id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17616	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.4.1-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 0x0000000201c44c80 (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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, 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, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 99)


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===== Log before crash start =====
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  

> cd /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS

Current working directory is:
/Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS  

> windowsize width 1000 height 1000

> nucleotides fill

> style nucleic stick

Changed 0 atom styles  

> open cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc

Opened cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc as #1, grid size
548,548,548, pixel 0.5, shown at level 6.93, step 4, values float32  

> rename #1 X_DH_map

> open XL_MCM_DH_final_v1_30042025.pdb

Chain information for XL_MCM_DH_final_v1_30042025.pdb #2  
---  
Chain | Description  
2 A | No description available  
3 B | No description available  
4 C | No description available  
5 D | No description available  
6 E | No description available  
7 F | No description available  
X | No description available  
Y | No description available  
  

> rename #2 X_DH

> open emdb:19618

Opened emdb 19618 as #3, grid size 400,400,400, pixel 1.08, shown at level
0.33, step 2, values float32, fit PDB 8s09  

> rename #3 H_DH_map_Costa

> open 8S09

8s09 title:  
H. sapiens MCM2-7 double hexamer bound to double stranded DNA [more info...]  
  
Chain information for 8s09 #4  
---  
Chain | Description | UniProt  
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904  
3 B | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808  
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863  
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734  
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821  
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719  
X | DNA (45-mer) |   
Y | DNA (45-mer) |   
  
Non-standard residues in 8s09 #4  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> rename #4 H_DH_Costa

> open emdb:43708

Opened emdb 43708 as #5, grid size 500,500,500, pixel 0.832, shown at level
0.1, step 2, values float32, fit PDB 8w0f  

> rename #5 H_DH_map_Bleichert

> open 8W0F

8w0f title:  
Cryo-EM structure of a human MCM2-7 double hexamer on dsDNA [more info...]  
  
Chain information for 8w0f #6  
---  
Chain | Description | UniProt  
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904  
3 B | DNA replication licensing factor MCM3 | MCM3_HUMAN 2-808  
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863  
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734  
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821  
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719  
O | DNA (47-MER) |   
S | DNA (47-MER) |   
  
Non-standard residues in 8w0f #6  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> rename #6 H_DH_Bleichert

> open emdb:32258

Opened emdb 32258 as #7, grid size 400,400,400, pixel 1.06, shown at level
0.5, step 2, values float32, fit PDB 7w1y  

> rename #7 H_DH_map_Zhai

> open 7W1Y

Summary of feedback from opening 7W1Y fetched from pdb  
---  
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain S  
Ignoring microheterogeneity for label_seq_id 2 in chain S  
Ignoring microheterogeneity for label_seq_id 3 in chain S  
Ignoring microheterogeneity for label_seq_id 4 in chain S  
Ignoring microheterogeneity for label_seq_id 5 in chain S  
93 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
7w1y title:  
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]  
  
Chain information for 7w1y #8  
---  
Chain | Description | UniProt  
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904  
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808  
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863  
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734  
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821  
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719  
S | DNA (49-MER) |   
  
Non-standard residues in 7w1y #8  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
DA — 2'-deoxyadenosine-5'-monophosphate  
MG — magnesium ion  
ZN — zinc ion  
  
2025 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> rename #8 H_DH_Zhai

> open emdb:19186

Opened emdb 19186 as #9, grid size 420,420,420, pixel 1.08, shown at level
0.02, step 2, values float32, fit PDB 8rif  

> rename #9 Y_DH_map_Miller

> open 8RIF

8rif title:  
Cryo-EM structure of the MCM double hexamer loaded onto dsDNA. [more info...]  
  
Chain information for 8rif #10  
---  
Chain | Description | UniProt  
2 A | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868  
3 B | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971  
4 C | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933  
5 D | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775  
6 E | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017  
7 F | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845  
X | DNA (53-MER) |   
Y | DNA (53-MER) |   
  
Non-standard residues in 8rif #10  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
ZN — zinc ion  
  

> rename #10 Y_DH_Miller

> transparency #1,3,5,7,9 60

> matchmaker #4/2 to #2/2 bring #3

Parameters  
---  
Chain pairing | bb  
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 X_DH, chain 2 (#2) with H_DH_Costa, chain 2 (#4), sequence
alignment score = 3374.7  
RMSD between 602 pruned atom pairs is 1.247 angstroms; (across all 692 pairs:
1.498)  
  

> matchmaker #6/2 to #2/2 bring #5

Parameters  
---  
Chain pairing | bb  
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 X_DH, chain 2 (#2) with H_DH_Bleichert, chain 2 (#6), sequence
alignment score = 3236.1  
RMSD between 621 pruned atom pairs is 0.633 angstroms; (across all 646 pairs:
0.877)  
  

> matchmaker #8/2 to #2/2 bring #7

Parameters  
---  
Chain pairing | bb  
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 X_DH, chain 2 (#2) with H_DH_Zhai, chain 2 (#8), sequence alignment
score = 3342.3  
RMSD between 644 pruned atom pairs is 0.653 angstroms; (across all 702 pairs:
1.557)  
  

> matchmaker #10/2 to #2/2 bring #9

Parameters  
---  
Chain pairing | bb  
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 X_DH, chain 2 (#2) with Y_DH_Miller, chain 2 (#10), sequence
alignment score = 2105.8  
RMSD between 515 pruned atom pairs is 1.084 angstroms; (across all 616 pairs:
1.831)  
  

