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Opened 10 hours ago
#20460 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.12rc202606060206 (2026-06-06 02:06:12 UTC)
Description
attempting to align 2 PDB
Log:
UCSF ChimeraX version: 1.12rc202606060206 (2026-06-06)
© 2016-2026 Regents of the University of California. All rights reserved.
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV1_gD_full_locking.cxs" format session
Log from Sat Jun 6 16:29:38 2026UCSF ChimeraX version: 1.12.dev202604220250
(2026-04-22)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 2C36 fromDatabase pdb format mmcif
Summary of feedback from opening 2C36 fetched from pdb
---
note | Fetching compressed mmCIF 2c36 from http://files.rcsb.org/download/2c36.cif
2c36 title:
Structure of unliganded HSV gD reveals a mechanism for receptor- mediated
activation of virus entry [more info...]
Chain information for 2c36 #1
---
Chain | Description | UniProt
A B | GLYCOPROTEIN D HSV-1 | VGLD_HHV1P 23-307
Non-standard residues in 2c36 #1
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
CL — chloride ion
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ZN — zinc ion
2c36 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
12 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open 3U82 fromDatabase pdb format mmcif
Summary of feedback from opening 3U82 fetched from pdb
---
note | Fetching compressed mmCIF 3u82 from http://files.rcsb.org/download/3u82.cif
3u82 title:
Binding of herpes simplex virus glycoprotein D to nectin-1 exploits host cell
adhesion [more info...]
Chain information for 3u82 #2
---
Chain | Description | UniProt
A | Envelope glycoprotein D | GD_HHV11 1-285
B | Poliovirus receptor-related protein 1 | PVRL1_HUMAN 30-335
14 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
4164 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui mousemode right "translate selected models"
> select add #2
4164 atoms, 4276 bonds, 531 residues, 1 model selected
Drag select of 1 residues
> select add #2
4173 atoms, 4276 bonds, 532 residues, 2 models selected
> view matrix models
> #1,1,0,0,3.4063,0,1,0,-3.5384,0,0,1,-15.333,#2,1,0,0,3.4063,0,1,0,-3.5384,0,0,1,-15.333
> view matrix models
> #1,1,0,0,1.9236,0,1,0,-2.2865,0,0,1,-14.648,#2,1,0,0,1.9236,0,1,0,-2.2865,0,0,1,-14.648
Drag select of 38 residues
> select add #2
4164 atoms, 4276 bonds, 531 residues, 1 model selected
> view matrix models #2,1,0,0,10.913,0,1,0,-5.4823,0,0,1,72.473
> select clear
> select add #2
4164 atoms, 4276 bonds, 531 residues, 1 model selected
> view matrix models #2,1,0,0,49.396,0,1,0,10.72,0,0,1,74.14
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.36377,0.23781,0.90062,93.031,0.2102,0.92097,-0.32808,-4.3201,-0.90746,0.30866,0.28503,95.517
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.36377,0.23781,0.90062,60.161,0.2102,0.92097,-0.32808,39.017,-0.90746,0.30866,0.28503,92.057
> select #2/B
2350 atoms, 2405 bonds, 300 residues, 1 model selected
> select #1/B
2378 atoms, 2211 bonds, 1 pseudobond, 511 residues, 2 models selected
> cartoon hide (#!1 & sel)
> hide (#!1 & sel) target a
Drag select of 61 atoms, 63 bonds
> hide sel target a
Drag select of 15 atoms, 13 bonds
Drag select of 17 atoms, 15 bonds
> hide sel target a
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> view matrix models #1,1,0,0,-1.9223,0,1,0,-10.557,0,0,1,-11.522
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.9967,0.07801,-0.022516,-2.9128,-0.077916,0.99695,0.005019,-6.3853,0.022839,-0.003248,0.99973,-12.683
> view matrix models
> #1,-0.94293,-0.29197,-0.16012,135,0.33274,-0.84487,-0.4189,79.3,-0.012978,-0.44828,0.8938,16.082
> view matrix models
> #1,-0.98397,0.14482,-0.10409,115.23,-0.14104,-0.98908,-0.042846,80.216,-0.10915,-0.027479,0.99364,-3.6143
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.98397,0.14482,-0.10409,116.77,-0.14104,-0.98908,-0.042846,34.526,-0.10915,-0.027479,0.99364,-7.383
> view matrix models
> #1,-0.98397,0.14482,-0.10409,129.19,-0.14104,-0.98908,-0.042846,34.931,-0.10915,-0.027479,0.99364,8.2471
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.65912,-0.68076,-0.31957,161.67,0.51961,-0.10506,-0.84792,30.444,0.54366,-0.72493,0.42297,47.06
