id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17005	ChimeraX bug report submission	chimerax-bug-report@…		"{{{
The following bug report has been submitted:
Platform:        macOS-15.3.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000036c32f000 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001ff30c840 (most recent call first):
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init
  File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, 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, PIL._imagingmath, PIL._webp, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.morph._morph (total: 65)


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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325.cxs

Opened cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc as #1.1, grid size
400,400,400, pixel 1.32, shown at level 0.0332, step 1, values float32  
Log from Tue Feb 25 11:58:40 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/tzviya/Documents/projects/mMIP/J325_spaca9_sh3_modeling.cxs

Opened cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc as #1.1, grid size
400,400,400, pixel 1.32, shown at level 0.0332, step 1, values float32  
Log from Mon Feb 24 14:02:57 2025 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 /Users/tzviya/Documents/projects/mMIP/J325_SPACA9_SH3.py

Failed opening file /Users/tzviya/Documents/projects/mMIP/J325_SPACA9_SH3.py:  
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to  
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene  
menu item, and change the resulting dialog's ""File Type"" to ChimeraX.  

> open /Volumes/nonshib-webdav/shared/mMIP/J325_SPACA9_SH3.py

Failed opening file /Volumes/nonshib-webdav/shared/mMIP/J325_SPACA9_SH3.py:  
ChimeraX cannot open a regular Chimera session. An exporter from Chimera to  
ChimeraX is available in the latest Chimera release. Use its File->Export
Scene  
menu item, and change the resulting dialog's ""File Type"" to ChimeraX.  

> cd /Users/tzviya/Documents/projects/mMIP

Current working directory is: /Users/tzviya/Documents/projects/mMIP  

> open
> /Users/tzviya/Documents/projects/mMIP/maps/cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc
> /Users/tzviya/Documents/projects/mMIP/maps/J325_007_volume_map_deepem_highRes_erase0.1_crop64.mrc

Opened cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc as #1.1, grid size
400,400,400, pixel 1.32, shown at level 0.0785, step 2, values float32  
Opened J325_007_volume_map_deepem_highRes_erase0.1_crop64.mrc as #1.2, grid
size 64,64,64, pixel 1.32, shown at level 0.000336, step 1, values float32  

> volume #1.2 level 0.005917

> close #1.2

> volume #1.1 step 1

> open /Users/tzviya/Documents/projects/mMIP/models/spaca9_q4v8p4_fitJ325.pdb

spaca9_q4v8p4_fitJ325.pdb title:  
Alphafold monomer V2.0 prediction for sperm acrosome-associated protein 9
(Q4V8P4) [more info...]  
  
Chain information for spaca9_q4v8p4_fitJ325.pdb #2  
---  
Chain | Description | UniProt  
A | sperm acrosome-associated protein 9 | SACA9_RAT 1-168  
  

> volume #1.1 color #b2b2b280

> open /Users/tzviya/Documents/projects/mMIP/models/f6pus4_fitJ325.pdb

f6pus4_fitJ325.pdb title:  
Alphafold monomer V2.0 prediction for SH3 domain-containing 21 (F6PUS4) [more
info...]  
  
Chain information for f6pus4_fitJ325.pdb #3  
---  
Chain | Description | UniProt  
A | SH3 domain-containing 21 | F6PUS4_RAT 1-544  
  

> open
> /Users/tzviya/Documents/projects/mMIP/models/GDP_kin_MT_MancMT_A1_fitJ325.pdb

Chain information for GDP_kin_MT_MancMT_A1_fitJ325.pdb #4  
---  
Chain | Description  
A C D J K L M P | No description available  
B E F G H I N O | No description available  
  

> open
> /Users/tzviya/Documents/projects/mMIP/models/GDP_kin_MT_MancMT_A13_fitJ325.pdb

Chain information for GDP_kin_MT_MancMT_A13_fitJ325.pdb #5  
---  
Chain | Description  
A C D J K L M P | No description available  
B E F G H I N O | No description available  
  

> show cartoons

> hide atoms

> save /Users/tzviya/Documents/projects/mMIP/J325_spaca9_sh3.cxs

> volume #1.1 level 0.03316

> ui tool show ""Show Sequence Viewer""

> sequence chain #2/A

Alignment identifier is 2/A  

> ui tool show ""Show Sequence Viewer""

> sequence chain #3/A

Alignment identifier is 3/A  

> ui mousemode right clip

> select #3/A:69-71,91-96,104-109,112-117

181 atoms, 183 bonds, 21 residues, 1 model selected  

> select #3/A:118-120

27 atoms, 27 bonds, 3 residues, 1 model selected  

> select clear

> select #3/A:124

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

> select #3/A:124-126

21 atoms, 23 bonds, 3 residues, 1 model selected  

> select #2/A:110-111

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

> select #2/A:110-114

41 atoms, 40 bonds, 5 residues, 1 model selected  

> select #2/A:2-35,46-55,60-86,91-104,121-124,127-133,137-157

965 atoms, 975 bonds, 117 residues, 1 model selected  

> select #2/A:58

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

> select #2/A:58

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

> select #2/A:57-58

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

> select #2/A:2-35,46-55,60-86,91-104,121-124,127-133,137-157

965 atoms, 975 bonds, 117 residues, 1 model selected  

> select #2/A:38

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

> select #2/A:38-40

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #2/A:2-35,46-55,60-86,91-104,121-124,127-133,137-157

965 atoms, 975 bonds, 117 residues, 1 model selected  

> open 8OU0

8ou0 title:  
bovine sperm endpiece singlet microtubules (one tubulin dimer and associated
microtubule inner proteins) [more info...]  
  
Chain information for 8ou0 #6  
---  
Chain | Description | UniProt  
A | Tubulin alpha-3 chain | TBA3_BOVIN 1-450  
B | Tubulin beta-4B chain | TBB4B_BOVIN 1-455  
C | Sperm acrosome associated 9 | A0A3Q1MYU9_BOVIN 1-224  
D | Stabilizer of axonemal microtubules 1 | A0A3S5ZPV0_BOVIN 38-514  
  
Non-standard residues in 8ou0 #6  
---  
GDP — guanosine-5'-diphosphate  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
  

> ui mousemode right rotate

> mmaker #6 to #2

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 spaca9_q4v8p4_fitJ325.pdb, chain A (#2) with 8ou0, chain C (#6),
sequence alignment score = 777.8  
RMSD between 148 pruned atom pairs is 0.761 angstroms; (across all 153 pairs:
0.903)  
  

> hide #!1 models

> hide #!6 models

> show #!6 models

> color #6 #011993ff

Drag select of 3 residues  

> select up

132 atoms, 132 bonds, 18 residues, 1 model selected  

> select up

3337 atoms, 3412 bonds, 426 residues, 1 model selected  

> select up

3365 atoms, 3442 bonds, 427 residues, 1 model selected  

> select up

8139 atoms, 8322 bonds, 1030 residues, 1 model selected  

> select down

3365 atoms, 3442 bonds, 427 residues, 1 model selected  

> hide sel cartoons

Drag select of 2 residues  

> select up

78 atoms, 82 bonds, 9 residues, 1 model selected  

> select up

3062 atoms, 3132 bonds, 391 residues, 1 model selected  

> select up

3122 atoms, 3193 bonds, 399 residues, 1 model selected  

> select up

3341 atoms, 3417 bonds, 428 residues, 1 model selected  

> select up

3374 atoms, 3451 bonds, 430 residues, 1 model selected  

> select up

8139 atoms, 8322 bonds, 1030 residues, 1 model selected  

> select down

3374 atoms, 3451 bonds, 430 residues, 1 model selected  

> hide sel cartoons

> select clear

[Repeated 1 time(s)]Drag select of 2 residues  

> select up

164 atoms, 168 bonds, 20 residues, 1 model selected  

> select up

8139 atoms, 8322 bonds, 1030 residues, 1 model selected  

> select down

164 atoms, 168 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> show #!1 models

> hide #!1 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #6/C

Alignment identifier is 6/C  
Drag select of 2 residues  

> select up

63 atoms, 63 bonds, 8 residues, 1 model selected  

> select up

1236 atoms, 1261 bonds, 153 residues, 1 model selected  

> select up

8139 atoms, 8322 bonds, 1030 residues, 1 model selected  

> select down

1236 atoms, 1261 bonds, 153 residues, 1 model selected  

> save /Users/tzviya/Documents/projects/mMIP/models/spaca9_bovine.pdb models
> #6 selectedOnly true relModel #1

> select #2/56

Nothing selected  

> select #2/C:56

Nothing selected  

> select #2 /C:56

Nothing selected  

> select #2/C

Nothing selected  

> select #2

1363 atoms, 1389 bonds, 168 residues, 1 model selected  

> select #2 /C

Nothing selected  

> select #2:56

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide #!6 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #4/A

Alignment identifier is 4/A  

> select #4/A:437

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

> select #4/A:1-437

3350 atoms, 3427 bonds, 1 pseudobond, 428 residues, 2 models selected  

> save /Users/tzviya/Documents/projects/mMIP/GDP_kin_MT_MancMT_A1 format fasta
> alignment 4/A

> ui tool show ""Show Sequence Viewer""

> sequence chain #4/H

Alignment identifier is 4/H  

> select #4/H:1-2

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

> select #4/H:1-436

3340 atoms, 3415 bonds, 426 residues, 1 model selected  

> save /Users/tzviya/Documents/projects/mMIP/MTalpha1a format fasta alignment
> 4/H

> select #4/A:153

8 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 72 residues  

> select up

1072 atoms, 1083 bonds, 138 residues, 1 model selected  

> select up

3340 atoms, 3415 bonds, 426 residues, 1 model selected  

> select up

3368 atoms, 3445 bonds, 427 residues, 1 model selected  

> select up

54008 atoms, 55248 bonds, 6856 residues, 1 model selected  

> select down

3368 atoms, 3445 bonds, 427 residues, 1 model selected  
Drag select of 6 residues  

> select up

3518 atoms, 3594 bonds, 445 residues, 1 model selected  

> select up

6439 atoms, 6587 bonds, 818 residues, 1 model selected  

> select up

6503 atoms, 6652 bonds, 827 residues, 1 model selected  

> select up

6718 atoms, 6872 bonds, 855 residues, 1 model selected  

> select up

6751 atoms, 6906 bonds, 857 residues, 1 model selected  

> select up

54008 atoms, 55248 bonds, 6856 residues, 1 model selected  

> select down

6751 atoms, 6906 bonds, 857 residues, 1 model selected  

> save /Users/tzviya/Documents/projects/mMIP/models/tubAB.pdb models #4-5
> selectedOnly true relModel #1.1

> open /Users/tzviya/Documents/projects/mMIP/models/tubAB.pdb

Summary of feedback from opening
/Users/tzviya/Documents/projects/mMIP/models/tubAB.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 21 21 GLY B 10 GLU B 27 1 18  
Start residue of secondary structure not found: HELIX 22 22 ASP B 41 GLU B 47
1 5  
Start residue of secondary structure not found: HELIX 23 23 ILE B 49 VAL B 51
1 3  
Start residue of secondary structure not found: HELIX 24 24 PRO B 72 SER B 80
1 9  
Start residue of secondary structure not found: HELIX 25 25 PRO B 89 ASN B 91
1 3  
443 messages similar to the above omitted  
  
Chain information for tubAB.pdb #7  
---  
Chain | Description  
A | No description available  
H | No description available  
  

> select clear

> hide #!4 models

> hide #!5 models

> ui tool show ""Show Sequence Viewer""

> sequence chain #7/A

Alignment identifier is 7/A  

> sequence chain #7/H

Alignment identifier is 7/H  

> open /Users/tzviya/Downloads/AF-P68370-F1-model_v4.pdb

AF-P68370-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for tubulin α-1A chain (P68370) [more
info...]  
  
Chain information for AF-P68370-F1-model_v4.pdb #8  
---  
Chain | Description | UniProt  
A | tubulin α-1A chain | TBA1A_RAT 1-451  
  

> mmaker #8 to #7/A

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 tubAB.pdb, chain A (#7) with AF-P68370-F1-model_v4.pdb, chain A
(#8), sequence alignment score = 2202.6  
RMSD between 403 pruned atom pairs is 0.876 angstroms; (across all 428 pairs:
1.266)  
  

> show #!1 models

> hide #!1 models

> show #!1 models

> save /Users/tzviya/Documents/projects/mMIP/J325_spaca9_sh3_modeling.cxs

——— End of log from Mon Feb 24 14:02:57 2025 ———

opened ChimeraX session  

> open /Users/tzviya/Documents/projects/mMIP/models/mMIP.pdb

Chain information for mMIP.pdb #9  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
H I | No description available  
  

> hide #2-3,8#!7,9 atoms

> show #2-3,8#!7,9 cartoons

> close #2

> hide #!1 models

> hide #!9 models

> show #!9 models

> hide #3 models

> show #3 models

> close #3

> hide #!7 models

> show #!7 models

> close #7

> close #8

> close #6

> close #4

> close #5

> hide #!1.1 models

> show #!1.1 models

> save /Users/tzviya/Documents/projects/mMIP/250225_mMIP_J325.cxs includeMaps
> true

——— End of log from Tue Feb 25 11:58:40 2025 ———

opened ChimeraX session  

> set bgColor gray

> set bgColor white

> lighting soft

> graphics silhouettes true

> hide #!1 models

> select ::name=""GTP""

64 atoms, 68 bonds, 2 residues, 1 model selected  

> show sel atoms

> select ::name=""GDP""

56 atoms, 60 bonds, 2 residues, 1 model selected  

> show sel atoms

> combine #9

> show #!1 models

> ui mousemode right translate

> select add #9

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> select subtract #9

Nothing selected  

> select add #2

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #2,1,0,0,3.9338,0,1,0,-4.6426,0,0,1,-65.158

> view matrix models #2,1,0,0,5.698,0,1,0,-2.2369,0,0,1,-80.89

> select add #3

30792 atoms, 31496 bonds, 4 pseudobonds, 3888 residues, 4 models selected  

> view matrix models
> #2,1,0,0,5.0696,0,1,0,-8.1136,0,0,1,-13.182,#3,1,0,0,-0.62849,0,1,0,-5.8767,0,0,1,67.708

> undo

> select subtract #2

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> view matrix models #3,1,0,0,-21.284,0,1,0,2.7018,0,0,1,79.961

> view matrix models #3,1,0,0,-20.559,0,1,0,1.1889,0,0,1,83.09

> ui tool show ""Fit in Map""

> fitmap #2 inMap #1.1

Fit molecule copy of mMIP.pdb (#2) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms  
average map value = 0.3073, steps = 84  
shifted from previous position = 6.43  
rotated from previous position = 0.148 degrees  
atoms outside contour = 2429, contour level = 0.033162  
  