> volume #1,3,5,7,9 step 1

> set bgColor white

> lighting soft

> lighting shadows true intensity 0.5

> volume #1,3,5,7,9 color #b2b2b29a

> color #*/2,A pink

> color #*/3,B dodger blue

> color #*/4,C olive drab

> color #*/5,D gold

> color #*/6,E orange

> color #*/7,F indigo

> color #*/X,S black

> color #*/Y,O light grey

> hide atoms

> show cartoons

> hide #*/X,Y #*/S,O cartoons

> show #*/X,Y #*/S,O atoms

> select #*/X,Y #*/S,O

12687 atoms, 13932 bonds, 390 pseudobonds, 502 residues, 9 models selected  

> style sel sphere

Changed 12687 atom styles  

> select clear

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 876 atom styles  

> color ::name=""ADP"" red

> show ::name=""ATP"" atoms

> style ::name=""ATP"" stick

Changed 888 atom styles  

> color ::name=""ATP"" red

> show ::name=""AGS"" atoms

> style ::name=""AGS"" stick

Changed 0 atom styles  

> color ::name=""AGS"" red

> show ::name=""Zn"" atoms

> style ::name=""Zn"" stick

Changed 50 atom styles  

> color ::name=""Zn"" byhetero

> show ::name=""Mg"" atoms

> style ::name=""Mg"" stick

Changed 50 atom styles  

> color ::name=""Mg"" byhetero

> volume #1 level 5

> color zone #1 near #2 distance 6.5

> volume splitbyzone #1

Opened X_DH_map 0 as #11.1, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 1 as #11.2, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 2 as #11.3, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 3 as #11.4, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 4 as #11.5, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 5 as #11.6, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 6 as #11.7, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 7 as #11.8, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 8 as #11.9, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 9 as #11.10, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 10 as #11.11, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  
Opened X_DH_map 11 as #11.12, grid size 548,548,548, pixel 0.5, shown at level
5, step 1, values float32  

> transparency #11 60

> volume #11 level 6.5

> volume #3 level 0.4

> color zone #3 near #4 distance 6.5

> volume splitbyzone #3

Opened H_DH_map_Costa 0 as #12.1, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 1 as #12.2, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 2 as #12.3, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 3 as #12.4, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 4 as #12.5, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 5 as #12.6, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 6 as #12.7, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 7 as #12.8, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 8 as #12.9, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 9 as #12.10, grid size 400,400,400, pixel 1.08, shown at
level 0.4, step 1, values float32  
Opened H_DH_map_Costa 10 as #12.11, grid size 400,400,400, pixel 1.08, shown
at level 0.4, step 1, values float32  
Opened H_DH_map_Costa 11 as #12.12, grid size 400,400,400, pixel 1.08, shown
at level 0.4, step 1, values float32  

> transparency #12 60

> volume #12 level 0.4

> volume #5 level 0.12

> color zone #5 near #6 distance 6.5

> volume splitbyzone #5

Opened H_DH_map_Bleichert 0 as #13.1, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 1 as #13.2, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 2 as #13.3, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 3 as #13.4, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 4 as #13.5, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 5 as #13.6, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 6 as #13.7, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 7 as #13.8, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 8 as #13.9, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 9 as #13.10, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 10 as #13.11, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  
Opened H_DH_map_Bleichert 11 as #13.12, grid size 500,500,500, pixel 0.832,
shown at level 0.12, step 1, values float32  

> transparency #13 60

> volume #13 level 0.12

> volume #7 level 0.7

> color zone #7 near #8 distance 6.5

> volume splitbyzone #7

Opened H_DH_map_Zhai 0 as #14.1, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 1 as #14.2, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 2 as #14.3, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 3 as #14.4, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 4 as #14.5, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 5 as #14.6, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 6 as #14.7, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 7 as #14.8, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 8 as #14.9, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 9 as #14.10, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 10 as #14.11, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  
Opened H_DH_map_Zhai 11 as #14.12, grid size 400,400,400, pixel 1.06, shown at
level 0.7, step 1, values float32  

> transparency #14 60

> volume #14 level 0.7

> volume #9 level 0.022

> color zone #9 near #10 distance 6.5

> volume splitbyzone #9

Opened Y_DH_map_Miller 0 as #15.1, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 1 as #15.2, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 2 as #15.3, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 3 as #15.4, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 4 as #15.5, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 5 as #15.6, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 6 as #15.7, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 7 as #15.8, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 8 as #15.9, grid size 420,420,420, pixel 1.08, shown at
level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 9 as #15.10, grid size 420,420,420, pixel 1.08, shown
at level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 10 as #15.11, grid size 420,420,420, pixel 1.08, shown
at level 0.022, step 1, values float32  
Opened Y_DH_map_Miller 11 as #15.12, grid size 420,420,420, pixel 1.08, shown
at level 0.022, step 1, values float32  

