #10/T:290 #12/Z:290

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #10/T:290 #12/Z:290

18 atoms, 16 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [266] RMSD: 1.278  
  

> show sel atoms

> select clear

> ui mousemode right select

Drag select of 6 atoms, 4 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 3 atoms, 2 bonds  

> color (#!10 & sel) byhetero

> select clear

Drag select of 2 atoms, 1 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 1 atoms  

> color (#!10 & sel) byhetero

> select clear

Drag select of 5 atoms, 4 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 8 atoms, 7 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 1 atoms  

> color (#!10 & sel) byhetero

> select clear

Drag select of 3 atoms, 2 bonds  

> select subtract #10/T:140@C

2 atoms, 1 bond, 1 residue, 3 models selected  

> color (#!12 & sel) byhetero

> select clear

Drag select of 3 atoms, 2 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 7 atoms, 7 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 1 atoms  

> color sel byhetero

> select clear

> select #10/T:248@OG

1 atom, 1 residue, 1 model selected  

> select add #12/Z:248@OG

2 atoms, 2 residues, 3 models selected  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 6 atoms, 5 bonds  

> color (#!10,12 & sel) byhetero

> select clear

Drag select of 1 atoms  

> color (#!10,12 & sel) byhetero

> select clear

> select add #12/Z:187@OG1

1 atom, 1 residue, 1 model selected  
Drag select of 34 atoms, 32 bonds  

> color (#!10,12 & sel) byhetero

> select clear

> select #12/Z:30@N

1 atom, 1 residue, 1 model selected  
Drag select of 1 atoms  

> select clear

> select #12/Z:30@N

1 atom, 1 residue, 1 model selected  

> color (#!12 & sel) forest green

> select clear

Drag select of 1 atoms  

> select add #10/T:30@N

2 atoms, 1 residue, 2 models selected  

> ui tool show ""Color Actions""

> color sel lemon chiffon

> select clear

> select #12/Z:30@O

1 atom, 1 residue, 1 model selected  

> color sel forest green

> select clear

Drag select of 1 atoms, 2 bonds  

> color sel lemon chiffon

> select clear

Drag select of 1 atoms  

> color sel forest green

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png"" width
> 1660 height 1174 supersample 3 transparentBackground true

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加AA .png"" width
> 1660 height 1591 supersample 3 transparentBackground true

> select add #10.12

2232 atoms, 291 residues, 1 model selected  

> select add #12.17

4464 atoms, 582 residues, 3 models selected  

> show sel cartoons

> ui mousemode right select

> select clear

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .png"" width 1660
> height 1591 supersample 3 transparentBackground true

> save ""/Users/wujingyi/Desktop/figure/figure4/state1_a1a2叠加 .cxs""

> open
> /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb

Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-3.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J K L M N O P | No description available  
I Q | No description available  
R | No description available  
S W | No description available  
T | No description available  
U X | No description available  
V | No description available  
Y | No description available  
Z | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!10,12-13 atoms

> show #!10,12-13 cartoons

Cell requested for row 11 is out of bounds for table with 47 rows! Resizing
table model.  