Position of copy of mMIP.pdb (#2) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99999721 -0.00128678 -0.00198245 1.01235758  
0.00128888 0.99999861 0.00105916 0.00170375  
0.00198108 -0.00106172 0.99999747 -80.49863569  
Axis -0.40936473 -0.76502812 0.49714434  
Axis point 30476.54375940 0.00000000 -7881.90973263  
Rotation angle (degrees) 0.14842204  
Shift along axis -40.43516816  
  

> fitmap #3 inMap #1.1

Fit molecule copy of mMIP.pdb (#3) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms  
average map value = 0.116, steps = 196  
shifted from previous position = 20.4  
rotated from previous position = 1.36 degrees  
atoms outside contour = 7964, contour level = 0.033162  
  
Position of copy of mMIP.pdb (#3) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99972609 -0.02313589 -0.00353325 6.98382522  
0.02312368 0.99972663 -0.00345891 -6.91791981  
0.00361231 0.00337626 0.99998778 82.42336252  
Axis 0.14449265 -0.15105400 0.97790826  
Axis point -243.27873956 -211.48115483 0.00000000  
Rotation angle (degrees) 1.35530384  
Shift along axis 82.65657778  
  

> view matrix models
> #3,0.99973,-0.023136,-0.0035332,7.0028,0.023124,0.99973,-0.0034589,-7.1344,0.0036123,0.0033763,0.99999,78.472

> fitmap #3 inMap #1.1

Fit molecule copy of mMIP.pdb (#3) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms  
average map value = 0.2768, steps = 80  
shifted from previous position = 1.28  
rotated from previous position = 1.72 degrees  
atoms outside contour = 2613, contour level = 0.033162  
  
Position of copy of mMIP.pdb (#3) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99997859 0.00644474 0.00113719 -2.22031144  
-0.00644424 0.99997914 -0.00044339 1.76633518  
-0.00114003 0.00043606 0.99999926 80.29757244  
Axis 0.06704098 0.17359332 -0.98253288  
Axis point 2396.61000487 -466.58030398 0.00000000  
Rotation angle (degrees) 0.37580898  
Shift along axis -78.73723315  
  

> select subtract #3

Nothing selected  

> select add #4

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> view matrix models #4,1,0,0,-38.631,0,1,0,3.7278,0,0,1,-106.8

> view matrix models #4,1,0,0,-38.427,0,1,0,5.7775,0,0,1,-138.91

> view matrix models #4,1,0,0,-38.282,0,1,0,7.1271,0,0,1,-155.79

> view matrix models #4,1,0,0,-0.74921,0,1,0,5.7378,0,0,1,-153.85

> view matrix models #4,1,0,0,-0.066444,0,1,0,5.4112,0,0,1,-151.76

> view matrix models #4,1,0,0,-4.6042,0,1,0,4.9323,0,0,1,-164.92

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> view matrix models #4,1,0,0,-4.3706,0,1,0,4.6142,0,0,1,-160.4

> fitmap #4 inMap #1.1

Fit molecule copy of mMIP.pdb (#4) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 15396 atoms  
average map value = 0.1853, steps = 80  
shifted from previous position = 5.58  
rotated from previous position = 0.274 degrees  
atoms outside contour = 3971, contour level = 0.033162  
  
Position of copy of mMIP.pdb (#4) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99998872 -0.00398943 -0.00257922 2.09099398  
0.00399068 0.99999192 0.00047929 -0.06625752  
0.00257729 -0.00048958 0.99999656 -160.90385628  
Axis -0.10144871 -0.53992501 0.83557713  
Axis point 18224.79317796 -2950.81942119 0.00000000  
Rotation angle (degrees) 0.27360012  
Shift along axis -134.62393736  
  

> select add #9

30792 atoms, 31496 bonds, 4 pseudobonds, 3888 residues, 4 models selected  

> select subtract #4

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> select subtract #9

Nothing selected  

> combine #9

> select add #5

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> select #5/A

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #5/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #5

13512 atoms, 13822 bonds, 2 pseudobonds, 1712 residues, 2 models selected  

> view matrix models #5,1,0,0,-38.857,0,1,0,-93.428,0,0,1,142.04

> hide #!1 models

> show #!1 models

> view matrix models
> #5,0.99426,0.10615,0.013394,-68.018,-0.10621,0.99433,0.0042454,-53.514,-0.012867,-0.0056436,0.9999,148.34

> view matrix models
> #5,0.96161,0.26505,0.07114,-113.9,-0.26439,0.96424,-0.018669,20.211,-0.073544,-0.00085621,0.99729,170.57

> ui mousemode right clip

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.84722,0.52498,0.081333,-141.06,-0.52137,0.85105,-0.062368,158.46,-0.10196,0.010435,0.99473,179.05

> view matrix models
> #5,0.69401,0.71552,0.079928,-132.38,-0.7085,0.69847,-0.10089,279.18,-0.12802,0.013391,0.99168,188.95

> view matrix models
> #5,0.69401,0.71552,0.079928,-148.18,-0.7085,0.69847,-0.10089,293.92,-0.12802,0.013391,0.99168,188.81

> view matrix models
> #5,0.62205,0.77117,0.13547,-152.2,-0.77018,0.6338,-0.071475,324.86,-0.14098,-0.059874,0.9882,213.5

> select #5/H

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #5/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> select #5/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #5/A

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!5 & sel)

> delete bonds (#!5 & sel)

> select add #5

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> view matrix models
> #5,0.62205,0.77117,0.13547,-120.33,-0.77018,0.6338,-0.071475,324.67,-0.14098,-0.059874,0.9882,157.83

> view matrix models
> #5,0.66535,0.74535,-0.04192,-73.236,-0.74106,0.66622,0.083552,256.25,0.090204,-0.024526,0.99562,60.986

> view matrix models
> #5,0.66535,0.74535,-0.04192,-60.997,-0.74106,0.66622,0.083552,278.03,0.090204,-0.024526,0.99562,68.893

> view matrix models
> #5,0.95573,0.24827,-0.15793,-15.839,-0.23442,0.96685,0.10125,13.251,0.17784,-0.059746,0.98224,48.752

> view matrix models
> #5,0.95573,0.24827,-0.15793,-16.865,-0.23442,0.96685,0.10125,17.715,0.17784,-0.059746,0.98224,37.101

> view matrix models
> #5,0.95573,0.24827,-0.15793,-18.36,-0.23442,0.96685,0.10125,16.724,0.17784,-0.059746,0.98224,38.06

> fitmap #5 inMap #1.1

Fit molecule copy of mMIP.pdb (#5) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.131, steps = 96  
shifted from previous position = 5.08  
rotated from previous position = 14.4 degrees  
atoms outside contour = 1961, contour level = 0.033162  
  
Position of copy of mMIP.pdb (#5) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.91834743 0.39575015 0.00445134 -92.66320147  
-0.39574163 0.91835794 -0.00269341 124.27123419  
-0.00515384 0.00071191 0.99998647 90.56129759  
Axis 0.00430204 0.01213454 -0.99991712  
Axis point 257.69116462 286.34114864 0.00000000  
Rotation angle (degrees) 23.31454797  
Shift along axis -89.44445883  
  

> combine #5

> select subtract #5

Nothing selected  

> select add #6

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> view matrix models
> #6,0.91835,0.39575,0.0044513,-107.04,-0.39574,0.91836,-0.0026934,143.78,-0.0051538,0.00071191,0.99999,17.562

> fitmap #6 inMap #1.1

Fit molecule copy of copy of mMIP.pdb (#6) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.06972, steps = 120  
shifted from previous position = 21  
rotated from previous position = 18 degrees  
atoms outside contour = 4139, contour level = 0.033162  
  
Position of copy of copy of mMIP.pdb (#6) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.98989843 0.12239790 0.07155313 -76.09738890  
-0.11440270 0.98767612 -0.10680778 43.04729272  
-0.08374436 0.09754298 0.99170169 29.11932259  
Axis 0.58517189 0.44470462 -0.67809414  
Axis point 503.50989628 447.50309023 0.00000000  
Rotation angle (degrees) 10.05581573  
Shift along axis -45.13236471  
  

> view matrix models
> #6,0.9899,0.1224,0.071553,-79.166,-0.1144,0.98768,-0.10681,44.1,-0.083744,0.097543,0.9917,17.998

> view matrix models
> #6,0.82543,0.56033,0.068499,-119.06,-0.56239,0.82675,0.014023,209.73,-0.048775,-0.050099,0.99755,37.529

> view matrix models
> #6,0.82543,0.56033,0.068499,-121.94,-0.56239,0.82675,0.014023,207.1,-0.048775,-0.050099,0.99755,39.628

> fitmap #6 inMap #1.1

Fit molecule copy of copy of mMIP.pdb (#6) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.1742, steps = 80  
shifted from previous position = 7  
rotated from previous position = 11.9 degrees  
atoms outside contour = 1538, contour level = 0.033162  
  
Position of copy of copy of mMIP.pdb (#6) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.92091360 0.38974558 0.00406478 -91.72390206  
-0.38973614 0.92092189 -0.00293383 122.21373240  
-0.00488679 0.00111762 0.99998744 10.35738873  
Axis 0.00519721 0.01148308 -0.99992056  
Axis point 255.60854812 287.08485186 0.00000000  
Rotation angle (degrees) 22.94030251  
Shift along axis -9.42988334  
  

> combine #5

> select add #7

13512 atoms, 13822 bonds, 2 pseudobonds, 1712 residues, 4 models selected  

> select subtract #6

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> view matrix models
> #7,0.91835,0.39575,0.0044513,-128.57,-0.39574,0.91836,-0.0026934,113.24,-0.0051538,0.00071191,0.99999,-66.615

> view matrix models
> #7,0.91835,0.39575,0.0044513,-128.66,-0.39574,0.91836,-0.0026934,110.3,-0.0051538,0.00071191,0.99999,-70.579

> view matrix models
> #7,0.91835,0.39575,0.0044513,-97.594,-0.39574,0.91836,-0.0026934,131.94,-0.0051538,0.00071191,0.99999,-76.842

> fitmap #7 inMap #1.1

Fit molecule copy of copy of mMIP.pdb (#7) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.07479, steps = 112  
shifted from previous position = 6.48  
rotated from previous position = 14 degrees  
atoms outside contour = 3994, contour level = 0.033162  
  
Position of copy of copy of mMIP.pdb (#7) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.79592567 0.60438871 0.03488002 -106.08919174  
-0.60466952 0.79647069 -0.00303608 233.31119526  
-0.02961589 -0.01867439 0.99938690 -64.82063147  
Axis -0.01291485 0.05326375 -0.99849696  
Axis point 287.71445014 271.00149999 0.00000000  
Rotation angle (degrees) 37.26044669  
Shift along axis 78.52035761  
  

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> view matrix models
> #7,0.79593,0.60439,0.03488,-105.63,-0.60467,0.79647,-0.0030361,233.33,-0.029616,-0.018674,0.99939,-56.277

> fitmap #7 inMap #1.1

Fit molecule copy of copy of mMIP.pdb (#7) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.1795, steps = 92  
shifted from previous position = 2.2  
rotated from previous position = 14.7 degrees  
atoms outside contour = 1459, contour level = 0.033162  
  
Position of copy of copy of mMIP.pdb (#7) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.92308918 0.38456910 0.00360195 -90.71929907  
-0.38456771 0.92309613 -0.00109779 119.75381467  
-0.00374712 -0.00037183 0.99999291 -69.75287743  
Axis 0.00094382 0.00955452 -0.99995391  
Axis point 252.33887914 286.53815501 0.00000000  
Rotation angle (degrees) 22.61804896  
Shift along axis 70.80822957  
  

> combine #5,6,7

Remapping chain ID 'B' in copy of copy of mMIP.pdb #6 to 'C'  
Remapping chain ID 'I' in copy of copy of mMIP.pdb #6 to 'J'  
Remapping chain ID 'B' in copy of copy of mMIP.pdb #7 to 'D'  
Remapping chain ID 'I' in copy of copy of mMIP.pdb #7 to 'K'  

> select add #8

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 4 models selected  

> select subtract #7

20268 atoms, 20733 bonds, 3 pseudobonds, 2568 residues, 2 models selected  

> close #8

> combine #7

> select add #8

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> view matrix models
> #8,0.92309,0.38457,0.0036019,-100.98,-0.38457,0.9231,-0.0010978,124.92,-0.0037471,-0.00037183,0.99999,-148.42

> fitmap #8 inMap #1.1

Fit molecule copy of copy of copy of mMIP.pdb (#8) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.154, steps = 104  
shifted from previous position = 11.7  
rotated from previous position = 0.148 degrees  
atoms outside contour = 1660, contour level = 0.033162  
  
Position of copy of copy of copy of mMIP.pdb (#8) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.92398309 0.38240908 0.00430702 -90.39185690  
-0.38241174 0.92399200 -0.00022055 119.07355107  
-0.00406399 -0.00144327 0.99999070 -149.39511898  
Axis -0.00159861 0.01094440 -0.99993883  
Axis point 250.31215151 285.50234805 0.00000000  
Rotation angle (degrees) 22.48451962  
Shift along axis 150.83366987  
  

> combine #5,6,7,8

Remapping chain ID 'B' in copy of copy of mMIP.pdb #6 to 'C'  
Remapping chain ID 'I' in copy of copy of mMIP.pdb #6 to 'J'  
Remapping chain ID 'B' in copy of copy of mMIP.pdb #7 to 'D'  
Remapping chain ID 'I' in copy of copy of mMIP.pdb #7 to 'K'  
Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #8 to 'E'  
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #8 to 'L'  

> select subtract #8

Nothing selected  

> select add #10

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> view matrix models
> #10,0.91835,0.39575,0.0044513,-134.3,-0.39574,0.91836,-0.0026934,92.516,-0.0051538,0.00071191,0.99999,100.1

> fitmap #10 inMap #1.1

Fit molecule combination (#10) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms  
average map value = 0.09391, steps = 220  
shifted from previous position = 5.13  
rotated from previous position = 24 degrees  
atoms outside contour = 10006, contour level = 0.033162  
  
Position of combination (#10) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.67734782 0.73564842 0.00461946 -126.09717895  
-0.73562348 0.67736317 -0.00610098 280.45778731  
-0.00761723 0.00073430 0.99997072 100.52087226  
Axis 0.00464562 0.00831670 -0.99995462  
Axis point 257.86060481 283.88237518 0.00000000  
Rotation angle (degrees) 47.36380401  
Shift along axis -98.76962602  
  

> combine #10

> select subtract #10

Nothing selected  

> select add #11

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> view matrix models
> #11,0.67735,0.73565,0.0046195,-175.92,-0.73562,0.67736,-0.006101,264.11,-0.0076172,0.0007343,0.99997,107.7