> transparency #15 60

> volume #15 level 0.022

> hide #4,6,8,10,12,13,14,15 models

> color ::name=""ADP"" byhetero

> color ::name=""ATP"" byhetero

> name xlMCM2_ZNF #2/2:306-356

""#2/2:306-356 "": contains extra trailing text  

> name xlMCM3_ZNF #2/3:140-195

""#2/3:140-195 "": contains extra trailing text  

> name xlMCM4_ZNF #2/4:293-342

""#2/4:293-342 "": contains extra trailing text  

> name xlMCM5_ZNF #2/5:163-224

""#2/5:163-224 "": contains extra trailing text  

> name xlMCM6_ZNF #2/6:153-202

""#2/6:153-202 "": contains extra trailing text  

> name xlMCM7_ZNF #2/7:177-227

""#2/7:177-227 "": contains extra trailing text  

> name xlMCM2_OB #2/2:405-422

""#2/2:405-422 "": contains extra trailing text  

> name xlMCM3_OB #2/3:243-258

""#2/3:243-258 "": contains extra trailing text  

> name xlMCM4_OB #2/4:392-408

""#2/4:392-408 "": contains extra trailing text  

> name xlMCM5_OB #2/5:275-286

""#2/5:275-286 "": contains extra trailing text  

> name xlMCM6_OB #2/6:254-264

""#2/6:254-264 "": contains extra trailing text  

> name xlMCM7_OB #2/7:280-293

""#2/7:280-293 "": contains extra trailing text  

> name xlMCM2_H2I #2/2:543-559

""#2/2:543-559 "": contains extra trailing text  

> name xlMCM3_H2I #2/3:380-395

""#2/3:380-395 "": contains extra trailing text  

> name xlMCM4_H2I #2/4:540-555

""#2/4:540-555 "": contains extra trailing text  

> name xlMCM5_H2I #2/5:417-432

""#2/5:417-432 "": contains extra trailing text  

> name xlMCM6_H2I #2/6:433-448

""#2/6:433-448 "": contains extra trailing text  

> name xlMCM7_H2I #2/7:405-432

""#2/7:405-432 "": contains extra trailing text  

> name xlMCM2_PS1 #2/2:593-605

""#2/2:593-605 "": contains extra trailing text  

> name xlMCM3_PS1 #2/3:434-439

""#2/3:434-439 "": contains extra trailing text  

> name xlMCM4_PS1 #2/4:594-599

""#2/4:594-599 "": contains extra trailing text  

> name xlMCM5_PS1 #2/5:471-476

""#2/5:471-476 "": contains extra trailing text  

> name xlMCM6_PS1 #2/6:487-491

""#2/6:487-491 "": contains extra trailing text  

> name xlMCM7_PS1 #2/7:468-474

""#2/7:468-474 "": contains extra trailing text  

> name xlMCM2_ATP #2/2:ATP

""#2/2:ATP "": contains extra trailing text  

> name xlMCM3_ADP #2/3:ADP

""#2/3:ADP "": contains extra trailing text  

> name xlMCM4_ATP #2/4:ATP

""#2/4:ATP "": contains extra trailing text  

> name xlMCM5_ATP #2/5:ATP

""#2/5:ATP "": contains extra trailing text  

> name xlMCM6_ATP #2/6:ATP

""#2/6:ATP "": contains extra trailing text  

> name xlMCM7_ATP #2/7:ATP

""#2/7:ATP "": contains extra trailing text  

> name xlMCM2_ATP_loop #2/2:508-525

""#2/2:508-525 "": contains extra trailing text  

> name xlMCM3_ATP_loop #2/3:346-362

""#2/3:346-362 "": contains extra trailing text  

> name xlMCM4_ATP_loop #2/4:506-522

""#2/4:506-522 "": contains extra trailing text  

> name xlMCM5_ATP_loop #2/5:383-399

""#2/5:383-399 "": contains extra trailing text  

> name xlMCM6_ATP_loop #2/6:399-415

""#2/6:399-415 "": contains extra trailing text  

> name xlMCM7_ATP_loop #2/7:382-397

""#2/7:382-397 "": contains extra trailing text  

> name DNA_bubble #2/X:22-38 #2/Y:24-38

""#2/X:22-38 #2/Y:24-38 "": contains extra trailing text  

> open cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc

Opened X_DH_map as #16, grid size 548,548,548, pixel 0.5, shown at level 6.93,
step 4, values float32  

> rename #16 X_DH_map_Mcm3

> open XL_MCM_DH_final_v1_30042025.pdb

Chain information for XL_MCM_DH_final_v1_30042025.pdb #17  
---  
Chain | Description  
2 A | No description available  
3 B | No description available  
4 C | No description available  
5 D | No description available  
6 E | No description available  
7 F | No description available  
X | No description available  
Y | No description available  
  

> rename #17 X_DH_Mcm3

> name xlMCM3_ATP_loop #17/3:346-362

""#17/3:346-362 "": contains extra trailing text  

> open cryosparc_P49_J1739_map_flipped.mrc

Opened cryosparc_P49_J1739_map_flipped.mrc as #18, grid size 500,500,500,
pixel 0.928, shown at level 0.0257, step 2, values float32  

> rename #18 X_DH_map_Mcm4

> open XL_MCM_DH_final_v1_30042025.pdb

Chain information for XL_MCM_DH_final_v1_30042025.pdb #19  
---  
Chain | Description  
2 A | No description available  
3 B | No description available  
4 C | No description available  
5 D | No description available  
6 E | No description available  
7 F | No description available  
X | No description available  
Y | No description available  
  

> rename #19 X_DH_Mcm4

> name xlMCM4_ATP_loop #19/4:506-522

""#19/4:506-522 "": contains extra trailing text  

> open cryosparc_P49_J1739_map_flipped.mrc

Opened X_DH_map_Mcm4 as #20, grid size 500,500,500, pixel 0.928, shown at
level 0.0257, step 2, values float32  

> rename #20 X_DH_map_Mcm5

> open XL_MCM_DH_final_v1_30042025.pdb

Chain information for XL_MCM_DH_final_v1_30042025.pdb #21  
---  
Chain | Description  
2 A | No description available  
3 B | No description available  
4 C | No description available  
5 D | No description available  
6 E | No description available  
7 F | No description available  
X | No description available  
Y | No description available  
  