> view matrix models
> #1,-0.76831,0.43248,-0.47187,136.7,0.060618,0.78305,0.61899,-103.46,0.6372,0.44698,-0.62785,84.674
> view matrix models
> #1,-0.98248,0.025355,-0.18463,140.71,-0.16057,0.38766,0.90771,-99.638,0.094587,0.92145,-0.3768,75.622
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.98248,0.025355,-0.18463,135.13,-0.16057,0.38766,0.90771,-59.244,0.094587,0.92145,-0.3768,70.638
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.99193,-0.062378,0.1104,114.02,0.080803,0.36003,0.92944,-73.872,-0.097723,0.93085,-0.35208,79.212
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.99193,-0.062378,0.1104,107.05,0.080803,0.36003,0.92944,-72.704,-0.097723,0.93085,-0.35208,82.111
> view matrix models
> #1,-0.99193,-0.062378,0.1104,114.49,0.080803,0.36003,0.92944,-93.699,-0.097723,0.93085,-0.35208,57.904
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.9571,0.28849,0.027023,105.65,0.26877,0.84906,0.45481,-83.486,0.10827,0.44256,-0.89018,111.31
> view matrix models
> #1,-0.94424,0.30785,-0.11683,116.4,0.29468,0.94837,0.11729,-60.158,0.1469,0.076325,-0.9862,131.83
> view matrix models
> #1,-0.94238,0.31033,-0.12494,116.89,0.2985,0.94864,0.10481,-59.325,0.15105,0.061479,-0.98661,132.21
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.94238,0.31033,-0.12494,117.63,0.2985,0.94864,0.10481,-30.747,0.15105,0.061479,-0.98661,147.91
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.94444,0.32578,-0.043662,110.21,0.27276,0.85091,0.44895,-54.711,0.18341,0.4121,-0.89249,124.11
> view matrix models
> #1,-0.94484,0.32551,-0.036316,109.62,0.27314,0.84426,0.46112,-55.505,0.18076,0.42576,-0.8866,123.21
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.94484,0.32551,-0.036316,107.15,0.27314,0.84426,0.46112,-64.24,0.18076,0.42576,-0.8866,119.63
> view matrix models
> #1,-0.94484,0.32551,-0.036316,106.11,0.27314,0.84426,0.46112,-64.181,0.18076,0.42576,-0.8866,125.67
> ui tool show Match→Align
> msa3d #1/A#2/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
24 residue pairs aligned
285 fully populated columns
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 199, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args, ma=self.match_align:
ma(apply=True))
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align
run(self.session, "msa3d " + ' '.join(args))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 155, in make_alignment
coords[seq] = column_atoms(seq, full_cols).scene_coords
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in column_atoms
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in <listcomp>
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'principal_atom'
AttributeError: 'NoneType' object has no attribute 'principal_atom'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select #2/B
2350 atoms, 2405 bonds, 300 residues, 1 model selected
> cartoon hide sel
> select add #2
4164 atoms, 4276 bonds, 531 residues, 1 model selected
> select add #1
9076 atoms, 8825 bonds, 6 pseudobonds, 1601 residues, 5 models selected
> select subtract #2
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> view matrix models
> #1,-0.94484,0.32551,-0.036316,78.784,0.27314,0.84426,0.46112,-98.282,0.18076,0.42576,-0.8866,101.33
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.89216,0.34963,-0.28601,96.076,0.30726,0.93384,0.18313,-80.114,0.33111,0.075506,-0.94057,111.2
> view matrix models
> #1,-0.8876,-0.11044,-0.44717,127.82,0.45344,-0.38012,-0.80616,47.982,-0.080945,-0.91832,0.38747,61.2
> view matrix models
> #1,-0.72558,-0.22625,-0.64988,140.38,0.61137,-0.64542,-0.45789,19.765,-0.31585,-0.72955,0.60662,48.529
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.72558,-0.22625,-0.64988,154.97,0.61137,-0.64542,-0.45789,58.622,-0.31585,-0.72955,0.60662,76.034
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.78266,-0.3287,-0.52858,151.99,0.44768,-0.88726,-0.11113,48.09,-0.43246,-0.32362,0.84158,46.59
> view matrix models
> #1,-0.93745,-0.34808,0.0054046,116.15,0.33548,-0.90742,-0.25307,67.435,0.092993,-0.23543,0.96743,2.1588
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.93745,-0.34808,0.0054046,134.19,0.33548,-0.90742,-0.25307,62.876,0.092993,-0.23543,0.96743,7.7984