> view matrix models
> #11,0.67735,0.73565,0.0046195,-174.86,-0.73562,0.67736,-0.006101,267.51,-0.0076172,0.0007343,0.99997,107.76

> fitmap #11 inMap #1.1

Fit molecule copy of combination (#11) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms  
average map value = 0.05089, steps = 260  
shifted from previous position = 8.09  
rotated from previous position = 25.8 degrees  
atoms outside contour = 15205, contour level = 0.033162  
  
Position of copy of combination (#11) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.28988911 0.95704848 0.00474406 -84.80672105  
-0.95701087 0.28992094 -0.00872055 447.93528473  
-0.00972140 -0.00201213 0.99995072 111.07403012  
Axis 0.00350470 0.00755721 -0.99996530  
Axis point 260.20382069 281.28339161 0.00000000  
Rotation angle (degrees) 73.14920495  
Shift along axis -107.98225509  
  

> combine #10

> select subtract #11

Nothing selected  

> select add #12

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> view matrix models
> #12,0.67735,0.73565,0.0046195,-110.27,-0.73562,0.67736,-0.006101,470.99,-0.0076172,0.0007343,0.99997,54.513

> view matrix models
> #12,0.99867,0.00086147,0.051551,-67.695,0.0069006,0.98863,-0.1502,149.75,-0.051095,0.15036,0.98731,38.268

> view matrix models
> #12,0.95499,-0.29001,0.062338,14.596,0.29203,0.95606,-0.025987,25.668,-0.052062,0.043022,0.99772,61.671

> view matrix models
> #12,0.95499,-0.29001,0.062338,42.695,0.29203,0.95606,-0.025987,40.061,-0.052062,0.043022,0.99772,58.514

> view matrix models
> #12,0.95431,-0.28981,0.07286,40.772,0.29267,0.95568,-0.032048,41.139,-0.060343,0.051907,0.99683,59.706

> view matrix models
> #12,0.95677,-0.28994,0.022956,49.99,0.29009,0.95699,-0.0032607,35.965,-0.021023,0.0097791,0.99973,54.295

> view matrix models
> #12,0.95677,-0.28994,0.022956,67.597,0.29009,0.95699,-0.0032607,19.101,-0.021023,0.0097791,0.99973,25.92

> fitmap #12 inMap #1.1

Fit molecule copy of combination (#12) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms  
average map value = 0.07201, steps = 128  
shifted from previous position = 21.7  
rotated from previous position = 1.37 degrees  
atoms outside contour = 16334, contour level = 0.033162  
  
Position of copy of combination (#12) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.95142820 -0.30774064 0.00894910 63.26891588  
0.30772849 0.95147027 0.00273846 -4.44752520  
-0.00935754 0.00014845 0.99995621 25.57250537  
Axis -0.00420629 0.02973079 0.99954909  
Axis point 48.16170512 198.33407674 0.00000000  
Rotation angle (degrees) 17.93111780  
Shift along axis 25.16261854  
  

> combine #5

> select subtract #12

Nothing selected  

> select add #13

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> view matrix models
> #13,0.91835,0.39575,0.0044513,-68.592,-0.39574,0.91836,-0.0026934,222.95,-0.0051538,0.00071191,0.99999,118.59

> view matrix models
> #13,0.7398,0.02313,-0.67243,303.25,-0.34513,0.87095,-0.34975,327.08,0.57757,0.49082,0.65231,-100.93

> view matrix models
> #13,0.8937,0.44749,0.032428,-80.5,-0.4318,0.87749,-0.20873,312.38,-0.12186,0.17254,0.97744,129.28

> fitmap #13 inMap #1.1

Fit molecule copy of copy of mMIP.pdb (#13) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.07907, steps = 96  
shifted from previous position = 5.21  
rotated from previous position = 7.79 degrees  
atoms outside contour = 4040, contour level = 0.033162  
  
Position of copy of copy of mMIP.pdb (#13) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.85267637 0.50100712 0.14810426 -111.64102628  
-0.46179706 0.85534842 -0.23478196 335.89371419  
-0.24430818 0.13179892 0.96069900 185.86327437  
Axis 0.33251954 0.35595092 -0.87334397  
Axis point 673.69137305 367.91650398 0.00000000  
Rotation angle (degrees) 33.45054758  
Shift along axis -79.88371484  
  

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> view matrix models
> #13,0.7894,0.59326,0.15776,-112.69,-0.54776,0.79674,-0.25527,388.23,-0.27713,0.1151,0.95391,204.19

> view matrix models
> #13,0.7894,0.59326,0.15776,-112.78,-0.54776,0.79674,-0.25527,389.55,-0.27713,0.1151,0.95391,204.7

> view matrix models
> #13,0.93252,-0.35174,0.081761,78.918,0.35045,0.9361,0.030152,-69.937,-0.087142,0.00053538,0.9962,146.96

> view matrix models
> #13,0.93252,-0.35174,0.081761,79.105,0.35045,0.9361,0.030152,-72.026,-0.087142,0.00053538,0.9962,145.5

> fitmap #13 inMap #1.1

Fit molecule copy of copy of mMIP.pdb (#13) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.1847, steps = 128  
shifted from previous position = 4.18  
rotated from previous position = 22.3 degrees  
atoms outside contour = 1726, contour level = 0.033162  
  
Position of copy of copy of mMIP.pdb (#13) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.73944390 -0.67320479 -0.00424649 257.24330528  
0.67321493 0.73944524 0.00155136 -137.61078825  
0.00209567 -0.00400594 0.99998978 111.02021230  
Axis -0.00412738 -0.00471030 0.99998039  
Axis point 305.95707423 264.37843466 0.00000000  
Rotation angle (degrees) 42.31631220  
Shift along axis 110.60448113  
  

> combine #13

> select subtract #13

Nothing selected  

> select add #14

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> view matrix models
> #14,0.73944,-0.6732,-0.0042465,242,0.67321,0.73945,0.0015514,-87.886,0.0020957,-0.0040059,0.99999,108.26

> fitmap #14 inMap #1.1

Fit molecule copy of copy of copy of mMIP.pdb (#14) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.1435, steps = 112  
shifted from previous position = 14.7  
rotated from previous position = 24.5 degrees  
atoms outside contour = 1834, contour level = 0.033162  
  
Position of copy of copy of copy of mMIP.pdb (#14) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.39312960 -0.91946420 -0.00589211 416.41983098  
0.91947507 0.39314485 -0.00165376 -104.02927569  
0.00383702 -0.00476751 0.99998128 101.75491661  
Axis -0.00169321 -0.00529054 0.99998457  
Axis point 286.69846749 263.85262924 0.00000000  
Rotation angle (degrees) 66.85073548  
Shift along axis 101.59863340  
  

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> ui mousemode right select

> select clear

> combine #13

> select add #15

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #15,0.73944,-0.6732,-0.0042465,208.82,0.67321,0.73945,0.0015514,-177.12,0.0020957,-0.0040059,0.99999,-93.853

> view matrix models
> #15,0.73944,-0.6732,-0.0042465,179.44,0.67321,0.73945,0.0015514,-175.86,0.0020957,-0.0040059,0.99999,-233.35

> view matrix models
> #15,0.73944,-0.6732,-0.0042465,245.49,0.67321,0.73945,0.0015514,-185.01,0.0020957,-0.0040059,0.99999,-255.79

> hide sel atoms

> view matrix models
> #15,0.73944,-0.6732,-0.0042465,249.56,0.67321,0.73945,0.0015514,-191.77,0.0020957,-0.0040059,0.99999,-241.83

> view matrix models
> #15,0.93909,-0.34083,0.044165,81.942,0.32849,0.92791,0.1763,-163.58,-0.10107,-0.15105,0.98335,-163.68

> view matrix models
> #15,0.92009,-0.38816,0.052597,97.35,0.37608,0.91294,0.15843,-172.07,-0.10951,-0.12599,0.98597,-167.22

> view matrix models
> #15,0.94006,-0.34041,0.020452,89.128,0.3391,0.93943,0.04981,-129.43,-0.036169,-0.039889,0.99855,-218.72

> view matrix models
> #15,0.93777,-0.33619,-0.086985,123.65,0.34328,0.93528,0.086034,-141.71,0.052432,-0.11054,0.99249,-233.31

> fitmap #15 inMap #1.1

Fit molecule copy of copy of copy of mMIP.pdb (#15) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.08735, steps = 172  
shifted from previous position = 6.88  
rotated from previous position = 20.7 degrees  
atoms outside contour = 3144, contour level = 0.033162  
  
Position of copy of copy of copy of mMIP.pdb (#15) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99996178 -0.00873777 -0.00031230 2.63630829  
0.00873778 0.99996183 0.00003151 -0.95549519  
0.00031201 -0.00003424 0.99999995 -240.15619250  
Axis -0.00375993 -0.03570192 0.99935541  
Axis point 1090.72787957 193.67875602 0.00000000  
Rotation angle (degrees) 0.50096669  
Shift along axis -239.97718956  
  

> combine #15

> view matrix models
> #15,0.99996,-0.0087378,-0.0003123,-28.199,0.0087378,0.99996,3.1511e-05,-39.322,0.00031201,-3.4238e-05,1,-233.42

> fitmap #15 inMap #1.1

Fit molecule copy of copy of copy of mMIP.pdb (#15) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.07215, steps = 108  
shifted from previous position = 5.31  
rotated from previous position = 22.4 degrees  
atoms outside contour = 3140, contour level = 0.033162  
  
Position of copy of copy of copy of mMIP.pdb (#15) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.92800351 0.37257140 0.00021964 -87.83331787  
-0.37256919 0.92799972 -0.00295282 116.00908582  
-0.00130397 0.00265839 0.99999562 -231.35294610  
Axis 0.00753018 0.00204467 -0.99996956  
Axis point 254.15601289 289.52985069 0.00000000  
Rotation angle (degrees) 21.87492174  
Shift along axis 230.92170241  
  

> ui mousemode right translate

> ui mousemode right select

> select clear

> hide atoms

> select clear

> hide #!1 models

> combine #12

> select add #17

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> close #17

> select add #11

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> select add #12

54048 atoms, 55288 bonds, 8 pseudobonds, 6848 residues, 4 models selected  

> select subtract #12

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> select subtract #11

Nothing selected  

> select add #10

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> select subtract #10

Nothing selected  

> select add #12

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> select subtract #12

Nothing selected  

> combine #12,14

Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #14 to 'F'  
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #14 to 'M'  

> select add #17

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> show #!1 models

> ui mousemode right ""translate selected models""

> view matrix models
> #17,0.95143,-0.30774,0.0089491,-72.445,0.30773,0.95147,0.0027385,-142.66,-0.0093575,0.00014845,0.99996,3.319

> view matrix models
> #17,0.95143,-0.30774,0.0089491,-73.257,0.30773,0.95147,0.0027385,-142.2,-0.0093575,0.00014845,0.99996,3.3405

> view matrix models
> #17,0.95143,-0.30774,0.0089491,-78.177,0.30773,0.95147,0.0027385,-143.48,-0.0093575,0.00014845,0.99996,4.266

> ui mousemode right ""rotate selected models""

> view matrix models
> #17,0.9508,-0.30972,0.0073568,-77.101,0.30971,0.95083,0.002236,-143.94,-0.0076876,0.00015244,0.99997,3.6428

> view matrix models
> #17,-0.89418,0.44103,0.077017,415.87,-0.41745,-0.88349,0.21254,499.13,0.16178,0.1579,0.97411,-89.398

> view matrix models
> #17,-0.89523,0.44561,6.7934e-05,433.85,-0.44517,-0.89433,-0.044681,574.28,-0.019849,-0.04003,0.999,17.686

> ui mousemode right ""translate selected models""

> view matrix models
> #17,-0.89523,0.44561,6.7934e-05,427.17,-0.44517,-0.89433,-0.044681,563.57,-0.019849,-0.04003,0.999,21.146

> ui mousemode right ""rotate selected models""

> view matrix models
> #17,-0.47251,0.86599,-0.16369,212.93,-0.87354,-0.48482,-0.04334,627.18,-0.11689,0.12251,0.98556,22.738

> view matrix models
> #17,-0.46584,0.87322,-0.14312,203.79,-0.87369,-0.47953,-0.082009,635.38,-0.14024,0.08684,0.9863,39.467

> view matrix models
> #17,-0.46756,0.88374,-0.019893,172.12,-0.88389,-0.46768,-0.0015532,616.91,-0.010676,0.016857,0.9998,4.3843

> fitmap #17 inMap #1.1

Fit molecule combination (#17) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.01657, steps = 196  
shifted from previous position = 8.66  
rotated from previous position = 16.9 degrees  
atoms outside contour = 28536, contour level = 0.033162  
  
Position of combination (#17) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.19195294 0.98140336 0.00122133 41.38432771  
-0.98136374 -0.19193360 -0.00930995 587.53282874  
-0.00890240 -0.00298564 0.99995590 0.46391723  
Axis 0.00322208 0.00515779 -0.99998151  
Axis point 262.56350360 276.73403491 0.00000000  
Rotation angle (degrees) 101.06750063  
Shift along axis 2.69980687  
  

> ui mousemode right ""translate selected models""

> view matrix models
> #17,-0.19195,0.9814,0.0012213,40.044,-0.98136,-0.19193,-0.00931,589.52,-0.0089024,-0.0029856,0.99996,36.113

> fitmap #17 inMap #1.1

Fit molecule combination (#17) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.01791, steps = 80  
shifted from previous position = 4.86  
rotated from previous position = 0.651 degrees  
atoms outside contour = 28024, contour level = 0.033162  
  
Position of combination (#17) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.18270821 0.98316498 0.00207464 37.16758709  
-0.98305348 -0.18265458 -0.01559271 587.23745022  
-0.01495126 -0.00488840 0.99987626 42.95155303  
Axis 0.00544382 0.00865876 -0.99994769  
Axis point 262.92091076 278.27079917 0.00000000  
Rotation angle (degrees) 100.52958842  
Shift along axis -37.66222630  
  

> ui mousemode right select

> select clear

> combine #12,14

Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #14 to 'F'  
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #14 to 'M'  

> select add #18

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #18,0.95143,-0.30774,0.0089491,29.725,0.30773,0.95147,0.0027385,31.014,-0.0093575,0.00014845,0.99996,18.702

> fitmap #18 inMap #1.1

Fit molecule combination (#18) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.0539, steps = 284  
shifted from previous position = 11.6  
rotated from previous position = 9.73 degrees  
atoms outside contour = 20989, contour level = 0.033162  
  