> rename #21 X_DH_Mcm5

> name xlMCM5_ATP_loop #21/5:383-399

""#21/5:383-399 "": contains extra trailing text  

> open cryosparc_P49_J1739_map_flipped.mrc

Opened X_DH_map_Mcm5 as #22, grid size 500,500,500, pixel 0.928, shown at
level 0.0257, step 2, values float32  

> rename #22 X_DH_map_Mcm6

> open XL_MCM_DH_final_v1_30042025.pdb

Chain information for XL_MCM_DH_final_v1_30042025.pdb #23  
---  
Chain | Description  
2 A | No description available  
3 B | No description available  
4 C | No description available  
5 D | No description available  
6 E | No description available  
7 F | No description available  
X | No description available  
Y | No description available  
  

> rename #23 X_DH_Mcm6

> name xlMCM6_ATP_loop #23/6:399-415

""#23/6:399-415 "": contains extra trailing text  

> open cryosparc_P49_J1739_map_flipped.mrc

Opened X_DH_map_Mcm6 as #24, grid size 500,500,500, pixel 0.928, shown at
level 0.0257, step 2, values float32  

> rename #24 X_DH_map_Mcm7

> open XL_MCM_DH_final_v1_30042025.pdb

Chain information for XL_MCM_DH_final_v1_30042025.pdb #25  
---  
Chain | Description  
2 A | No description available  
3 B | No description available  
4 C | No description available  
5 D | No description available  
6 E | No description available  
7 F | No description available  
X | No description available  
Y | No description available  
  

> rename #25 X_DH_Mcm7

> name xlMCM7_ATP_loop #25/7:382-397

""#25/7:382-397 "": contains extra trailing text  

> matchmaker xlMCM3_ATP_loop to #2/2 bring #16

Missing or invalid ""matchAtoms"" argument: invalid atoms specifier  

> matchmaker xlMCM4_ATP_loop to #2/2 bring #18

Missing or invalid ""matchAtoms"" argument: invalid atoms specifier  

> matchmaker xlMCM5_ATP_loop to #2/2 bring #20

Missing or invalid ""matchAtoms"" argument: invalid atoms specifier  

> matchmaker xlMCM6_ATP_loop to #2/2 bring #22

Missing or invalid ""matchAtoms"" argument: invalid atoms specifier  

> matchmaker xlMCM7_ATP_loop to #2/2 bring #24

Missing or invalid ""matchAtoms"" argument: invalid atoms specifier  

> volume #16-24 step 1

> volume #1,3,5,7,9 color #b2b2b29a

> color #*/2,A pink

> color #*/3,B dodger blue

> color #*/4,C olive drab

> color #*/5,D gold

> color #*/6,E orange

> color #*/7,F indigo

> color #*/X,S black

> color #*/Y,O light grey

> hide atoms

> show cartoons

> hide #*/X,Y #*/S,O cartoons

> show #*/X,Y #*/S,O atoms

> select #*/X,Y #*/S,O

30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected  

> style sel sphere

Changed 30937 atom styles  

> select clear

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 1266 atom styles  

> color ::name=""ADP"" red

> show ::name=""ATP"" atoms

> style ::name=""ATP"" stick

Changed 3038 atom styles  

> color ::name=""ATP"" red

> show ::name=""AGS"" atoms

> style ::name=""AGS"" stick

Changed 0 atom styles  

> color ::name=""AGS"" red

> show ::name=""Zn"" atoms

> style ::name=""Zn"" stick

Changed 100 atom styles  

> color ::name=""Zn"" byhetero

> show ::name=""Mg"" atoms

> style ::name=""Mg"" stick

Changed 110 atom styles  

> color ::name=""Mg"" byhetero

> volume #16 level 5

> color zone #16 near #17 distance 6.5

> volume splitbyzone #16

Opened X_DH_map_Mcm3 0 as #26.1, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 1 as #26.2, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 2 as #26.3, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 3 as #26.4, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 4 as #26.5, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 5 as #26.6, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 6 as #26.7, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 7 as #26.8, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 8 as #26.9, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 9 as #26.10, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 10 as #26.11, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 11 as #26.12, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  

> transparency #26 60

> volume #26 level 6.5

> volume #18 level 5

> color zone #18 near #19 distance 6.5

> volume splitbyzone #18

Opened X_DH_map_Mcm7 0 as #27.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 1 as #27.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 2 as #27.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 3 as #27.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 4 as #27.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 5 as #27.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 6 as #27.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 7 as #27.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 8 as #27.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 9 as #27.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 10 as #27.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  
Opened X_DH_map_Mcm7 11 as #27.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  

> transparency #27 60

> volume #27 level 6.5

> volume #20 level 5

> color zone #20 near #21 distance 6.5

> volume splitbyzone #20

Opened X_DH_map_Mcm7 0 as #28.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 1 as #28.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 2 as #28.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 3 as #28.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 4 as #28.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 5 as #28.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 6 as #28.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 7 as #28.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 8 as #28.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 9 as #28.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 10 as #28.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  
Opened X_DH_map_Mcm7 11 as #28.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  

> transparency #28 60

> volume #28 level 6.5

> volume #22 level 5

> color zone #22 near #23 distance 6.5

> volume splitbyzone #22

Opened X_DH_map_Mcm7 0 as #29.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 1 as #29.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 2 as #29.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 3 as #29.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 4 as #29.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 5 as #29.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 6 as #29.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 7 as #29.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 8 as #29.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 9 as #29.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 10 as #29.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  
Opened X_DH_map_Mcm7 11 as #29.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  