> hide #!12 models

> hide #!10 models

> select add #13

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #13

26 models selected  

> select add #13.2

3805 atoms, 498 residues, 1 model selected  

> select add #13.3

7598 atoms, 994 residues, 2 models selected  

> select add #13.4

11420 atoms, 1494 residues, 3 models selected  

> color (#!13 & sel) #0099ccff

> select subtract #13.2

7615 atoms, 996 residues, 4 models selected  

> select subtract #13.3

3822 atoms, 500 residues, 3 models selected  

> select subtract #13.4

1 model selected  

> select add #13.5

3597 atoms, 469 residues, 1 model selected  

> select add #13.6

7202 atoms, 939 residues, 2 models selected  

> select add #13.7

10788 atoms, 1407 residues, 3 models selected  

> color (#!13 & sel) #e9d49bff

> select subtract #13.5

7191 atoms, 938 residues, 4 models selected  

> select subtract #13.6

3586 atoms, 468 residues, 3 models selected  

> select subtract #13.7

1 model selected  

> select add #13.8

2282 atoms, 289 residues, 1 model selected  

> color (#!13 & sel) #002befff

> color (#!13 & sel) #2befc8ff

> select subtract #13.8

1 model selected  

> select add #13.9

535 atoms, 74 residues, 1 model selected  

> select add #13.10

1062 atoms, 147 residues, 2 models selected  

> select add #13.11

1597 atoms, 221 residues, 3 models selected  

> select add #13.12

2132 atoms, 295 residues, 4 models selected  

> select add #13.13

2667 atoms, 369 residues, 5 models selected  

> select add #13.14

3202 atoms, 443 residues, 6 models selected  

> select add #13.15

3737 atoms, 517 residues, 7 models selected  

> select add #13.16

4272 atoms, 591 residues, 8 models selected  

> select add #13.17

4807 atoms, 665 residues, 9 models selected  

> select add #13.18

5334 atoms, 738 residues, 10 models selected  

> color (#!13 & sel) #f5ccdcff

> select add #13

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected  

> select subtract #13

26 models selected  

> select add #13.21

1588 atoms, 265 residues, 1 model selected  

> select add #13.27

3130 atoms, 543 residues, 2 models selected  

> color (#!13 & sel) forest green

> select clear

> select add #13.22

747 atoms, 150 residues, 1 model selected  

> select add #13.26

1959 atoms, 301 residues, 2 models selected  

> select subtract #13.26

747 atoms, 150 residues, 3 models selected  

> select add #13.25

1812 atoms, 300 residues, 2 models selected  

> color (#!13 & sel) #c5c5ecff

> select clear

> select add #13.23

764 atoms, 152 residues, 1 model selected  

> select add #13.26

1976 atoms, 303 residues, 2 models selected  

> color (#!13 & sel) #9e7bbaff

> select clear

> select add #13.20

365 atoms, 74 residues, 1 model selected  

> select subtract #13.20

1 model selected  

> select add #13

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected  

> select subtract #13.2

34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected  

> select add #13.2

38578 atoms, 35235 bonds, 3 pseudobonds, 5349 residues, 27 models selected  

> select subtract #13.9

38043 atoms, 34692 bonds, 3 pseudobonds, 5275 residues, 28 models selected  

> select subtract #13.10

37516 atoms, 34157 bonds, 3 pseudobonds, 5202 residues, 27 models selected  

> select subtract #13.12

36981 atoms, 33614 bonds, 3 pseudobonds, 5128 residues, 26 models selected  

> select subtract #13.11

36446 atoms, 33071 bonds, 3 pseudobonds, 5054 residues, 25 models selected  

> select subtract #13.13

35911 atoms, 32528 bonds, 3 pseudobonds, 4980 residues, 24 models selected  

> select subtract #13.14

35376 atoms, 31985 bonds, 3 pseudobonds, 4906 residues, 23 models selected  

> select subtract #13.15

34841 atoms, 31442 bonds, 3 pseudobonds, 4832 residues, 22 models selected  

> select subtract #13.16

34306 atoms, 30899 bonds, 3 pseudobonds, 4758 residues, 21 models selected  

> select subtract #13.17

33771 atoms, 30356 bonds, 3 pseudobonds, 4684 residues, 20 models selected  

> select subtract #13.18

33244 atoms, 29821 bonds, 3 pseudobonds, 4611 residues, 19 models selected  

> select subtract #13.21

31656 atoms, 28218 bonds, 1 pseudobond, 4346 residues, 18 models selected  

> select subtract #13.27

30114 atoms, 26668 bonds, 4068 residues, 16 models selected  

> hide sel cartoons

> select clear

> select add #13.21

1588 atoms, 265 residues, 1 model selected  

> select add #13.27

3130 atoms, 543 residues, 2 models selected  

> color (#!13 & sel) dark gray

> select clear

> select add #13.9

535 atoms, 74 residues, 1 model selected  

> select add #13.10

1062 atoms, 147 residues, 2 models selected  

> select add #13.11

1597 atoms, 221 residues, 3 models selected  

> select add #13.12

2132 atoms, 295 residues, 4 models selected  

> select add #13.13

2667 atoms, 369 residues, 5 models selected  

> select add #13.14

3202 atoms, 443 residues, 6 models selected  

> select add #13.15

3737 atoms, 517 residues, 7 models selected  

> select add #13.16

4272 atoms, 591 residues, 8 models selected  

> select add #13.17

4807 atoms, 665 residues, 9 models selected  

> select add #13.18

5334 atoms, 738 residues, 10 models selected  

> hide sel cartoons

> select add #13

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected  

> select subtract #13

26 models selected  

> select add #13.21

1588 atoms, 265 residues, 1 model selected  

> hide sel cartoons

> show #!4 models

> hide #!4 models

> show #!5 models

> show #!6 models

> cartoon style (#!13 & sel) modeHelix tube sides 20

> select clear

> select add #13

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected  

> select subtract #13

26 models selected  

> select add #13.21

1588 atoms, 265 residues, 1 model selected  

> select add #13.27

3130 atoms, 543 residues, 2 models selected  

> ui tool show ""Color Actions""