Position of combination (#18) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.88606217 -0.46342271 0.01154214 81.94349086  
0.46315726 0.88605153 0.01995085 -24.45721374  
-0.01947261 -0.01233187 0.99973434 23.54299380  
Axis -0.03480013 0.03343329 0.99883490  
Axis point 92.51162554 155.56762230 0.00000000  
Rotation angle (degrees) 27.63455309  
Shift along axis 19.84623440  
  

> ui mousemode right select

> select clear

> select add #18

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #18,0.88606,-0.46342,0.011542,79.125,0.46316,0.88605,0.019951,-23.29,-0.019473,-0.012332,0.99973,23.043

> fitmap #18 inMap #1.1

Fit molecule combination (#18) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.0601, steps = 268  
shifted from previous position = 1.61  
rotated from previous position = 11.3 degrees  
atoms outside contour = 19659, contour level = 0.033162  
  
Position of combination (#18) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.77878484 -0.62728335 0.00312637 159.62792323  
0.62727014 0.77878988 0.00430041 -54.32746429  
-0.00513237 -0.00138802 0.99998587 15.21207519  
Axis -0.00453408 0.00658280 0.99996805  
Axis point 157.00903224 199.20696745 0.00000000  
Rotation angle (degrees) 38.85096442  
Shift along axis 14.13019601  
  

> ui mousemode right select

> select clear

> ui mousemode right translate

> select add #13

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #14

Nothing selected  

> hide #!1 models

> combine #15

> select add #19

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> show #!1 models

> ui mousemode right ""translate selected models""

> view matrix models
> #19,0.928,0.37257,0.00021964,-128.53,-0.37257,0.928,-0.0029528,93.424,-0.001304,0.0026584,1,-223.74

> fitmap #19 inMap #1.1

Fit molecule copy of copy of copy of copy of mMIP.pdb (#19) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.04699, steps = 132  
shifted from previous position = 6.57  
rotated from previous position = 24.1 degrees  
atoms outside contour = 3818, contour level = 0.033162  
  
Position of copy of copy of copy of copy of mMIP.pdb (#19) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.69527060 0.71864073 0.01242166 -129.84753010  
-0.71865323 0.69535578 -0.00422819 271.84628200  
-0.01167603 -0.00598713 0.99991391 -216.44469674  
Axis -0.00122361 0.01676364 -0.99985873  
Axis point 251.47565000 286.94307088 0.00000000  
Rotation angle (degrees) 45.95125175  
Shift along axis 221.13013689  
  

> combine #19

> view matrix models
> #19,0.69527,0.71864,0.012422,-177.39,-0.71865,0.69536,-0.0042282,255.75,-0.011676,-0.0059871,0.99991,-213.91

> view matrix models
> #19,0.69527,0.71864,0.012422,-179.19,-0.71865,0.69536,-0.0042282,254.74,-0.011676,-0.0059871,0.99991,-209.18

> fitmap #20 inMap #1.1

Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.04699, steps = 40  
shifted from previous position = 0.00402  
rotated from previous position = 0.013 degrees  
atoms outside contour = 3816, contour level = 0.033162  
  
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.69542748 0.71848898 0.01241843 -129.86861265  
-0.71850078 0.69551296 -0.00428509 271.76777536  
-0.01171597 -0.00594269 0.99991371 -216.44114025  
Axis -0.00115336 0.01679273 -0.99985833  
Axis point 251.45364269 286.99041394 0.00000000  
Rotation angle (degrees) 45.93874108  
Shift along axis 221.12398487  
  

> view matrix models
> #19,0.69527,0.71864,0.012422,-178.89,-0.71865,0.69536,-0.0042282,261.93,-0.011676,-0.0059871,0.99991,-209.48

> fitmap #20 inMap #1.1

Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.04699, steps = 48  
shifted from previous position = 0.0074  
rotated from previous position = 0.00959 degrees  
atoms outside contour = 3820, contour level = 0.033162  
  
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.69536855 0.71854355 0.01255987 -129.90722454  
-0.71855666 0.69545546 -0.00424659 271.78795436  
-0.01178619 -0.00607203 0.99991211 -216.39135109  
Axis -0.00127004 0.01693865 -0.99985572  
Axis point 251.39726178 286.98315528 0.00000000  
Rotation angle (degrees) 45.94344635  
Shift along axis 221.12884016  
  

> view matrix models
> #19,0.69527,0.71864,0.012422,-180.29,-0.71865,0.69536,-0.0042282,267.95,-0.011676,-0.0059871,0.99991,-206.69

> fitmap #20 inMap #1.1

Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.047, steps = 28  
shifted from previous position = 0.0217  
rotated from previous position = 0.0421 degrees  
atoms outside contour = 3808, contour level = 0.033162  
  
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.69554773 0.71837981 0.01199240 -129.74039638  
-0.71838499 0.69563025 -0.00464276 271.82119325  
-0.01167754 -0.00538590 0.99991731 -216.57782319  
Axis -0.00051716 0.01647224 -0.99986419  
Axis point 251.66821453 287.10024367 0.00000000  
Rotation angle (degrees) 45.92912660  
Shift along axis 221.09300848  
  

> view matrix models
> #19,0.69527,0.71864,0.012422,-184.77,-0.71865,0.69536,-0.0042282,265.6,-0.011676,-0.0059871,0.99991,-213.91

> fitmap #20 inMap #1.1

Fit molecule copy of copy of copy of copy of copy of mMIP.pdb (#20) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.047, steps = 44  
shifted from previous position = 0.0201  
rotated from previous position = 0.0246 degrees  
atoms outside contour = 3819, contour level = 0.033162  
  
Position of copy of copy of copy of copy of copy of mMIP.pdb (#20) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.69556138 0.71836150 0.01229335 -129.85008341  
-0.71837194 0.69564571 -0.00433745 271.69944317  
-0.01166767 -0.00581424 0.99991503 -216.48831772  
Axis -0.00102774 0.01667511 -0.99986043  
Axis point 251.48084555 287.01887579 0.00000000  
Rotation angle (degrees) 45.92805692  
Shift along axis 221.12217190  
  

> fitmap #19 inMap #1.1

Fit molecule copy of copy of copy of copy of mMIP.pdb (#19) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 6756 atoms  
average map value = 0.0242, steps = 144  
shifted from previous position = 7.29  
rotated from previous position = 27.8 degrees  
atoms outside contour = 5127, contour level = 0.033162  
  
Position of copy of copy of copy of copy of mMIP.pdb (#19) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.27989392 0.96002981 0.00147331 -78.76596403  
-0.96000243 0.27989711 -0.00727654 452.62020727  
-0.00739807 0.00062227 0.99997244 -210.57996062  
Axis 0.00411382 0.00462035 -0.99998086  
Axis point 261.24373181 278.91082498 0.00000000  
Rotation angle (degrees) 73.74685351  
Shift along axis 212.34316488  
  

> select subtract #19

Nothing selected  

> hide #!1 models

> combine #18

> select add #21

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> show #!1 models

> view matrix models
> #21,0.77878,-0.62728,0.0031264,107.47,0.62727,0.77879,0.0043004,-52.825,-0.0051324,-0.001388,0.99999,14.869

> fitmap #21 inMap #1.1

Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.03306, steps = 132  
shifted from previous position = 6.71  
rotated from previous position = 1.48 degrees  
atoms outside contour = 23844, contour level = 0.033162  
  
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.76290093 -0.64650884 -0.00291382 120.30300561  
0.64651056 0.76287001 0.00731003 -50.42745423  
-0.00250313 -0.00746065 0.99996904 14.75429938  
Axis -0.01142266 -0.00031760 0.99993471  
Axis point 128.98149204 139.01530296 0.00000000  
Rotation angle (degrees) 40.28213266  
Shift along axis 13.39517164  
  

> view matrix models
> #21,0.7629,-0.64651,-0.0029138,116.45,0.64651,0.76287,0.00731,-50.167,-0.0025031,-0.0074607,0.99997,8.3401

> fitmap #21 inMap #1.1

Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.03428, steps = 92  
shifted from previous position = 6.58  
rotated from previous position = 1.67 degrees  
atoms outside contour = 23612, contour level = 0.033162  
  
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.78085806 -0.62470372 0.00244108 103.89248144  
0.62469984 0.78086185 0.00221019 -45.38135287  
-0.00328686 -0.00020090 0.99999458 0.39692860  
Axis -0.00192977 0.00458448 0.99998763  
Axis point 116.63158139 125.39318365 0.00000000  
Rotation angle (degrees) 38.66086914  
Shift along axis -0.01161494  
  

> view matrix models
> #21,0.78086,-0.6247,0.0024411,101.64,0.6247,0.78086,0.0022102,-49.183,-0.0032869,-0.0002009,0.99999,0.76612

> view matrix models
> #21,0.78086,-0.6247,0.0024411,103.13,0.6247,0.78086,0.0022102,-47.679,-0.0032869,-0.0002009,0.99999,1.9671

> fitmap #21 inMap #1.1

Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.03429, steps = 76  
shifted from previous position = 2.9  
rotated from previous position = 0.501 degrees  
atoms outside contour = 23597, contour level = 0.033162  
  
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.78629491 -0.61784690 0.00234998 100.27042055  
0.61784275 0.78629834 0.00229112 -44.07511402  
-0.00326334 -0.00034958 0.99999462 0.42777996  
Axis -0.00213699 0.00454261 0.99998740  
Axis point 113.85006090 122.91088875 0.00000000  
Rotation angle (degrees) 38.15948972  
Shift along axis 0.01328137  
  

> ui mousemode right translate

> select add #12

60804 atoms, 62199 bonds, 9 pseudobonds, 7704 residues, 4 models selected  

> select subtract #21

27024 atoms, 27644 bonds, 4 pseudobonds, 3424 residues, 2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,0.95056,-0.31028,-0.013065,68.648,0.31045,0.95049,0.013818,-7.4782,0.008131,-0.017191,0.99982,23.127

> view matrix models
> #12,0.95096,-0.30908,0.012172,63.106,0.30914,0.95101,-0.0036414,-3.5763,-0.010451,0.0072258,0.99992,24.33

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> ui mousemode right ""rotate selected models""

> view matrix models
> #12,0.94854,-0.31391,0.041559,59.189,0.31463,0.94914,-0.011803,-3.5352,-0.03574,0.024271,0.99907,29.96

> view matrix models
> #12,0.95186,-0.30347,0.043221,55.168,0.30428,0.95249,-0.013431,-0.1243,-0.037092,0.025936,0.99898,30.094

> view matrix models
> #12,0.95653,-0.29154,-0.0071929,60.835,0.29163,0.95627,0.022435,-3.5437,0.00033774,-0.023557,0.99972,27.551

> view matrix models
> #12,0.98515,-0.17102,0.015264,17.354,0.1709,0.98525,0.0086594,37.573,-0.016519,-0.0059222,0.99985,29.694

> fitmap #12 inMap #1.1

Fit molecule copy of combination (#12) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms  
average map value = 0.07142, steps = 68  
shifted from previous position = 1.95  
rotated from previous position = 0.512 degrees  
atoms outside contour = 16349, contour level = 0.033162  
  
Position of copy of combination (#12) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.98428426 -0.17628369 0.01041885 18.21216227  
0.17625703 0.98433820 0.00343118 37.72041326  
-0.01086053 -0.00154086 0.99993984 27.02973678  
Axis -0.01407645 0.06024444 0.99808440  
Axis point -193.18177269 122.84908368 0.00000000  
Rotation angle (degrees) 10.17228645  
Shift along axis 28.99404110  
  

> view matrix models
> #12,0.68107,-0.73011,-0.055529,274.65,0.72706,0.68331,-0.06694,-83.343,0.086817,0.0052171,0.99621,-10.303

> fitmap #12 inMap #1.1

Fit molecule copy of combination (#12) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 27024 atoms  
average map value = 0.1813, steps = 240  
shifted from previous position = 2.63  
rotated from previous position = 20.4 degrees  
atoms outside contour = 6296, contour level = 0.033162  
  
Position of copy of combination (#12) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.39547743 -0.91846630 -0.00415484 414.70478352  
0.91847472 0.39547956 0.00033083 -104.22047056  
0.00133929 -0.00394695 0.99999132 22.49425611  
Axis -0.00232874 -0.00299089 0.99999282  
Axis point 286.50241902 263.00199113 0.00000000  
Rotation angle (degrees) 66.70445099  
Shift along axis 21.84006730  
  

> select subtract #12

Nothing selected  

> select add #13

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #13

Nothing selected  

> select add #14

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #15

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #15

Nothing selected  

> select add #16

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #16

Nothing selected  

> select add #18

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> close #18

> select add #21

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> close #21

> hide #!1 models

> combine #12,14

Remapping chain ID 'B' in copy of copy of copy of mMIP.pdb #14 to 'F'  
Remapping chain ID 'I' in copy of copy of copy of mMIP.pdb #14 to 'M'  

> select add #14

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select add #12

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 4 models selected  

> select subtract #12

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #14

Nothing selected  

> select add #16

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #16

Nothing selected  

> select add #18

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> show #!1 models

> ui mousemode right ""translate selected models""

> view matrix models
> #18,0.39548,-0.91847,-0.0041548,391.86,0.91847,0.39548,0.00033083,-61.349,0.0013393,-0.003947,0.99999,17.009

> view matrix models
> #18,0.39548,-0.91847,-0.0041548,376.6,0.91847,0.39548,0.00033083,-73.639,0.0013393,-0.003947,0.99999,19.239

> fitmap #18 inMap #1.1

Fit molecule combination (#18) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.101, steps = 248  
shifted from previous position = 8.19  
rotated from previous position = 23.4 degrees  
atoms outside contour = 12500, contour level = 0.033162  
  
Position of combination (#18) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.00120286 -0.99997416 -0.00708817 538.94908965  
0.99999892 -0.00119682 -0.00085618 -13.28514814  
0.00084767 -0.00708919 0.99997451 14.24127601  
Axis -0.00311651 -0.00396792 0.99998727  
Axis point 276.10634935 262.55672068 0.00000000  
Rotation angle (degrees) 90.06947604  
Shift along axis 12.61416877  
  

> combine #18

> select subtract #18

Nothing selected  

> select add #21

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> view matrix models
> #21,-0.0012029,-0.99997,-0.0070882,490.37,1,-0.0011968,-0.00085618,-18.727,0.00084767,-0.0070892,0.99997,18.737

> view matrix models
> #21,-0.0012029,-0.99997,-0.0070882,487.99,1,-0.0011968,-0.00085618,-16.81,0.00084767,-0.0070892,0.99997,10.834

> fitmap #21 inMap #1.1

Fit molecule copy of combination (#21) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.05597, steps = 340  
shifted from previous position = 12.9  
rotated from previous position = 25.4 degrees  
atoms outside contour = 17879, contour level = 0.033162  
  
Position of copy of combination (#21) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.42959365 -0.90298497 -0.00821209 624.86464353  
0.90302128 -0.42958918 -0.00239117 130.57074241  
-0.00136864 -0.00844292 0.99996342 6.00394474  
Axis -0.00335086 -0.00378923 0.99998721  
Axis point 271.20018359 262.65113487 0.00000000  
Rotation angle (degrees) 115.44279338  
Shift along axis 3.41527099  
  

> combine #21

> select subtract #21

Nothing selected  

> select add #22

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,581.58,0.90302,-0.42959,-0.0023912,138.79,-0.0013686,-0.0084429,0.99996,63.504

> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,571.18,0.90302,-0.42959,-0.0023912,133.6,-0.0013686,-0.0084429,0.99996,69.381

> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,580.41,0.90302,-0.42959,-0.0023912,123.84,-0.0013686,-0.0084429,0.99996,73.036

> view matrix models
> #22,-0.42959,-0.90298,-0.0082121,576.44,0.90302,-0.42959,-0.0023912,115.44,-0.0013686,-0.0084429,0.99996,74.706

> ui mousemode right select

> select clear

> select #22/K

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> select #22/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!22 & sel)

> delete bonds (#!22 & sel)

> undo

Undo failed, probably because structures have been modified.  