> transparency #29 60

> volume #29 level 6.5

> volume #24 level 5

> color zone #24 near #25 distance 6.5

> volume splitbyzone #24

Opened X_DH_map_Mcm7 0 as #30.1, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 1 as #30.2, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 2 as #30.3, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 3 as #30.4, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 4 as #30.5, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 5 as #30.6, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 6 as #30.7, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 7 as #30.8, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 8 as #30.9, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 9 as #30.10, grid size 500,500,500, pixel 0.928, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm7 10 as #30.11, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  
Opened X_DH_map_Mcm7 11 as #30.12, grid size 500,500,500, pixel 0.928, shown
at level 5, step 1, values float32  

> transparency #30 60

> volume #30 level 6.5

> color ::name=""ADP"" byhetero

> color ::name=""ATP"" byhetero

> view n-term_front

Expected an objects specifier or a view name or a keyword  

> view c-term_front

Expected an objects specifier or a view name or a keyword  

> view

> view matrix camera

Missing ""camera"" keyword's argument  

> view name c-term_front

> turn y 180

> view name n-term_front

> turn y 180

> view c-term_front

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true

> turn y 180

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true

> transparency #11 0

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!11 models

> show #!11 models

> hide #!17 models

> hide #!19 models

> hide #!23 models

> hide #!21 models

> hide #!27 models

> hide #!25 models

> hide #!26 models

> hide #!28 models

> hide #!29 models

> hide #!30 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> transparency #11 60

> transparency #11 50

> transparency #11 60

> transparency #11 0

> hide #!2 models

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true

> turn y-180

Expected an axis vector or a keyword  

> turn y 180

> view c-term front

Expected an objects specifier or a view name or a keyword  

> view c-term_front

> view cN-term_front

Expected an objects specifier or a view name or a keyword  

> view N-term_front

Expected an objects specifier or a view name or a keyword  

> view n-term_front

> view c-term_front

> view n-term_front

> view c-term_front

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true

> turn x 180

> turn x 90

> turn x 270

> show #!2 models

> view n-term_front

> transparency #11 60

> clip front -4 back 15

> clip off

> clip front -4 back 20

> clip off

> clip front -4 back 30

> clip off

> clip front -4 back 10

> clip off

> clip front -4 back 15

> clip off

> hide #*/X,Y #*/S,O cartoons

> show #*/X,Y #*/S,O atoms

> select #*/X,Y #*/S,O

30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected  

> style sel stick

Changed 30937 atom styles  

> show sel atoms

> color sel byhetero

> transparency #11 60

> select clear

> show #*/X,Y #*/S,O cartoons

> show #*/X,Y #*/S,O atoms

> select #*/X,Y #*/S,O

30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected  

> style sel stick

Changed 30937 atom styles  

> show sel atoms

> color sel byhetero

> transparency #11 60

> select clear

> clip front -4 back 15

> clip off

> clip front -4 back 20

> clip off

> hide #*/X,Y #*/S,O cartoons

> show #*/X,Y #*/S,O atoms

> select #*/X,Y #*/S,O

30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected  

> style sel sphere

Changed 30937 atom styles  

> select clear

> color #*/X,S black

> color #*/Y,O light grey

> clip front -4 back 15

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_clip.png
> width 2000 height 1352 supersample 3 transparentBackground true

> turn y 180

> clip off

> clip front -4 back 15

> clip off

> view c-term_front

> clip front -4 back 15

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_clip_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true

> clip off

> turn x,y 90

Expected an axis vector or a keyword  

> turn y 90 x 90

Expected 'forever' or an integer >= 1 or a keyword  

> turn y 90

> view c-term_front

> turn y 90

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_top_view_cartoon_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true

> clip front -4 back 15

> clip off

> clip front -2 back 15

> clip off

> clip front 2 back 15

> clip off

> clip front 10

> clip off

> clip front 2

> clip off

> clip back 1

> clip off

> clip front -10

> clip off

> clip front -1

> clip off

> view c-term_front

> hide #!2 models

> view n-term_front

> transparency #11 0

> clip front -4 back 15

> clip off

> clip front -3 back 15

> clip off

> clip front -3 back 10

> clip off

> ui tool show ""Side View""

> hide #!11.4 models

> show #!11.4 models

> hide #!11.4 models

> hide #!11.3 models

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_clip_with_side_view.png
> width 2000 height 1352 supersample 3 transparentBackground true

> turn y 180

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_clip_with_side_view_turn_180.png
> width 2000 height 1352 supersample 3 transparentBackground true

> view n-term_front

> save /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM-
> DH_back-map_cut-through.png supersample 5 transparentBackground true

> show #!11.4 models

> show #!11.3 models

> clip off

> hide #!11.1 models

> hide #!11.2 models

> hide #!11.3 models

> hide #!11.4 models

> hide #!11.5 models

> hide #!11.6 models

> hide #!11.7 models

> hide #!11.8 models

> hide #!11.9 models

> hide #!11.10 models

> view n-term

Expected an objects specifier or a view name or a keyword  

> view n-term_front

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_surface.png
> width 2000 height 1352 supersample 3 transparentBackground true