> color sel light slate gray

> color sel lavender

> color sel light steel blue

> select clear

> color light steel blue

> undo

> select #13/Z:241

5 atoms, 4 bonds, 1 residue, 1 model selected  

> color #13.27 #b0bed1ff

> color #13.27 #b8c6daff

> undo

> select subtract #13.27

1 model selected  

> select add #13.27

1542 atoms, 278 residues, 1 model selected  

> color (#!13 & sel) #b8c6daff

> color (#!13 & sel) #b4c2d5ff

> color (#!13 & sel) #b0bed1ff

> color (#!13 & sel) #b0bdd0ff

> color (#!13 & sel) #b0bed0ff

> color (#!13 & sel) #adbbcdff

> color (#!13 & sel) #abb9cbff

> color (#!13 & sel) #aab7c9ff

> color (#!13 & sel) #abb8caff

> color (#!13 & sel) #adbaccff

> color (#!13 & sel) #adbacdff

> color (#!13 & sel) #afbdd0ff

> color (#!13 & sel) #afbdd5ff

> color (#!13 & sel) #afbdd9ff

> color (#!13 & sel) #afbddbff

> color (#!13 & sel) #afbde0ff

> color (#!13 & sel) #afbddfff

> color (#!13 & sel) #afbdddff

> color (#!13 & sel) #afbddbff

> color (#!13 & sel) #afbdd9ff

> color (#!13 & sel) #afbdd5ff

> color (#!13 & sel) #afbdd3ff

> color (#!13 & sel) #afbdd2ff

> color (#!13 & sel) #a9bdd2ff

> color (#!13 & sel) #a3bdd2ff

> color (#!13 & sel) #a5bdd2ff

> color (#!13 & sel) #abbdd2ff

> color (#!13 & sel) #afbdd2ff

> color (#!13 & sel) #aebdd2ff

> color (#!13 & sel) #abbdd2ff

> color (#!13 & sel) #abb9d2ff

> color (#!13 & sel) #abb6d2ff

> color (#!13 & sel) #abb5d2ff

> color (#!13 & sel) #abb7d2ff

> color (#!13 & sel) #abb9d2ff

> color (#!13 & sel) #abbad2ff

> color (#!13 & sel) #abbbd2ff

> color (#!13 & sel) #abbdd2ff

> select subtract #13.27

1 model selected  

> select add #13.27

1542 atoms, 278 residues, 1 model selected  

> color (#!13 & sel) #abbdd2ff

> color (#!13 & sel) #abbdd5ff

> color (#!13 & sel) #abbdd8ff

> color (#!13 & sel) #abbdddff

> color (#!13 & sel) #abbde3ff

> color (#!13 & sel) #abbde9ff

> color (#!13 & sel) #abbdeeff

> color (#!13 & sel) #abbdecff

> color (#!13 & sel) #abbdebff

> color (#!13 & sel) #abbde1ff

> color (#!13 & sel) #abbdd4ff

> color (#!13 & sel) #abbdd3ff

> color (#!13 & sel) #abbdd2ff

> color (#!13 & sel) #abbdd7ff

> select subtract #13.27

1 model selected  

> select clear

> select #13/Z:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> style (#!13 & sel) stick

Changed 11 atom styles  

> select clear

> select add #13.10

527 atoms, 73 residues, 1 model selected  

> select add #13.11

1062 atoms, 147 residues, 2 models selected  

> select add #13.12

1597 atoms, 221 residues, 3 models selected  

> select add #13.13

2132 atoms, 295 residues, 4 models selected  

> select add #13.14

2667 atoms, 369 residues, 5 models selected  

> select add #13.15

3202 atoms, 443 residues, 6 models selected  

> select add #13.16

3737 atoms, 517 residues, 7 models selected  

> select add #13.17

4272 atoms, 591 residues, 8 models selected  

> select add #13.18

4799 atoms, 664 residues, 9 models selected  
Alignment identifier is 2  
Alignment identifier is 3  

> select #13/I,Q:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #13/I,Q:59-60

28 atoms, 26 bonds, 4 residues, 1 model selected  

> select #13/I,Q:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #13/I,Q:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> hide sel cartoons

> style (#!13 & sel) stick

Changed 18 atom styles  

> select clear

> select #13/P,O,N,L-M,K,J:59

63 atoms, 56 bonds, 7 residues, 1 model selected  

> select #13/P,O,N,L-M,K,J:59

63 atoms, 56 bonds, 7 residues, 1 model selected  

> show sel atoms

> style (#!13 & sel) stick

Changed 63 atom styles  

> select clear

> select #10/T:290 #12/Z:290

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #10/T:290 #12/Z:290

18 atoms, 16 bonds, 2 residues, 2 models selected  
1 [ID: 1] region chains T,Z [266] RMSD: 1.278  
  