> fitmap #22 inMap #1.1

Fit molecule copy of copy of combination (#22) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 30398 atoms  
average map value = 0.02916, steps = 264  
shifted from previous position = 2.78  
rotated from previous position = 28.1 degrees  
atoms outside contour = 21704, contour level = 0.033162  
  
Position of copy of copy of combination (#22) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.80387257 -0.59473385 -0.00897490 642.98685850  
0.59479470 -0.80384427 -0.00732480 317.85442028  
-0.00285812 -0.01122643 0.99993290 77.76277501  
Axis -0.00327992 -0.00514209 0.99998140  
Axis point 269.15610307 265.17125528 0.00000000  
Rotation angle (degrees) 143.50338205  
Shift along axis 74.01794744  
  

> select #21/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> combine #21,F

Expected a keyword  

> combine #21 chain F

Expected a keyword  

> combine #21/F

> select add #23

37162 atoms, 38015 bonds, 6 pseudobonds, 4709 residues, 4 models selected  

> select add #21

67560 atoms, 69110 bonds, 10 pseudobonds, 8560 residues, 4 models selected  

> select subtract #21

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> select #23/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select ~sel & ##selected

30398 atoms, 31095 bonds, 4 pseudobonds, 3851 residues, 2 models selected  

> delete atoms (#!23 & sel)

> delete bonds (#!23 & sel)

> select add #23

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  
Drag select of 1.1 cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc , 5714
residues, 7 pseudobonds  

> ui mousemode right select

> select clear

> select add #23

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #23,-0.42959,-0.90298,-0.0082121,586.77,0.90302,-0.42959,-0.0023912,83.501,-0.0013686,-0.0084429,0.99996,-320.28

> view matrix models
> #23,-0.42959,-0.90298,-0.0082121,556.83,0.90302,-0.42959,-0.0023912,103.87,-0.0013686,-0.0084429,0.99996,-328.1

> view matrix models
> #23,-0.42959,-0.90298,-0.0082121,570.1,0.90302,-0.42959,-0.0023912,111.07,-0.0013686,-0.0084429,0.99996,-327.98

> fitmap #23 inMap #1.1

Fit molecule copy of copy of combination (#23) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 3382 atoms  
average map value = 0.01308, steps = 180  
shifted from previous position = 14  
rotated from previous position = 32.9 degrees  
atoms outside contour = 2973, contour level = 0.033162  
  
Position of copy of copy of combination (#23) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.52942860 -0.67404595 -0.51513824 766.06264894  
0.79718952 -0.60296644 -0.03033719 203.02877966  
-0.29016241 -0.42672419 0.85657005 -49.88052356  
Axis -0.25735777 -0.14606755 0.95521267  
Axis point 336.21048140 268.85362634 0.00000000  
Rotation angle (degrees) 129.63633520  
Shift along axis -274.45459932  
  

> view matrix models
> #23,-0.52943,-0.67405,-0.51514,763.46,0.79719,-0.60297,-0.030337,202.11,-0.29016,-0.42672,0.85657,-47.97

> ui mousemode right ""rotate selected models""

> view matrix models
> #23,-0.82462,-0.56346,0.050188,608.53,0.55267,-0.82139,-0.14098,390.69,0.12066,-0.088519,0.98874,-335.4

> ui mousemode right ""translate selected models""

> view matrix models
> #23,-0.82462,-0.56346,0.050188,614.38,0.55267,-0.82139,-0.14098,392.57,0.12066,-0.088519,0.98874,-341.27

> volume #1.1 level 0.001

> volume #1.1 level 0.003

> volume #1.1 level 0.004

> fitmap #23 inMap #1.1

Fit molecule copy of copy of combination (#23) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 3382 atoms  
average map value = 0.01274, steps = 96  
shifted from previous position = 3.6  
rotated from previous position = 16.7 degrees  
atoms outside contour = 1812, contour level = 0.004  
  
Position of copy of copy of combination (#23) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.87017564 -0.44942131 -0.20202685 713.98361465  
0.47070005 -0.87942587 -0.07107466 408.76977632  
-0.14572517 -0.15694148 0.97679760 -223.22976300  
Axis -0.09274550 -0.06081193 0.99383106  
Axis point 298.45853927 282.12040068 0.00000000  
Rotation angle (degrees) 152.42454274  
Shift along axis -312.92951996  
  

> view matrix models
> #23,-0.87018,-0.44942,-0.20203,714.41,0.4707,-0.87943,-0.071075,409.36,-0.14573,-0.15694,0.9768,-229.75

> fitmap #23 inMap #1.1

Fit molecule copy of copy of combination (#23) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 3382 atoms  
average map value = 0.01257, steps = 64  
shifted from previous position = 3.36  
rotated from previous position = 7.76 degrees  
atoms outside contour = 1838, contour level = 0.004  
  
Position of copy of copy of combination (#23) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.87354920 -0.48065584 -0.07669265 671.47024620  
0.48652745 -0.86687837 -0.10868732 415.44877038  
-0.01424201 -0.13225680 0.99111317 -287.61505607  
Axis -0.02431137 -0.06441638 0.99762693  
Axis point 281.14529676 284.41867596 0.00000000  
Rotation angle (degrees) 151.00443136  
Shift along axis -330.01859062  
  

> combine #22,23

> select subtract #23

Nothing selected  

> select add #24

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> view matrix models
> #24,-0.80387,-0.59473,-0.0089749,612.49,0.59479,-0.80384,-0.0073248,280.95,-0.0028581,-0.011226,0.99993,74.57

> fitmap #24 inMap #1.1

Fit molecule combination (#24) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.01205, steps = 384  
shifted from previous position = 9.8  
rotated from previous position = 27.2 degrees  
atoms outside contour = 18208, contour level = 0.004  
  
Position of combination (#24) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.98697450 -0.16069695 -0.00760400 572.12203713  
0.16077362 -0.98693156 -0.01085994 486.58996009  
-0.00575947 -0.01194101 0.99991212 69.67555414  
Axis -0.00336280 -0.00573767 0.99997789  
Axis point 266.48122736 266.64522925 0.00000000  
Rotation angle (degrees) 170.75021625  
Shift along axis 64.95818797  
  

> volume #1.1 level 0.005

> combine #24

> select subtract #24

Nothing selected  

> select add #25

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> view matrix models
> #25,-0.98697,-0.1607,-0.007604,551.3,0.16077,-0.98693,-0.01086,438.35,-0.0057595,-0.011941,0.99991,67.639

> ui mousemode right translate

> ui mousemode right ""translate selected models""

> view matrix models
> #25,-0.98697,-0.1607,-0.007604,551.63,0.16077,-0.98693,-0.01086,437.99,-0.0057595,-0.011941,0.99991,60.543

> fitmap #25 inMap #1.1

Fit molecule copy of combination (#25) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.009276, steps = 628  
shifted from previous position = 4.62  
rotated from previous position = 28.9 degrees  
atoms outside contour = 22263, contour level = 0.005  
  
Position of copy of combination (#25) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.94154414 0.33686184 -0.00432765 422.49183700  
-0.33679215 -0.94150302 -0.01196275 611.53282250  
-0.00810429 -0.00980594 0.99991908 60.63488626  
Axis 0.00320160 0.00560609 -0.99997916  
Axis point 264.41741689 269.27191030 0.00000000  
Rotation angle (degrees) 160.31589794  
Shift along axis -55.85266880  
  

> combine #25

> select subtract #25

Nothing selected  

> select add #26

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> view matrix models
> #26,-0.94154,0.33686,-0.0043277,446.93,-0.33679,-0.9415,-0.011963,569.93,-0.0081043,-0.0098059,0.99992,52.542

> view matrix models
> #26,-0.94154,0.33686,-0.0043277,428.59,-0.33679,-0.9415,-0.011963,556.36,-0.0081043,-0.0098059,0.99992,53.504

> fitmap #26 inMap #1.1

Fit molecule copy of copy of combination (#26) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.007022, steps = 104  
shifted from previous position = 3.31  
rotated from previous position = 2 degrees  
atoms outside contour = 25242, contour level = 0.005  
  
Position of copy of copy of combination (#26) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.95026704 0.31141250 -0.00384925 439.65229916  
-0.31111051 -0.94976568 -0.03399137 550.87260223  
-0.01424122 -0.03110334 0.99941472 59.48970101  
Axis 0.00463854 0.01669081 -0.99984994  
Axis point 264.00014804 240.82107314 0.00000000  
Rotation angle (degrees) 161.86191257  
Shift along axis -48.24691788  
  

> ui mousemode right ""rotate selected models""

> view matrix models
> #26,-0.60937,0.79282,-0.010013,200.53,-0.79197,-0.60923,-0.040335,651.95,-0.038079,-0.016649,0.99914,65.063

> ui mousemode right ""translate selected models""

> view matrix models
> #26,-0.60937,0.79282,-0.010013,204.74,-0.79197,-0.60923,-0.040335,653.98,-0.038079,-0.016649,0.99914,65.144

> fitmap #26 inMap #1.1

Fit molecule copy of copy of combination (#26) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.009403, steps = 84  
shifted from previous position = 5.42  
rotated from previous position = 1.76 degrees  
atoms outside contour = 22377, contour level = 0.005  
  
Position of copy of copy of combination (#26) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.60102643 0.79922908 0.00034392 199.56459754  
-0.79916027 -0.60096892 -0.01338786 654.35871538  
-0.01049328 -0.00832131 0.99991032 51.55653882  
Axis 0.00316970 0.00677989 -0.99997199  
Axis point 263.27041174 277.50609625 0.00000000  
Rotation angle (degrees) 126.94459845  
Shift along axis -46.48605565  
  

> ui mousemode right select

> select clear

> volume #1.1 level 0.0337

> hide #!1 models

> view orient

> show #!1 models

> select add #8

6756 atoms, 6911 bonds, 1 pseudobond, 856 residues, 2 models selected  

> select subtract #8

Nothing selected  

> hide #!1 models

> show #!1 models

> select add #17

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> close #17

> hide #!1 models

> combine #11,19

Remapping chain ID 'B' in copy of copy of copy of copy of mMIP.pdb #19 to 'F'  
Remapping chain ID 'I' in copy of copy of copy of copy of mMIP.pdb #19 to 'M'  

> show #!1 models

> select add #26

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> select subtract #26

Nothing selected  

> select add #17

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> ui mousemode right ""translate selected models""

> view matrix models
> #17,0.28989,0.95705,0.0047441,-121.68,-0.95701,0.28992,-0.0087206,474.47,-0.0097214,-0.0020121,0.99995,107.23

> view matrix models
> #17,0.28989,0.95705,0.0047441,-132.86,-0.95701,0.28992,-0.0087206,466.95,-0.0097214,-0.0020121,0.99995,108.49

> ui mousemode right ""rotate selected models""

> view matrix models
> #17,-0.078654,0.99622,-0.036905,2.5,-0.99687,-0.078283,0.01138,565.11,0.0084475,0.037685,0.99925,92.477

> view matrix models
> #17,-0.082784,0.99656,0.0043514,-2.7379,-0.99653,-0.08274,-0.0094033,569.4,-0.0090109,-0.0051147,0.99995,108.95

> fitmap #17 inMap #1.1

Fit molecule combination (#17) to map
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) using 33780 atoms  
average map value = 0.01866, steps = 136  
shifted from previous position = 12.2  
rotated from previous position = 5.86 degrees  
atoms outside contour = 27889, contour level = 0.0337  
  
Position of combination (#17) relative to
cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.18396201 0.98293286 0.00098391 37.36525773  
-0.98288208 -0.18394209 -0.01039835 586.20602886  
-0.01003990 -0.00287997 0.99994545 120.79298247  
Axis 0.00382447 0.00560762 -0.99997696  
Axis point 262.52417572 277.74486119 0.00000000  
Rotation angle (degrees) 100.60163059  
Shift along axis -117.36007511  
  

> ui mousemode right select

> select clear

> ui mousemode right translate

> hide #!1 models

> select add #26

33780 atoms, 34555 bonds, 5 pseudobonds, 4280 residues, 2 models selected  

> select #26/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!26 & sel)

> delete bonds (#!26 & sel)

> select #25/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!25 & sel)

> delete bonds (#!25 & sel)

> show #!1 models

> select #24/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!24 & sel)

> delete bonds (#!24 & sel)

> select #23/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!23 & sel)

> delete bonds (#!23 & sel)

> hide #!1 models

> save /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325_tubulinbuild.cxs

> select #2/A#3/A#4/A#9/A

13528 atoms, 13840 bonds, 4 pseudobonds, 1716 residues, 8 models selected  

> color sel ivory

> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B

81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected  

> color sel ivory

> select #17/F#18/F#21/F

10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected  

> color sel ivory

> select #10/K#11/K#12/K#17/K#18/K#21/K#22/K#24/K#25/K#26/K

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> select #17/M#18/M#21/M#22/M#24/M#25/M#26/M