> show #!11.10 models

> show #!11.9 models

> show #!11.8 models

> show #!11.7 models

> show #!11.6 models

> hide #!11.6 models

> show #!11.5 models

> show #!11.6 models

> show #!11.4 models

> show #!11.3 models

> show #!11.2 models

> transparency #11 60

> show #!2 models

> view c-term_front

> turn y 90

> transparency #11.4 0

> clip off

> view c-term_front

> turn y 90

> clip front -4 back 15

> clip off

> clip front -4 back 80

> clip off

> clip front 20 back 10

clip back plane is in front of front plane  

> clip off

> clip front -1 back 10

> clip off

> clip front 10 back 10

clip back plane is in front of front plane  

> clip off

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 1266 atom styles  

> color ::name=""ADP"" black

> volume #1 level 5

> color zone #1 near #2 distance 6.5

> volume splitbyzone #1

Opened X_DH_map_Mcm3 0 as #31.1, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 1 as #31.2, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 2 as #31.3, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 3 as #31.4, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 4 as #31.5, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 5 as #31.6, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 6 as #31.7, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 7 as #31.8, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 8 as #31.9, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 9 as #31.10, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 10 as #31.11, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 11 as #31.12, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 12 as #31.13, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 13 as #31.14, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 14 as #31.15, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 15 as #31.16, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  

> transparency #31 60

> volume #31 level 6.5

> hide #!11 models

> hide #!11.2 models

> hide #!11.3 models

> hide #!11.4 models

> hide #!11.5 models

> hide #!11.6 models

> hide #!11.7 models

> hide #!11.8 models

> hide #!11.9 models

> hide #!11.10 models

> hide #!11.11 models

> hide #!11.12 models

> hide #!31 models

> show #!31 models

> hide #!31 models

> show #!31 models

> hide #!31 models

> show #!31 models

> hide #!31.11 models

> show #!31.11 models

> hide #!31.11 models

> show #!31.11 models

> hide #!31.11 models

> show #!31.11 models

> hide #!31.11 models

> show #!31.11 models

> close #31

> show #!11 models

> show #!11.1 models

> show #!11.2 models

> hide #!11.2 models

> hide #!11.1 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 1266 atom styles  

> color ::name=""ADP"" Dim grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color ::name=""ADP"" dim_grey

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 1266 atom styles  

> color ::name=""ADP"" Dim Gray

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color ::name=""ADP"" Dim_Gray

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> show ::name=""ADP"" atoms

> select ADP

Expected an objects specifier or a keyword  

> select ADP atom

Expected an objects specifier or a keyword  

> ui tool show ""Color Actions""

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 1266 atom styles  

> color ::name=""ADP"" Gray

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> select ::name=""ADP""

1266 atoms, 1342 bonds, 38 residues, 10 models selected  

> color (#!2 & sel) dim gray

> select clear

> show ::name=""ADP"" atoms

> style ::name=""ADP"" stick

Changed 1266 atom styles  

> color ::name=""ADP"" dim gray

> volume #1 level 5

> color zone #1 near #2 distance 6.5

> volume splitbyzone #1

Opened X_DH_map_Mcm3 0 as #31.1, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 1 as #31.2, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 2 as #31.3, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 3 as #31.4, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 4 as #31.5, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 5 as #31.6, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 6 as #31.7, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 7 as #31.8, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 8 as #31.9, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 9 as #31.10, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 10 as #31.11, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 11 as #31.12, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 12 as #31.13, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 13 as #31.14, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 14 as #31.15, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 15 as #31.16, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  
Opened X_DH_map_Mcm3 16 as #31.17, grid size 548,548,548, pixel 0.5, shown at
level 5, step 1, values float32  

> transparency #31 60

> volume #31 level 6.5

> hide #!31.6 models

> show #!31.6 models

> hide #!31.6 models

> show #!31.6 models

> hide #!31.11 models

> show #!31.11 models

> hide #!31.11 models

> show #!31.11 models

> hide #!31.6 models

> show #!31.6 models

> hide #!31.5 models

> show #!31.5 models

> hide #!31.5 models

> show #!31.5 models

> hide #!31.5 models

> show #!31.5 models

> transparency #31.5, 31.6, 31.11 0

> transparency #31.5 0

> transparency #31.4 0

> transparency #31.11 0

> hide #!31.7 models

> hide #!31.6 models

> show #!31.6 models

> hide #!31.6 models

> show #!31.6 models

> hide #!31.5 models

> show #!31.5 models

> hide #!31.5 models

> show #!31.5 models

> transparency #31.11 0

> select add #31.11

4 models selected  

> transparency sel 0

> select subtract #31.11

Nothing selected  

> select add #31.11

4 models selected  

> select subtract #31.11

Nothing selected  

> select add #31.11

4 models selected  

> select subtract #31.11

Nothing selected  

> select add #31.11

4 models selected  

> select subtract #31.11

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select ATP

Expected an objects specifier or a keyword  

> select add #31.11

4 models selected  

> select add #31.6

7 models selected  

> select add #31.5

10 models selected  

> select transperencey 0

Expected an objects specifier or a keyword  

> select transparency 0

Expected an objects specifier or a keyword  

> select transparency 0

Expected an objects specifier or a keyword  

> transparency #31.5.1#31.6.1#31.11.1 0

> transparency #31.5.1#31.6.1#31.11.1 60

> transparency #31.5.1#31.6.1#31.11.1 0

> select clear

> show ::name=""ATP"" atoms

> style ::name=""ATP"" stick

Changed 3038 atom styles  

> color ::name=""ATP"" red

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_top_view_cartoon_surface_ATP_ADP_colored.png
> width 2000 height 1352 supersample 3 transparentBackground true