> show #!5-6,13 atoms

> hide #!5-6,13 atoms

> undo

Drag select of 4 atoms, 5 bonds  

> select clear

> select add #13.9

535 atoms, 74 residues, 1 model selected  

> select subtract #13.9

1 model selected  

> select add #13.10

527 atoms, 73 residues, 1 model selected  

> select subtract #13.10

1 model selected  

> select add #13.9

535 atoms, 74 residues, 1 model selected  
Alignment identifier is 13/H  

> select #13/H:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #13/H:59

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel atoms

> style (#!13 & sel) stick

Changed 9 atom styles  

> select clear

> open
> /Users/wujingyi/Desktop/rfxATPase_PDB/J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb

Chain information for J437_state1_hydrolysis_2.94A_7.88w-coot-4.pdb #14  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H J K L M N O P | No description available  
I Q | No description available  
R | No description available  
S W | No description available  
T | No description available  
U X | No description available  
V | No description available  
Y | No description available  
Z | No description available  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> hide #!5-6,13-14 atoms

> select add #14

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 2 models selected  

> show sel surfaces

> hide sel surfaces

> select subtract #14.2

34773 atoms, 35235 bonds, 3 pseudobonds, 4851 residues, 28 models selected  

> select subtract #14.3

30980 atoms, 31384 bonds, 3 pseudobonds, 4355 residues, 27 models selected  

> select subtract #14.4

27158 atoms, 27504 bonds, 3 pseudobonds, 3855 residues, 26 models selected  

> select subtract #14.5

23561 atoms, 23844 bonds, 3 pseudobonds, 3386 residues, 25 models selected  

> select subtract #14.6

19956 atoms, 20176 bonds, 3 pseudobonds, 2916 residues, 24 models selected  

> select subtract #14.7

16370 atoms, 16527 bonds, 3 pseudobonds, 2448 residues, 23 models selected  

> select subtract #14.8

14088 atoms, 14217 bonds, 3 pseudobonds, 2159 residues, 22 models selected  

> select subtract #14.27

12546 atoms, 12667 bonds, 2 pseudobonds, 1881 residues, 21 models selected  

> select subtract #14.26

11334 atoms, 11445 bonds, 2 pseudobonds, 1730 residues, 20 models selected  

> select subtract #14.25

10269 atoms, 10378 bonds, 2 pseudobonds, 1580 residues, 19 models selected  

> select subtract #14.24

9904 atoms, 10014 bonds, 2 pseudobonds, 1506 residues, 18 models selected  

> select subtract #14.23

9140 atoms, 9251 bonds, 2 pseudobonds, 1354 residues, 17 models selected  

> select subtract #14.22

8393 atoms, 8505 bonds, 2 pseudobonds, 1204 residues, 16 models selected  

> select subtract #14.21

6805 atoms, 6902 bonds, 939 residues, 14 models selected  

> select subtract #14.20

6440 atoms, 6538 bonds, 865 residues, 13 models selected  

> select subtract #14.19

5548 atoms, 5636 bonds, 748 residues, 12 models selected  

> show sel atoms

> hide sel atoms

> show sel cartoons

> color (#!14 & sel) #f5ccdcff

Cell requested for row 13 is out of bounds for table with 41 rows! Resizing
table model.  

> select add #14

38578 atoms, 39098 bonds, 3 pseudobonds, 5349 residues, 12 models selected  

> select subtract #14

26 models selected  

> hide #!13 models

> hide #!6 models

> hide #!5 models

Drag select of 738 residues  
Alignment identifier is 1  
Alignment identifier is 4  

> show #!13 models

> show #!5 models

> show #!6 models

> select #14/P,O,N,L-M,K,J,H:76

64 atoms, 56 bonds, 8 residues, 1 model selected  

> select #14/P,O,N,L-M,K,J,H

4280 atoms, 4344 bonds, 592 residues, 1 model selected  

> hide sel cartoons

> select #14/P,O,N,L-M,K,J,H:59

72 atoms, 64 bonds, 8 residues, 1 model selected  

> select #14/P,O,N,L-M,K,J,H:59

72 atoms, 64 bonds, 8 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> select #14/I,Q:75

22 atoms, 20 bonds, 2 residues, 1 model selected  

> select #14/I,Q

1054 atoms, 1070 bonds, 146 residues, 1 model selected  

> hide sel cartoons

> select #14/I,Q:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> select #14/I,Q:59

18 atoms, 16 bonds, 2 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> select clear

> style #5-6,13-14 ball

Changed 89937 atom styles  

> style #5-6,13-14 stick

Changed 89937 atom styles  

> select clear


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,6
      Model Number: MRX63CH/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 10151.101.3
      OS Loader Version: 10151.101.3

Software:

    System Software Overview:

      System Version: macOS 14.4 (23E214)
      Kernel Version: Darwin 23.4.0
      Time since boot: 46天3小时39分钟

Graphics/Displays:

    Apple M3 Pro:

      Chipset Model: Apple M3 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Redmi 27 NU:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Resolution: 3024 x 1964
          UI Looks like: 1512 x 982 @ 120.00Hz
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	new	normal		Unassigned