> view matrix models
> #1,-0.93745,-0.34808,0.0054046,134.81,0.33548,-0.90742,-0.25307,63.104,0.092993,-0.23543,0.96743,6.9425
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.89951,-0.31276,0.30507,105.68,0.23313,-0.93413,-0.27028,71.515,0.36951,-0.172,0.91317,-6.847
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.89951,-0.31276,0.30507,101.6,0.23313,-0.93413,-0.27028,72.531,0.36951,-0.172,0.91317,-8.3189
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.89907,-0.3103,0.30885,101.15,0.23415,-0.93688,-0.25966,71.677,0.36993,-0.16114,0.91498,-8.9289
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.89907,-0.3103,0.30885,100.24,0.23415,-0.93688,-0.25966,77.531,0.36993,-0.16114,0.91498,-12.425
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.8404,-0.54186,-0.010584,133.29,0.39205,-0.59435,-0.70217,92.555,0.37419,-0.59426,0.71193,21.838
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.8404,-0.54186,-0.010584,128.48,0.39205,-0.59435,-0.70217,86.68,0.37419,-0.59426,0.71193,20.236
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.89687,-0.44211,-0.012456,127.92,0.31477,-0.61825,-0.7202,93.609,0.31071,-0.64985,0.69365,27.65
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.89687,-0.44211,-0.012456,127.52,0.31477,-0.61825,-0.7202,95.437,0.31071,-0.64985,0.69365,29.561
> view matrix models
> #1,-0.89687,-0.44211,-0.012456,124.44,0.31477,-0.61825,-0.7202,92.625,0.31071,-0.64985,0.69365,32.887
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.65267,-0.75749,-0.015254,123.17,0.48571,-0.40288,-0.77574,78.977,0.58147,-0.51371,0.63087,17.266
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.65267,-0.75749,-0.015254,131.65,0.48571,-0.40288,-0.77574,74.387,0.58147,-0.51371,0.63087,17.936
> view matrix models
> #1,-0.65267,-0.75749,-0.015254,132.85,0.48571,-0.40288,-0.77574,82.595,0.58147,-0.51371,0.63087,11.574
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.63655,-0.75476,0.15853,117,0.67528,-0.64475,-0.35817,45.724,0.37255,-0.12094,0.9201,-16.667
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.63655,-0.75476,0.15853,115.14,0.67528,-0.64475,-0.35817,39.093,0.37255,-0.12094,0.9201,-17.536
> ui tool show Match→Align
> msa3d #2/A#1/A cutoffDistance 10 maxIterations none refChain #1/A
Match→Align cutoff: 10.0, in column if within cutoff of: any
67 residue pairs aligned
285 fully populated columns
285 fully populated columns in at least 3 column stetches
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align
run(self.session, "msa3d " + ' '.join(args))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 129, in make_alignment
ref_atoms = column_atoms(ref_seq, culled)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in column_atoms
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in <listcomp>
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'principal_atom'
AttributeError: 'NoneType' object has no attribute 'principal_atom'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> view matrix models
> #1,-0.63655,-0.75476,0.15853,79.974,0.67528,-0.64475,-0.35817,54.278,0.37255,-0.12094,0.9201,14.061
> view matrix models
> #1,-0.63655,-0.75476,0.15853,77.116,0.67528,-0.64475,-0.35817,55.517,0.37255,-0.12094,0.9201,16.633
> view matrix models
> #1,-0.63655,-0.75476,0.15853,76.966,0.67528,-0.64475,-0.35817,55.451,0.37255,-0.12094,0.9201,16.657
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99264,-0.021188,0.11925,-42.472,-0.051118,-0.96588,0.2539,57.803,0.1098,-0.25813,-0.95985,197.41
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99264,-0.021188,0.11925,-9.9361,-0.051118,-0.96588,0.2539,41.251,0.1098,-0.25813,-0.95985,170.95
> view matrix models
> #1,0.99264,-0.021188,0.11925,-11.819,-0.051118,-0.96588,0.2539,44.491,0.1098,-0.25813,-0.95985,168.23
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99668,-0.031962,0.074832,-7.8394,-0.038582,-0.99531,0.088763,59.012,0.071644,-0.091355,-0.99324,166.64
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99668,-0.031962,0.074832,-5.6357,-0.038582,-0.99531,0.088763,60.039,0.071644,-0.091355,-0.99324,165.89
> select clear
> ui mousemode right "rotate selected models"
> select add #2