> clip off

> view c-term_front

> ui tool show ""Side View""

> hide #!31 models

> hide #!31.1 models

> hide #!31.2 models

> hide #!31.3 models

> hide #!31.4 models

> hide #!31.5 models

> hide #!31.6 models

> hide #!31.8 models

> hide #!31.9 models

> hide #!31.10 models

> hide #!31.11 models

> hide #!31.12 models

> hide #!31.13 models

> hide #!31.14 models

> hide #!31.15 models

> hide #!31.16 models

> hide #!31.17 models

> show #!11.1 models

> show #!11.2 models

> show #!11.3 models

> show #!11.4 models

> show #!11.5 models

> show #!11.6 models

> show #!11.7 models

> show #!11.8 models

> show #!11.9 models

> show #!11.10 models

> show #!11.11 models

> show #!11.12 models

> hide #!11.4 models

> hide #!11.3 models

> show #!11.3 models

> show #!11.4 models

> hide #!11.4 models

> show #!11.4 models

> hide #!11.4 models

> show #!11.4 models

> hide #!11.4 models

> show #!11.4 models

> hide #!11.4 models

> hide #!11.3 models

> show #!11.3 models

> show #!11.4 models

> hide #!11 models

> view c-term_front

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon.png
> width 2000 height 1352 supersample 3 transparentBackground true

> view n-term_front

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_turn.png
> width 2000 height 1352 supersample 3 transparentBackground true

> show #!11 models

> show #!2 models

> select DNA_bubble

Expected an objects specifier or a keyword  

> view sel

No objects specified.  

> transparency #11 60

> select #2/X,Y

3650 atoms, 3933 bonds, 114 residues, 1 model selected  

> style sel stick

Changed 3650 atom styles  

> color sel byhetero

> hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models

> select clear

> view mcm5_dna_melt

Expected an objects specifier or a view name or a keyword  

> select mcm5_dna_melt

Expected an objects specifier or a keyword  

> show sel atoms

> color sel byhetero

> select clear

> name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 110 atom styles  

> color sel byhetero

> select clear

> view mcm5_dna_melt

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 110 atom styles  

> color sel byhetero

> select clear

> view mcm5_dna_melt

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select H

456356 atoms, 56737 residues, 7 models selected  

> hide (#!2 & sel) target a

> select clear

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_1.png
> width 2000 height 1352 supersample 3 transparentBackground true

> turn y 180

> clip off

> name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 110 atom styles  

> color sel byhetero

> select clear

> view mcm5_dna_melt

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> select H

456356 atoms, 56737 residues, 7 models selected  

> hide (#!2 & sel) target a

> select clear

> show #*/X,Y #*/S,O cartoons

> hide #*/X,Y #*/S,O cartoons

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_2.png
> width 2000 height 1352 supersample 3 transparentBackground true

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> style sel sphere

Changed 110 atom styles  

> select clear

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_3.png
> width 2000 height 1352 supersample 3 transparentBackground true

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 110 atom styles  

> color sel byhetero

> select clear

> select H

456356 atoms, 56737 residues, 7 models selected  

> hide (#!2 & sel) target a

> select clear

> hide #!11

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_4.png
> width 2000 height 1352 supersample 3 transparentBackground true

> nucleotides #!2 tube/slab shape muffler

> nucleotides #!2 tube/slab shape ellipsoid

> nucleotides #!2 slab

> style nucleic & #!2 stick

Changed 3650 atom styles  

> nucleotides #!2 fill

> style nucleic & #!2 stick

Changed 3650 atom styles  

> nucleotides #!2 atoms

> style nucleic & #!2 stick

Changed 3650 atom styles  

> nucleotides #!2 tube/slab shape ellipsoid

> nucleotides #!2 tube/slab shape muffler

> nucleotides #!2 ladder

> nucleotides #!2 stubs

> nucleotides #!2 slab

> style nucleic & #!2 stick

Changed 3650 atom styles  

> nucleotides #!2 fill

> style nucleic & #!2 stick

Changed 3650 atom styles  

> nucleotides #!2 atoms

> style nucleic & #!2 stick

Changed 3650 atom styles  

> show #!11

> show #!2 models

> select DNA_bubble

Expected an objects specifier or a keyword  

> view sel

No objects specified.  

> transparency #11 60

> select #2/X,Y

3650 atoms, 3933 bonds, 114 residues, 1 model selected  

> style sel stick

Changed 3650 atom styles  

> color sel byhetero

> hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models

> select clear

> name DNA_bubble #2/X:22-38 #2/Y:24-38

> show #!2 models

> select DNA_bubble

1024 atoms, 1099 bonds, 32 residues, 1 model selected  

> view sel

> transparency #11 60

> select #2/X,Y

3650 atoms, 3933 bonds, 114 residues, 1 model selected  

> style sel stick

Changed 3650 atom styles  

> color sel byhetero

> hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models

> select clear

> hide #!11 models

> hide #!11.1 models

> show #!11 models

> show #!11.1 models

> hide #!11.1 models

> hide #!11.2 models

> hide #!11.3 models

> hide #!11.4 models

> hide #!11.5 models

> hide #!11.6 models

> hide #!11.7 models

> hide #!11.8 models

> hide #!11.9 models

> hide #!11.10 models

> hide #!11.11 models

> show #!11.11 models

> show #!11.10 models

> show #!11.9 models

> show #!11.8 models

> show #!11.7 models

> show #!11.6 models

> show #!11.5 models

> show #!11.4 models

> show #!11.3 models

> show #!11.2 models

> show #!11.1 models

> view mcm5_dna_melt

> select mcm5_dna_melt

110 atoms, 106 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> hide #!11.11 models