23618 atoms, 24157 bonds, 2989 residues, 7 models selected  

> select #10/L#11/L#12/L#17/L#18/L#21/L#22/L#24/L#25/L#26/L

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I

80976 atoms, 82824 bonds, 10248 residues, 24 models selected  

> select #2/H#3/H#4/H#9/H

13496 atoms, 13804 bonds, 1708 residues, 4 models selected  

> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I

80976 atoms, 82824 bonds, 10248 residues, 24 models selected  

> color sel dim gray

> select #17/M#18/M#21/M#22/M#24/M#25/M#26/M

23618 atoms, 24157 bonds, 2989 residues, 7 models selected  

> color sel dim gray

> select #10/K#11/K#12/K#17/K#18/K#21/K#22/K#24/K#25/K#26/K

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> color sel dim gray

> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> color sel dim gray

> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B

81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected  

> select #2/C#3/C#4/C#9/C#10/C#11/C#12/C#17/C#18/C#21/C#22/C#24/C#25/C#26/C

39272 atoms, 40164 bonds, 10 pseudobonds, 4962 residues, 24 models selected  

> color sel ivory

> select #2/D#3/D#4/D#9/D#10/D#11/D#12/D#17/D#18/D#21/D#22/D#24/D#25/D#26/D

35904 atoms, 36740 bonds, 10 pseudobonds, 4546 residues, 24 models selected  

> color sel ivory

> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E

33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected  

> color sel ivory

> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E

33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected  

> select #17/F#18/F#21/F

10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected  

> select #2/H#3/H#4/H#9/H

13496 atoms, 13804 bonds, 1708 residues, 4 models selected  

> color sel dim gray

> select #10/L#11/L#12/L#17/L#18/L#21/L#22/L#24/L#25/L#26/L

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> color sel dim gray

> ui mousemode right select

> select clear

> ui mousemode right ""translate selected models""

> ui mousemode right translate

> select #2/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> color sel #FFA200

> select #4/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> color sel #FFA200

> select #3/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> color sel #FFA200

> select #4/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select #2/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select #9/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> color sel #FFA200

> select #2/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #00BFFF

> select #3/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #00BFFF

> select #4/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #00BFFF

> select #9/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #00BFFF

> ui mousemode right select

> select clear

> ui mousemode right translate

> view orient

> graphics ortho

Expected a keyword  

> camera ortho

> view orient

> select #9/A

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!22 models

> hide #!17 models

> hide #!11 models

> hide #!19 models

> ui mousemode right select

> select clear

> ui mousemode right translate

> view orient

> turny90

Unknown command: turny90  

> turn y 90

> show #!2-10,12-16,18,20-21 surfaces

> hide #!21 models

> hide #!20 models

> hide #!10 models

> view orient

> turn y 90

> view orient

> ui tool show ""Side View""

> turn y 90

> save Surface_Top.tif pixelSize 0.1 transparentBackground true

> lighting soft

> cd /Users/jojudernatz/Desktop/mMIP_Model/ForFigures

Current working directory is: /Users/jojudernatz/Desktop/mMIP_Model/ForFigures  

> save Surface_Top.tif pixelSize 0.1 transparentBackground true

> show #!10 models

> show #!11 models

> show #!17 models

> show #!19 models

> show #!20 models

> show #!21 models

> show #!22 models

> show #!24 models

> show #!25 models

> show #!26 models

> hide surfaces

> view orient

> select #2/A#3/A#4/A#9/A

13528 atoms, 13840 bonds, 4 pseudobonds, 1716 residues, 8 models selected  

> color sel #AAFF7F

> select add #1

13528 atoms, 13840 bonds, 4 pseudobonds, 1716 residues, 15 models selected  

> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B

81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected  

> color sel #AAFF7F

> select #10/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #12/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #17/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #18/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #21/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #22/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #22/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #22/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #24/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #25/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #26/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E

33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected  

> color sel #AAFF7F

> select #17/F#18/F#21/F

10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected  

> color sel #AAFF7F

> select #11/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #10/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> select #10/E#11/E#12/E#17/E#18/E#21/E#22/E#24/E#25/E#26/E

33820 atoms, 34600 bonds, 10 pseudobonds, 4290 residues, 20 models selected  

> select #2/D#3/D#4/D#9/D#10/D#11/D#12/D#17/D#18/D#21/D#22/D#24/D#25/D#26/D

35904 atoms, 36740 bonds, 10 pseudobonds, 4546 residues, 24 models selected  

> select #10/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #11/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #12/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #18/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #21/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #21/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #22/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #24/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #25/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #26/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #17/D

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select
> #2/B#3/B#4/B#5/B#6/B#7/B#8/B#9/B#10/B#11/B#12/B#13/B#14/B#15/B#16/B#17/B#18/B#19/B#20/B#21/B#22/B#24/B#25/B#26/B

81168 atoms, 83040 bonds, 24 pseudobonds, 10296 residues, 48 models selected  

> color sel lime

> color sel #AAFF7F

> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I

80976 atoms, 82824 bonds, 10248 residues, 24 models selected  

> color sel lime

> ui mousemode right select

> select clear

> select
> #2/I#3/I#4/I#5/I#6/I#7/I#8/I#9/I#10/I#11/I#12/I#13/I#14/I#15/I#16/I#17/I#18/I#19/I#20/I#21/I#22/I#24/I#25/I#26/I

80976 atoms, 82824 bonds, 10248 residues, 24 models selected  

> color sel olive drab

> select #2/H#3/H#4/H#9/H

13496 atoms, 13804 bonds, 1708 residues, 4 models selected  

> color sel olive drab

> select #17/F#18/F#21/F

10146 atoms, 10380 bonds, 3 pseudobonds, 1287 residues, 6 models selected  

> select #10/J#11/J#12/J#17/J#18/J#21/J#22/J#24/J#25/J#26/J

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> color sel olive drab

> select #10/K#11/K#12/K#17/K#18/K#21/K#22/K#24/K#25/K#26/K

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> color sel olive drab

> select #10/L#11/L#12/L#17/L#18/L#21/L#22/L#24/L#25/L#26/L

33740 atoms, 34510 bonds, 4270 residues, 10 models selected  

> color sel olive drab

> select #17/M#18/M#21/M#22/M#24/M#25/M#26/M

23618 atoms, 24157 bonds, 2989 residues, 7 models selected  

> color sel olive drab

> select #2/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #FFA200

> select #3/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #FFA200

> select #4/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #FFA200

> select #9/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel #FFA200

> ui mousemode right select

> select clear

> view orient

> select add #1

3 models selected  

> color sel #FFA200

> show #!1 models

> color sel #AAFF7F

> color #1.1 #b2b2b2ff models

> color sel #AAFF7F

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26 distance
> 4

> hide #!2 models

> hide #!4 models

> hide #!3 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!17 models

> hide #!16 models

> hide #!18 models

> hide #!19 models

> hide #!20 models

> hide #!21 models

> hide #!22 models

> hide #!24 models

> hide #!25 models

> hide #!26 models

> hide #!1 models

> show #!9 models

> show #!7 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> hide #!7 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!12 models

> show #!1 models

> show #!13 models

> hide #!13 models

> hide #!1 models

> show #!13 models

> hide #!13 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!16 models

> hide #!15 models

> hide #!13 models

> hide #!14 models

> show #!13 models

> show #!14 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!18 models

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> show #!20 models

> hide #!20 models

> show #!21 models

> hide #!21 models

> show #!22 models

> hide #!22 models

> show #!24 models

> hide #!24 models

> show #!26 models

> hide #!26 models

> show #!11 models

> hide #!11 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!5 models

> show #!15 models

> show #!7 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!5 models

> hide #!4 models

> show #!4 models

> hide #!16 models

> show #!16 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!12 models

> show #!12 models

> hide #!9 models

> show #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> view orient

> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16 range 4

> show #!1 models

> select #2/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel deep sky blue

> select #3/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel deep sky blue

> select #4/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel deep sky blue

> select #9/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel deep sky blue

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!3 models

> show #!2 models

> hide sel cartoons

> show #!4 models

> show sel cartoons

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26 distance
> 4

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!9 models

> select add #9

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 3 models selected  

> select subtract #9

6 models selected  

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!16 models

> view orient

> turn y 90

Drag select of 1.1 cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc  

> select clear

> ui mousemode right translate

> view orient

> turn y 90

> ui tool show ""Side View""

> view orient

> turn y 90

> show #!13 models

> hide #!13 models

> show #!9 models

> hide #!9 models

> combine #9

> select #26/C

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> show #!26 models

> hide #!26 models

> show #!9 models

> hide #!9 models

> combine #9

> hide #!23 models

> close #23

> select add #27

18778 atoms, 19208 bonds, 3 pseudobonds, 2373 residues, 4 models selected  

> select #27/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select ~sel & ##selected

14033 atoms, 14357 bonds, 2 pseudobonds, 1776 residues, 2 models selected  

> delete atoms (#!27 & sel)

> delete bonds (#!27 & sel)

> select add #27

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> ui mousemode right ""translate selected models""

> view matrix models #27,1,0,0,-3.1829,0,1,0,-0.39177,0,0,1,-0.39631

> view matrix models #27,1,0,0,-3.5992,0,1,0,-0.062122,0,0,1,-1.3011

> view matrix models #27,1,0,0,-3.6142,0,1,0,-0.093856,0,0,1,-1.3889

> view matrix models #27,1,0,0,-7.0572,0,1,0,-0.67889,0,0,1,-0.81126

> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16,27 range 4

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4

> hide #!27 models

> view orient

> turn y 90

> save greentubs_density_top.tif pixelSize 0.1 transparentBackground true

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4.2

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4.5

> color zone #1 near
> #2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
> distance 4

> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16,27 range 4.5

> volume zone #1 nearAtoms #2,3,4,9,12,13,14,16,27 range 5

> save
> /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325_tubulinbuild_colors.cxs
> includeMaps true

> view orient

> turn y 90

> view orient

> turn y 90

> turn x 90

> turn z 90

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!12 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!15 models

> show #!14 models

> hide #!14 models

> show #!18 models

> hide #!18 models

> show #!19 models

> hide #!19 models

> show #!21 models

> hide #!21 models

> show #!20 models

> hide #!20 models

> show #!19 models

> hide #!19 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!16 models

> hide #!16 models

> show #!14 models

> hide #!14 models

> show #!13 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> show #!9 models

> hide #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> volume zone #1 nearAtoms #2,3,4,5,6,7,8,9,12,13,14,15,16,27 range 5

> hide #!15 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> save greentubs_density_top2.tif pixelSize 0.1 transparentBackground true

> view orient

> hide #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!27 models

> hide #!27 models

> show #!26 models

> select subtract #27

Nothing selected  

> show #!25 models

> show #!24 models

> show #!22 models

> show #!21 models

> show #!20 models

> show #!19 models

> show #!18 models

> show #!17 models

> show #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #!12 models

> show #!11 models

> show #!9 models

> show #!10 models

> show #!8 models

> view orient

> select #26/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel target a

> hide sel cartoons

> select #25/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #24/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #22/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> save greentubs_SS_front.tif pixelSize 0.1 transparentBackground true

> show sel surfaces

> hide sel surfaces

> select add #22

30398 atoms, 31095 bonds, 4 pseudobonds, 3851 residues, 3 models selected  

> select subtract #22

1 model selected  

> show #!2-22,24-26 cartoons

> save greentubs_SS_front2.tif pixelSize 0.1 transparentBackground true

> show #!2-22,24-26 surfaces

> hide #!2-22,24-26 surfaces

> cartoon style width 2.5 thickness 0.7

> select #26/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #25/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #24/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #22/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> save greentubs_SS_front3.tif pixelSize 0.1 transparentBackground true

> ui mousemode right select

Drag select of 23 residues  

> select clear

Drag select of 30 residues  

> view orient

Drag select of 22 residues  

> select clear

Drag select of 8 residues  

> select clear

Drag select of 8 residues  

> hide sel cartoons

Drag select of 5 residues  

> hide sel cartoons

Drag select of 1 residues  
Drag select of 3 residues  

> hide sel cartoons

> select clear

Drag select of 7 residues  

> select subtract #3/C:161

45 atoms, 6 residues, 2 models selected  

> select add #3/C:163

53 atoms, 7 bonds, 7 residues, 2 models selected  

> select add #3/C:161

62 atoms, 15 bonds, 8 residues, 2 models selected  

> select subtract #3/C:161

53 atoms, 7 bonds, 7 residues, 2 models selected  

> hide sel cartoons

> select clear

Drag select of 1 residues  

> hide sel cartoons

Drag select of 1 residues  

> hide sel cartoons

Drag select of 7 residues  

> hide sel cartoons

> view orient

> turn x 90

> show #!1 models

> hide #1.1.1 models

> show #1.1.1 models

> hide #!1 models

> show #!1 models

> volume zone

Missing or invalid ""volumes"" argument: empty atom specifier  

> volume #1.1 level 0.08317

> volume #1.1 level 0.07493

> volume #1.1 level 0.0337

> volume zone off

Missing or invalid ""volumes"" argument: invalid density maps specifier  

> volume zone #1 off

Expected a keyword  

> volume zone #1

Missing required ""near_atoms"" argument  

> volume zone #1 nearAtoms #2-26

> hide #!1 models

> view orient

> select add #3

15450 atoms, 15748 bonds, 2 pseudobonds, 1951 residues, 4 models selected  

> select subtract #3

54 atoms, 7 residues, 8 models selected  

> view orient

> graphics silhouettes false

> graphics silhouettes true

> select #2/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> show sel cartoons

> select #3/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #13/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> show sel cartoons

> hide sel cartoons

> select #13/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #14/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #14/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #18/M

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #18/F

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #5/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #10/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #11/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #17/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> hide sel cartoons

> select #5/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #10/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #11/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #17/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> view orient

> select #3/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> view orient

> save greentubs_SS_front.tif pixelSize 0.1 transparentBackground true

> ui mousemode right select

Drag select of 46105 residues, 53 pseudobonds  

> show sel surfaces

> save greentubs_SS_front2.tif pixelSize 0.1 transparentBackground true

> hide sel surfaces

> show sel surfaces

> select clear

> save greentubs_SS_front2.tif pixelSize 0.1 transparentBackground true

> hide #!2-22,24-26 surfaces

> view orient

> ui tool show ""Show Sequence Viewer""

> sequence chain #9/D #2/D #3/D #4/D

Alignment identifier is 1  

> select #9/D:68 #2/D:68 #3/D:68 #4/D:68

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #9/D #2/D #3/D #4/D

2084 atoms, 2140 bonds, 256 residues, 4 models selected  
1 [ID: 1] region 4 chains [1-64] RMSD: 146.177  
  

> select #9/D:117 #2/D:117 #3/D:117 #4/D:117

28 atoms, 28 bonds, 4 residues, 4 models selected  

> select #9/D:117-121 #2/D:117-121 #3/D:117-121 #4/D:117-121

164 atoms, 168 bonds, 20 residues, 4 models selected  
1 [ID: 1] region 4 chains [50-54] RMSD: 146.184  
  