> show #!11.11 models

> hide #!11.8 models

> hide #!11.9 models

> hide #!11.6 models

> hide #!11.2 models

> select H

456356 atoms, 56737 residues, 7 models selected  

> hide (#!2 & sel) target a

> select clear

> save
> /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_5.png
> width 2000 height 1352 supersample 3 transparentBackground true

> hide #!1-30 target m

> show #!2 models

> view #2/2:ATP

> turn x 270

> clip front -5 back 10 position #2/2:ATP

> show #!11.3 models

> show #!11.4 models

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface sel

> transparency (#!2 & sel) 60

> surface style #!2.2 mesh

> select clear

> hide #!1-31 target m

> show #!2 models

> view #2/2:ATP

> turn x 270

> clip front -5 back 10 position #2/2:ATP

> show #!11.3 models

> show #!11.4 models

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface sel

> transparency (#!2 & sel) 60

> surface style #!2.2 mesh

> show #!11.9 models

> show #!11.8 models

> show #!11.6 models

> show #!11.2 models

> select clear

> hide #!1-31 target m

> show #!2 models

> view #2/2:ATP

> turn x 270

> clip front -5 back 10 position #2/2:ATP

> show #!11.3 models

> show #!11.4 models

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface sel

> transparency (#!2 & sel) 60

> surface style #!2.2 mesh

> select clear

> color ::name=""ADP"" byhetero

> color ::name=""ATP"" byhetero

> clip off

> hide #!1-31 target m

> show #!2 models

> view #2/2:ATP

> turn x 270

> clip front -5 back 10 position #2/2:ATP

> show #!11.3 models

> show #!11.4 models

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface sel

> transparency (#!2 & sel) 60

> surface style #!2.2 mesh

> select clear

> hide #!1-30 target m

> show #!2 models

> view #2/2:ATP

> turn x 270

> clip front -5 back 10 position #2/2:ATP

> show #!11.3 models

> show #!11.4 models

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface sel

> transparency (#!2 & sel) 60

> surface style #!2.2 mesh

> turn y 180

> select clear

> clip off

> hide #!1-30 target m

> show #!2 models

> view #2/2:ATP

> turn x 270

> clip front -5 back 10 position #2/2:ATP

> show #!11.3 models

> show #!11.4 models

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface sel

> transparency (#!2 & sel) 60

> surface style #!2.2 mesh

> turn y 180

> select clear

> clip off

> hide #!1-30 target m

> show #!2 models

> view #2/3:ADP

> turn x 270

> clip front -5 back 10 position #2/3:ADP

> show #!11.5 models

> show #!11.6 models

> hide #!11.3 models

> show #!11.3 models

> hide #!11.3 models

> show #!11.3 models

> hide #!11.3 models

> show #!11.3 models

> hide #!11.3 models

> show #!11.3 models

> hide #!11.4 models

> show #!11.4 models

> hide #!11.4 models

> show #!11.4 models

> clip off

> view #2/2:ATP

> hide #!11 mesh

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #!11 surfaces mesh

Expected ',' or a keyword  

> surface style #!2.2 surface

Missing or invalid ""style"" argument: Should be one of 'dot', 'mesh', or
'solid'  

> surface style #!2.2 mesh

> hide #!11.1 models

> hide #!11.2 models

> hide #!11.3 models

> hide #!11.5 models

> hide #!11.6 models

> hide #!11.7 models

> hide #!11.8 models

> hide #!11.9 models

> hide #!11.10 models

> hide #!11.11 models

> hide #!11.12 models

> select #11.4

4 models selected  

> color #11.4.1 light gray

> color #11.4 light gray

> select #11.4

4 models selected  

> surface hidePatches #11.4.1

> select clear

> select #11.4

4 models selected  

> surface style #11.4 solid

> select #2/2:ATP

43 atoms, 45 bonds, 1 residue, 1 model selected  

> surface hidePatches (#!2 & sel)

> select #11.4

4 models selected  

> surface style #11.4 mesh

> select clear

> select #11.4

2 models selected  

> select color blue

Expected an objects specifier or a keyword  

> color #11.4.1 blue

> select clear

> show #!11.3 models

> hide #!11.3 models

> show #!11.3 models

> hide #!11.3 models

> show #!11.3 models

> select #11.3

2 models selected  

> select #11.3

2 models selected  

> surface style #11.3 mesh

> color #11.3 blue

> select clear

> hide #!11.3 models

> show #!11.3 models

> undo

> select #11.3

2 models selected  

> surface style #11.3 mesh

> color #11.3 blue

> 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 - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.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: MRX33DK/A
      Chip: Apple M3 Pro
      Total Number of Cores: 11 (5 performance and 6 efficiency)
      Memory: 18 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 23 days, 19 hours, 38 minutes

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:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG FHD:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 100.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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
    biopython: 1.83
    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-Clipper: 0.23.1
    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-ISOLDE: 1.8
    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-PhenixUI: 1.3.7
    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
    DiffFit: 0.6.2
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    fsspec: 2024.10.0
    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
    mpmath: 1.3.0
    mrcfile: 1.5.0
    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
    Send2Trash: 1.8.3
    SEQCROW: 1.8.16
    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
    sympy: 1.13.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    torch: 2.2.1
    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	closed	normal		Window Toolkit		duplicate						all	ChimeraX