> ui mousemode right translate

> show sel atoms

> style sel stick

Changed 164 atom styles  

> color sel byhetero

> show #!1 models

> volume zone #1 nearAtoms #9/C,D

> select add #4

15519 atoms, 15874 bonds, 2 pseudobonds, 1959 residues, 9 models selected  

> select add #3

30874 atoms, 31580 bonds, 4 pseudobonds, 3898 residues, 15 models selected  

> select add #2

46229 atoms, 47286 bonds, 6 pseudobonds, 5837 residues, 21 models selected  

> select subtract #2

30833 atoms, 31538 bonds, 4 pseudobonds, 3893 residues, 24 models selected  

> select subtract #3

15437 atoms, 15790 bonds, 2 pseudobonds, 1949 residues, 16 models selected  

> select subtract #4

41 atoms, 42 bonds, 5 residues, 8 models selected  

> select add #9

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 3 models selected  

> select subtract #9

6 models selected  

> select add #9

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> select ~sel

419115 atoms, 428722 bonds, 59 pseudobonds, 53076 residues, 50 models selected  

> hide sel & #!2-8,10-22,24-26 cartoons

> hide sel & #!2-8,10-22,24-26 atoms

> ui mousemode right select

> select clear

> view orient

> volume zone #1 nearAtoms #9/C,D range 6

> color #1 #b2b2b24e models

> select clear

> ui mousemode right translate

> select #9/D:101 #2/D:101 #3/D:101 #4/D:101

32 atoms, 28 bonds, 4 residues, 4 models selected  

> select #9/D:101-109 #2/D:101-109 #3/D:101-109 #4/D:101-109

308 atoms, 320 bonds, 36 residues, 4 models selected  
1 [ID: 1] region 4 chains [34-42] RMSD: 146.185  
  

> select #9/D:74-75 #2/D:74-75 #3/D:74-75 #4/D:74-75

76 atoms, 76 bonds, 8 residues, 4 models selected  

> select #9/D:74-78 #2/D:74-78 #3/D:74-78 #4/D:74-78

188 atoms, 196 bonds, 20 residues, 4 models selected  
1 [ID: 1] region 4 chains [7-11] RMSD: 146.199  
  

> select #9/D:74 #2/D:74 #3/D:74 #4/D:74

44 atoms, 44 bonds, 4 residues, 4 models selected  

> select #9/D:74 #2/D:74 #3/D:74 #4/D:74

44 atoms, 44 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [7] RMSD: 146.189  
  

> show sel atoms

> color sel byhetero

> style sel stick

Changed 44 atom styles  

> select add #9

15429 atoms, 15781 bonds, 2 pseudobonds, 1947 residues, 9 models selected  

> select subtract #9

33 atoms, 33 bonds, 3 residues, 12 models selected  

> hide sel atoms

> hide #!1 models

> ui mousemode right select

> select #9/D:118

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

> hide sel atoms

> select #9/D:120

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

> select #9/D:121

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

> hide sel atoms

> select #9/D:117

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

> select #9/D:68 #2/D:68 #3/D:68 #4/D:68

36 atoms, 32 bonds, 4 residues, 4 models selected  

> select #9/D:68 #2/D:68 #3/D:68 #4/D:68

36 atoms, 32 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [1] RMSD: 146.156  
  

> show sel atoms

> style sel stick

Changed 36 atom styles  

> show #!1 models

> select #1.1

2 models selected  

> hide #!1 models

> select #9/D:78

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

> select #9/D:79

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

> select #9/D:82 #2/D:82 #3/D:82 #4/D:82

32 atoms, 28 bonds, 4 residues, 4 models selected  

> select #9/D:82 #2/D:82 #3/D:82 #4/D:82

32 atoms, 28 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [15] RMSD: 146.204  
  

> show sel atoms

> style sel stick

Changed 32 atom styles  

> select #9/D:77

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

> select #9/D:78

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

> select #9/D:72 #2/D:72 #3/D:72 #4/D:72

28 atoms, 24 bonds, 4 residues, 4 models selected  

> select #9/D:72-77 #2/D:72-77 #3/D:72-77 #4/D:72-77

220 atoms, 224 bonds, 24 residues, 4 models selected  
1 [ID: 1] region 4 chains [5-10] RMSD: 146.191  
  

> select #9/D:75 #2/D:75 #3/D:75 #4/D:75

32 atoms, 28 bonds, 4 residues, 4 models selected  

> select #9/D:75-81 #2/D:75-81 #3/D:75-81 #4/D:75-81

228 atoms, 236 bonds, 28 residues, 4 models selected  
1 [ID: 1] region 4 chains [8-14] RMSD: 146.207  
  

> select #9/D:75 #2/D:75 #3/D:75 #4/D:75

32 atoms, 28 bonds, 4 residues, 4 models selected  

> select #9/D:75-79 #2/D:75-79 #3/D:75-79 #4/D:75-79

180 atoms, 184 bonds, 20 residues, 4 models selected  
1 [ID: 1] region 4 chains [8-12] RMSD: 146.204  
  

> select #9/D:76 #2/D:76 #3/D:76 #4/D:76

48 atoms, 48 bonds, 4 residues, 4 models selected  

> select #9/D:76 #2/D:76 #3/D:76 #4/D:76

48 atoms, 48 bonds, 4 residues, 4 models selected  
1 [ID: 1] region 4 chains [9] RMSD: 146.198  
  

> show sel atoms

> style sel stick

Changed 48 atom styles  

> select add #9

15432 atoms, 15784 bonds, 2 pseudobonds, 1947 residues, 9 models selected  

> select subtract #9

36 atoms, 36 bonds, 3 residues, 12 models selected  

> hide sel atoms

> color sel byhetero

> select clear

> color #!2-22,24-26 byhetero

> select add #2

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> select add #3

30792 atoms, 31496 bonds, 4 pseudobonds, 3888 residues, 10 models selected  

> select add #4

46188 atoms, 47244 bonds, 6 pseudobonds, 5832 residues, 18 models selected  

> hide sel atoms

> select clear

> select #9/D:130

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

> select #9/D:129

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

> select #9/D:125-126 #2/D:125-126 #3/D:125-126 #4/D:125-126

56 atoms, 60 bonds, 8 residues, 4 models selected  

> select #9/D:125-126 #2/D:125-126 #3/D:125-126 #4/D:125-126

56 atoms, 60 bonds, 8 residues, 4 models selected  
1 [ID: 1] region 4 chains [58-59] RMSD: 146.142  
  

> select #9/D:125 #2/D:125 #3/D:125 #4/D:125

28 atoms, 28 bonds, 4 residues, 4 models selected  

> select #9/D:125 #2/D:125 #3/D:125 #4/D:125

28 atoms, 28 bonds, 4 residues, 4 models selected  

> show sel atoms

> color sel byhetero

> style sel stick

Changed 28 atom styles  

> select add #9

15417 atoms, 15769 bonds, 2 pseudobonds, 1947 residues, 9 models selected  

> select subtract #9

21 atoms, 21 bonds, 3 residues, 12 models selected  

> hide sel atoms

> select clear

> select #9/C:153

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

> show sel atoms

> style sel stick

Changed 5 atom styles  

> select #9/C:154

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

> show sel atoms

> style sel stick

Changed 10 atom styles  

> show #!1 models

> hide #!1 models

> select clear

> select #9/D:78

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

> select #9/D:79

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #9/C:91

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

> style sel stick

Changed 7 atom styles  

> show sel atoms

> select #9/C:90

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> color sel byhetero

> select #9/D:79

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

> select #9/D:71 #2/D:71 #3/D:71 #4/D:71

44 atoms, 40 bonds, 4 residues, 4 models selected  

> select #9/D:71-76 #2/D:71-76 #3/D:71-76 #4/D:71-76

228 atoms, 232 bonds, 24 residues, 4 models selected  
1 [ID: 1] region 4 chains [4-9] RMSD: 146.184  
  

> select #9/D:75

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

> show sel atoms

> color sel byhetero

> style sel stick

Changed 8 atom styles  

> select clear

> show #!1 models

> select #1.1

2 models selected  

> hide #!1 models

> select #9/D:78

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

> select #9/D:77

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

> show sel atoms

> color sel byhetero

> style sel stick

Changed 9 atom styles  

> select clear

> select #9/D:77

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

> show #!1 models

> select clear

> hide #!1 models

> select #9/C:156

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> select #9/C:154

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

> select #9/C:157

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> show #!1 models

> select #9/D:103

4 atoms, 3 bonds, 1 residue, 1 model selected  

> hide #!1 models

> select #9/D:115

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

> select #9/D:117

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

> select #9/D:116

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

> select #9/D:116

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

> show sel atoms

> style sel stick

Changed 11 atom styles  

> select #9/D:104

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 14 atom styles  

> show #!1 models

> hide #!1 models

> select #9/C:157

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

> hide sel atoms

> select #9/C:158

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

> show sel atoms

> style sel stick

Changed 8 atom styles  

> select clear

> select #9/C:159

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

> select #9/C:157

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

> select clear

> select #9/C:92

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

> select #9/D:104

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #9/D:69-71,91-96,104-109,112-117 #2/D:69-71,91-96,104-109,112-117
> #3/D:69-71,91-96,104-109,112-117 #4/D:69-71,91-96,104-109,112-117

724 atoms, 732 bonds, 84 residues, 4 models selected  

> select clear

> select #9/D:105

14 atoms, 15 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 14 atom styles  

> select #9/D:103

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!1 models

> hide #!1 models

> select #9/D:115

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select #9/D:116

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

> select #9/D:79

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

> select #9/D:68

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

> hide sel atoms

> select #9/D:82

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

> hide sel atoms

> select #9/C:156

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

> hide sel atoms

> select #9/C:90

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

> hide sel atoms

> select #9/D:77

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

> hide sel atoms

> select #9/D:105

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #9/D:75

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

> hide sel atoms

> select #9/D:76

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #9/C:90

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

> select #9/C:91

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

> select #9/C:92

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

> select #9/C:89

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #9/C:90

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

> show sel atoms

> hide sel atoms

> select #9/C:91

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

> select #9/C:92

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

> select add #9/C:91

14 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #9/C:90

21 atoms, 19 bonds, 3 residues, 2 models selected  

> hide sel cartoons

> show sel atoms

> style sel stick

Changed 21 atom styles  

> hide sel atoms

> show sel cartoons

> select #9/C:91

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

> show sel atoms

> show #!1 models

> select #1.1

2 models selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #9/D:79

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

> select #9/D:79

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

> select #9/D:77

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

> show #!1 models

> select #1.1

2 models selected  

> hide #!1 models

> select #9/D:119

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

> select #9/C:156

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

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select #9/C:153

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

> select #9/C:157

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

> show #!1 models

> select clear

> save
> /Users/jojudernatz/Desktop/mMIP_Model/250225_mMIP_J325_tubulinbuild_close.cxs
> includeMaps true

> volume #1.1 level 0.037

> volume #1.1 level 0.005

> hide #!1 models

> select #9/C:157

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

> show sel atoms

> show #!1 models

> hide #!1 models

> hide sel atoms

> select clear

> select #9/C:158

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

> hide sel atoms

> select #9/D:79

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

> hide sel atoms

> select #9/C:91

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

> hide sel atoms

> select #9/D:74

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

> select #9/C:156

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

> hide sel atoms

> select #9/D:117

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

> hide sel atoms

> select #9/D:115

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

> hide sel atoms

> select #9/D:116

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

> hide sel atoms

> show #!1 models

> select #9/C:160

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

> hide sel cartoons

Drag select of 1.1 cryosparc_P11_J325_007_volume_map_deepem_highRes.mrc , 4
atoms, 5 residues, 4 bonds  

> select clear

> ui mousemode right translate

> hide #!1 models

> ui mousemode right select

> select #9/D:74

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

> select add #9/C:153

16 atoms, 15 bonds, 2 residues, 2 models selected  

> hide sel atoms

> show #!1 models

> select clear

> ui mousemode right translate

> hide #!1 models

> ui mousemode right select

> select #9/C:150

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

> show #!1 models

> hide #!1 models

> show sel atoms

> style sel sphere

Changed 9 atom styles  

> style sel stick

Changed 9 atom styles  

> select #9/C:149

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

> show sel atoms

> style sel stick

Changed 9 atom styles  

> show #!1 models

> hide sel atoms

> hide #!1 models

> select #9/C:150

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

> hide sel atoms

> select clear

> select #9/D:76

12 atoms, 12 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select #9/D:104

14 atoms, 15 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #!1 models

> view orient

> volume zone #1 nearAtoms #9/C,D range 5

> volume #1.1 level 0.0337

> volume zone #1 nearAtoms #9/C,D range 4

> select clear

> hide #!2-22,24-26 atoms

> volume zone #1 nearAtoms #9/C,D range 4.4

> volume zone #1 nearAtoms #9/C,D range 4

> volume zone #1 nearAtoms #9/C,D range 3.5

> color zone #1 near #9/C,D range 4

Expected a keyword  

> color zone #1 near #9/C,D distance 4

> hide #!2-22,24-26 atoms

> color #!2-22,24-26 bychain

> undo

> color zone #1 near #9/C,D distance 4

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #9/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> color sel #FFA200

> select #4/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> select #9/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> color sel deep sky blue

> select clear

> ui mousemode right translate

> color zone #1 near #9/C,D distance 4

> color #1.1.1 #b2b2b21d

> view orient

> color zone #1 near #9/C,D distance 4

> hide #!9 models

> show #!9 models

> color zone #1 near #9 distance 4

> select #9/A

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #9/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> color sel #AAFF7F

> select #9/H

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> color sel olive drab

> select #9/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> color sel olive drab

> ui mousemode right select

> ui mousemode right ""translate selected models""

> ui mousemode right translate

> color zone #1 near #9 distance 4

> volume zone #1 nearAtoms #9 range 3.5

> hide #!9 models

> show #!27 models

> volume zone #1 nearAtoms #9,27 range 3.5

> hide #!27 models

> color zone #1 near #9,27 distance 4

> view

> view orient

> volume zone #1 nearAtoms #9,27 range 4

> volume zone #1 nearAtoms #9,27 range 5

> view orient

> turn y 90

> color zone #1 near #9,27 distance 5

> view orient

> turn y 90

> turn x 90

> turn y 90

> turn y -45

> turn y 5

> turn x 5

> turn y 5

> turn y -5

> turn z -5

> volume #1.1 level 0.04195

> view orient

> turn z 90

> turn y 90

> hide #!1 models

> show #!9 models

> ui mousemode right select

> select clear

> view orient

> turn y 90

> hide #!10 models

> show #!10 models

> show #!27 models

> hide #!27 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!26 models

> view orient

> turn x 90

> show #!2-22,24-26 cartoons

> view orient

> turn y 90

> turn x 90

> turn z 90

> turn x 90

> ui mousemode right clip

> save greentubs_SS_top.tif pixelSize 0.1 transparentBackground true

> view orient

> hide #!8 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> show #!6 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> hide #!16 models

> hide #!17 models

> show #!17 models

> hide #!18 models

> hide #!17 models

> hide #!19 models

> hide #!20 models

> hide #!21 models

> hide #!22 models

> hide #!24 models

> hide #!25 models

> hide #!26 models

> hide #!6 models

> hide #!9 models

> show #!9 models

> view orient

> open /Users/jojudernatz/Downloads/pdb8ou0.ent

pdb8ou0.ent title:  
Bovine sperm endpiece singlet microtubules (one tubulin dimer and associated
microtubule inner proteins) [more info...]  
  
Chain information for pdb8ou0.ent #23  
---  
Chain | Description | UniProt  
A | α-tubulin 3 | TBA3_BOVIN 1-450  
B | tubulin β-2C chain | TBB4B_BOVIN 1-455  
C | sperm acrosome associated 9 |   
D | stabilizer of axonemal microtubules 1 |   
  
Non-standard residues in pdb8ou0.ent #23  
---  
GDP — guanosine-5'-diphosphate  
GTP — guanosine-5'-triphosphate  
MG — magnesium ion  
  

> select add #23

8139 atoms, 8322 bonds, 7 pseudobonds, 1030 residues, 4 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #23,1,0,0,-63.846,0,1,0,14.323,0,0,1,0

> view matrix models #23,1,0,0,168.66,0,1,0,27.315,0,0,1,6.913

> view matrix models
> #23,0.98541,0.088231,0.14557,127.01,-0.15324,0.087534,0.9843,82.47,0.074104,-0.99225,0.099777,364.15

> view matrix models
> #23,0.86937,0.48809,0.07724,77.288,0.41645,-0.80778,0.41719,255.74,0.26602,-0.33053,-0.90553,358.61

> view matrix models
> #23,0.71893,0.68416,0.12272,58.641,0.63872,-0.5806,-0.50492,322.81,-0.27419,0.44138,-0.8544,296.84

> view matrix models
> #23,0.78783,0.61051,0.081225,67.349,0.61386,-0.7677,-0.18386,311.68,-0.049889,0.19471,-0.97959,324.93

> view matrix models
> #23,0.78783,0.61051,0.081225,62.882,0.61386,-0.7677,-0.18386,360.97,-0.049889,0.19471,-0.97959,399.78

> view matrix models
> #23,0.78783,0.61051,0.081225,76.733,0.61386,-0.7677,-0.18386,322.84,-0.049889,0.19471,-0.97959,357.66

> view matrix models
> #23,0.78783,0.61051,0.081225,42.312,0.61386,-0.7677,-0.18386,318.76,-0.049889,0.19471,-0.97959,409.7

> view matrix models
> #23,0.78783,0.61051,0.081225,48.674,0.61386,-0.7677,-0.18386,348.66,-0.049889,0.19471,-0.97959,418.53

> ui tool show Matchmaker

> matchmaker #!23 to #9

Computing secondary structure  
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 mMIP.pdb, chain A (#9) with pdb8ou0.ent, chain A (#23), sequence
alignment score = 2098.3  
RMSD between 423 pruned atom pairs is 0.947 angstroms; (across all 427 pairs:
0.972)  
  

> ui mousemode right select

> select clear

> show #!1 models

> hide #!1 models

Drag select of 10 residues  

> select subtract #9/C:159

73 atoms, 9 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> hide #!1 models

> select add #9/C:159

80 atoms, 7 bonds, 10 residues, 2 models selected  

> select add #9/C:158

88 atoms, 14 bonds, 11 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> hide #!1 models

> select #9/C:157

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

> hide sel cartoons

Drag select of 377 residues, 64 atoms, 5 pseudobonds, 61 bonds  
Drag select of 2 residues  

> select clear

> ui mousemode right translate

> view orient

> show #!1 models

> hide #!1 models

> hide #!9,23 atoms

> select #23/B

3365 atoms, 3442 bonds, 427 residues, 1 model selected  

> hide sel cartoons

> select #23/A

3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected  

> hide sel cartoons

> select #23/D

164 atoms, 168 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> select #23/C

1236 atoms, 1261 bonds, 1 pseudobond, 153 residues, 2 models selected  

> color sel dim grey

> ui mousemode right select

> select clear

> hbonds #!9,23 reveal true

3460 hydrogen bonds found  

> ~hbonds

> hide #!9,23 atoms

> select clear

> select #9/C:92

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

> select #23/C:93

7 atoms, 6 bonds, 1 residue, 1 model selected  
Drag select of 36 residues  

> select clear

> view orient

> select clear

Drag select of 1 pseudobonds  

> hide #!9,23 cartoons

> show #!9,23 cartoons

> hide #!9,23 atoms

No visible atoms selected  

> select clear

> ~label #9,23 residues

> ~label #9,23 atoms

> label delete

> select clear

Drag select of 7 residues  

> select clear

Drag select of 8 residues  

> hide sel cartoons

Drag select of 3 residues  

> select add #9/C:157

35 atoms, 8 bonds, 4 residues, 2 models selected  

> hide sel cartoons

> select #23/D

164 atoms, 168 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> select #9/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> hide sel cartoons

> select #9/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> show sel cartoons

> select #23/A

3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected  

> hide sel cartoons

> select #23/A

3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected  

> show sel cartoons

> color sel ivory

> select #23/B

3365 atoms, 3442 bonds, 427 residues, 1 model selected  

> color sel dim grey

> select clear

> select #23/A

3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected  

> color sel dim grey

> select clear

> view orient

> turn y 90

> turn y -90

> turn x -90

> turn z -90

> turn y -90

> morph #23,9 frames 40

models have different number of chains, 4 (Morph - pdb8ou0.ent #/A,Morph -
pdb8ou0.ent #/B,Morph - pdb8ou0.ent #/C,Morph - pdb8ou0.ent #/D) and 6
(mMIP.pdb #9/A,mMIP.pdb #9/B,mMIP.pdb #9/C,mMIP.pdb #9/D,mMIP.pdb
#9/H,mMIP.pdb #9/I)  

> combine #9

> hide #!28 models

> show #!28 models

> show #!27 models

> hide #!27 models

> hide #!9 models

> select #28/A

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> select #28/B

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!28 & sel)

> delete bonds (#!28 & sel)

> select #28/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select #28/D

521 atoms, 535 bonds, 64 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #28/I

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #28/C

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> color sel ivory

> select #23/C

1236 atoms, 1261 bonds, 1 pseudobond, 153 residues, 2 models selected  

> color sel ivory

> select clear

> show #!9 models

> view orient

> turn z -90

> turn y -90

> morph #23,28 frames 40

models have different number of chains, 4 (Morph - pdb8ou0.ent #/A,Morph -
pdb8ou0.ent #/B,Morph - pdb8ou0.ent #/C,Morph - pdb8ou0.ent #/D) and 3 (copy
of mMIP.pdb #28/A,copy of mMIP.pdb #28/C,copy of mMIP.pdb #28/H)  

> select add #28

8119 atoms, 8302 bonds, 1 pseudobond, 1024 residues, 2 models selected  

> hide #!28 models

> show #!28 models

> hide #!9 models

> hide #!23 models

> show #!9 models

> hide #!9 models

> select clear

> show #!23 models

> morph #23,28 frames 40

models have different number of chains, 4 (Morph - pdb8ou0.ent #/A,Morph -
pdb8ou0.ent #/B,Morph - pdb8ou0.ent #/C,Morph - pdb8ou0.ent #/D) and 3 (copy
of mMIP.pdb #28/A,copy of mMIP.pdb #28/C,copy of mMIP.pdb #28/H)  

> select #23/D

164 atoms, 168 bonds, 20 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> view orient

> turn z -90

> turn y -90

> show #!9 models

> morph #23,28 frames 40

Computed 41 frame morph #29  

> coordset #29 1,41

> hide #!9 models

> close #29

> show #!28 models

> show #!27 models

> hide #!27 models

> show #!23 models

> ui tool show Matchmaker

> matchmaker #!23 to #28

Computing secondary structure  
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 copy of mMIP.pdb, chain A (#28) with pdb8ou0.ent, chain A (#23),
sequence alignment score = 2098.3  
RMSD between 423 pruned atom pairs is 0.947 angstroms; (across all 427 pairs:
0.972)  
  

> morph #23,28 cartesian true frames 40

Computed 41 frame morph #29  

> coordset #29 1,41

> view orient

> show #!28 models

> view orient

> close #29

> show #!23 models

> view orient

> select #23/A

3374 atoms, 3451 bonds, 6 pseudobonds, 430 residues, 3 models selected  

> delete atoms (#!23 & sel)

> delete bonds (#!23 & sel)

> select #23/B

3365 atoms, 3442 bonds, 427 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #28/A

3382 atoms, 3460 bonds, 1 pseudobond, 429 residues, 2 models selected  

> delete atoms (#!28 & sel)

> delete bonds (#!28 & sel)

> select #28/H

3374 atoms, 3451 bonds, 427 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!9 models

> morph #23,28 frames 40

Computed 41 frame morph #29  

> coordset #29 1,41

> label delete

> select add #29

1223 atoms, 1245 bonds, 1 pseudobond, 153 residues, 2 models selected  

> color sel ivory

> select clear

Drag select of 105 residues  

> select clear

> ui mousemode right translate

> view orient

> turn y -90

> turn z -90

> turn y -90

> movie record

> movie encode /Users/jojudernatz/Desktop/movie1.mp4 framerate 25.0

Movie saved to /Users/jojudernatz/Desktop/movie1.mp4  
  

> movie record

> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0

Error processing trigger ""new frame"":  
Movie encoding failed because no images were recorded.  

> movie record

> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0

Error processing trigger ""new frame"":  
Movie encoding failed because no images were recorded.  

> movie record

> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0

Error processing trigger ""new frame"":  
Movie encoding failed because no images were recorded.  

> turn y -90

> movie record

> movie encode /Users/jojudernatz/Desktop/movie2.mp4 framerate 25.0

Error processing trigger ""new frame"":  
Movie encoding failed because no images were recorded.  

> movie record

Already recording a movie  

> movie encode

Movie saved to /Users/jojudernatz/Desktop/movie.mp4  
  

> select add #29

1223 atoms, 1245 bonds, 1 pseudobond, 153 residues, 2 models selected  

> show sel atoms

> show #!28 models

> hide #!28 models

> select add #28

2586 atoms, 2636 bonds, 1 pseudobond, 321 residues, 3 models selected  

> show sel & #!29 atoms

> select subtract #29

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select subtract #28

Nothing selected  

> select add #28

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select subtract #28

Nothing selected  

> select add #27

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> select subtract #27

Nothing selected  

> select add #9

15396 atoms, 15748 bonds, 2 pseudobonds, 1944 residues, 2 models selected  

> select subtract #9

6 models selected  

> hide #!9 models

> show #!28 models

> select add #28

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 1363 atom styles  

> show sel cartoons

> hide sel atoms

> ui mousemode right select

Drag select of 3 residues  
Drag select of 6 residues  

> select add #28/C:159

80 atoms, 7 bonds, 10 residues, 1 model selected  

> select add #28/C:158

88 atoms, 14 bonds, 11 residues, 1 model selected  

> hide sel cartoons

Drag select of 65 residues, 90 atoms, 77 bonds  

> select clear

> select add #28

1363 atoms, 1391 bonds, 168 residues, 1 model selected  

> show sel atoms

Drag select of 30 atoms, 29 bonds  

> select add #28/C:166@O

31 atoms, 30 bonds, 5 residues, 1 model selected  

> hide sel atoms

Drag select of 40 atoms, 39 bonds  

> hide sel atoms

Drag select of 5 atoms, 2 bonds  
Drag select of 7 atoms, 7 bonds  

> select add #28/C:159@CA

82 atoms, 78 bonds, 11 residues, 1 model selected  

> hide sel atoms

Drag select of 4 atoms, 4 bonds  

> select add #28/C:158@CD1

87 atoms, 83 bonds, 11 residues, 1 model selected  

> hide sel atoms

Drag select of 4 atoms, 1 residues, 3 bonds  

> select add #28/C:157@CG

95 atoms, 88 bonds, 12 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select clear

Drag select of 2 atoms, 1 bonds  

> hide sel atoms

> view orient

> select clear

> turn y -90

> show #!9 models

> view orient

> turn z -90

> turn y -90

> ui mousemode right translate

> ui mousemode right select

Drag select of 22 residues, 1 atoms  

> select subtract #28/C:131@NH2

183 atoms, 22 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 183 atom styles  

> select clear

> open /Users/jojudernatz/Downloads/mMIP_real_space_refined_013-coot-0.pdb

Summary of feedback from opening
/Users/jojudernatz/Downloads/mMIP_real_space_refined_013-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY H 10 HIS H 28 1 19  
Start residue of secondary structure not found: HELIX 2 2 ASP H 41 GLN H 43 1
3  
Start residue of secondary structure not found: HELIX 3 3 ILE H 47 VAL H 49 1
3  
Start residue of secondary structure not found: HELIX 4 4 GLY H 71 SER H 78 1
8  
Start residue of secondary structure not found: HELIX 5 5 PRO H 87 ASN H 89 1
3  
43 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 72 72 GLY B 144 ASP B 160
1 17  
Start residue of secondary structure not found: HELIX 73 73 GLU B 183 THR B
194 1 12  
Start residue of secondary structure not found: HELIX 74 74 ASN B 206 ARG B
215 1 10  
Start residue of secondary structure not found: HELIX 75 75 TYR B 224 ILE B
238 1 15  
Start residue of secondary structure not found: HELIX 76 76 THR B 239 SER B
241 1 3  
Start residue of secondary structure not found: HELIX 77 77 LEU B 252 PHE B
255 1 4  
42 messages similar to the above omitted  
  
Chain information for mMIP_real_space_refined_013-coot-0.pdb #30  
---  
Chain | Description  
A AA | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> style #!9,28-30 stick

Changed 33305 atom styles  

> hide #!28 models

> hide #!29 models

> show #!9,30 cartoons

> hide #!9,30 atoms

> dssp true

Expected a structures specifier or a keyword  

> dssp #30 true

Expected a keyword  

> dssp #30

Computing secondary structure  

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!1 models

> hide #!1 models

> select clear

> ui mousemode right translate


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac16,7
      Model Number: Z1FU000R8Y/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 48 GB
      System Firmware Version: 11881.81.4
      OS Loader Version: 11881.81.4

Software:

    System Software Overview:

      System Version: macOS 15.3.1 (24D70)
      Kernel Version: Darwin 24.3.0
      Time since boot: 12 days, 1 hour, 57 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        HP Z24nf G2:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 75.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    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: 2.3
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-MutationScores: 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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    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: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    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: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	new	normal		Unassigned