4164 atoms, 4276 bonds, 531 residues, 1 model selected
> select add #1
9076 atoms, 8825 bonds, 6 pseudobonds, 1601 residues, 5 models selected
> select subtract #2
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> view matrix models
> #1,0.9955,-0.050142,-0.080459,8.3878,-0.040117,-0.99176,0.12171,57.179,-0.085898,-0.11793,-0.9893,175.66
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9955,-0.050142,-0.080459,10.417,-0.040117,-0.99176,0.12171,56.823,-0.085898,-0.11793,-0.9893,174.41
> select clear
> ui tool show Match→Align
> msa3d #2/A#1/A cutoffDistance 10 maxIterations none minStretch 1 refChain
> #1/A
Match→Align cutoff: 10.0, in column if within cutoff of: any
231 residue pairs aligned
285 fully populated columns
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 199, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args, ma=self.match_align:
ma(apply=True))
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align
run(self.session, "msa3d " + ' '.join(args))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 129, in make_alignment
ref_atoms = column_atoms(ref_seq, culled)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in column_atoms
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in <listcomp>
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'principal_atom'
AttributeError: 'NoneType' object has no attribute 'principal_atom'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui mousemode right "rotate selected models"
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> view matrix models
> #1,0.98262,-0.1584,-0.096768,16.847,-0.14711,-0.98248,0.1144,63.226,-0.11319,-0.098178,-0.98871,175.15
> select clear
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> view matrix models
> #1,0.98337,-0.13115,-0.12567,18.185,-0.11639,-0.98612,0.11838,61.266,-0.13945,-0.10179,-0.98498,176.48
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98337,-0.13115,-0.12567,18.11,-0.11639,-0.98612,0.11838,60.633,-0.13945,-0.10179,-0.98498,177.04
> select clear
[Repeated 4 time(s)]
> select #1/A:307
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B
2350 atoms, 2405 bonds, 300 residues, 1 model selected
> cartoon sel
> color sel orange
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #2
4164 atoms, 4276 bonds, 531 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97757,-0.15039,-0.14742,21.061,-0.12783,-0.98006,0.15215,58.172,-0.16737,-0.12989,-0.9773,179.1
> select clear
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.97757,-0.15039,-0.14742,20.023,-0.12783,-0.98006,0.15215,58.001,-0.16737,-0.12989,-0.9773,179.03
> view matrix models
> #1,0.97757,-0.15039,-0.14742,20.058,-0.12783,-0.98006,0.15215,57.586,-0.16737,-0.12989,-0.9773,179.51
> select clear
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV_gD_Nec1_compare.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> select clear
> select #2/A
1814 atoms, 1871 bonds, 231 residues, 1 model selected
> ui tool show AlphaFold
Populating font family aliases took 382 ms. Replace uses of missing font
family "Harding" with one that exists to avoid this cost.
> select #2/A
1814 atoms, 1871 bonds, 231 residues, 1 model selected
> select clear
> select #2/A
1814 atoms, 1871 bonds, 231 residues, 1 model selected
> select clear
> select #2/A
1814 atoms, 1871 bonds, 231 residues, 1 model selected
> select clear
> alphafold predict
> PVLDQLTDPPGVRRVYHIQAGLPDPFQPPSLPITVYYAVLERACRSVLLNAPSEAPQIVRGASEDVRKQPYNLTIAWFRMGGNCAIPITVMEYTECSYNKSLGACPIRTQPRWNYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFILEHRAKGSCKYALPLRIPPSACLSPQAYQQGVTVDSIGMLPRFIPENQRTVAVYSLKIAGWHGPKAPYTSTLLPPELSETPNATQPELAPEDPEDSALLEDPVG,MGNGLWFVGVIILGVAWGQVHDWTEQTDPWFLDGLGMDRMYWRDTNTGRLWLPNTPDPQKPPRGFLAPPDELNLTTASLPLLRWYEERFCFVLVTTAEFPRDPGQLLYIPKTYLLGRPPNASLPAPTTVEPTAQPPPSVAPLKGLLHNPAASVLLRSRAWVTFSAVPDPEALTFPRGDNVATASHPSGPRDTPPPRPPVGARRHPTTELDITHLHNASTTWLATRGLLRSPGRYVYFSPSASTWPVGIWTTGELVLGCDAALVRARYGREFMGLVISMHDSPPVEVMVVPAGQTLDRVGDPADENPPGALPGPPGGPRYRVFVLGSLTRADNGSALDALRRVGGYPEEGTNYAQFLSRAYAEFFSGDAGAEQGPRPPLFWRLTGLLATSGFAFVNAAHANGAVCLSDLLGFLAHSRALAGLAARGAAGCAADSVFFNVSVLDPTARLQLEARLQHLVAEILEREQSLALHALGYQLAFVLDSPSAYDAVAPSAAHLIDALYAEFLGGRVLTTPVVHRALFYASAVLRQPFLAGVPSAVQRERARRSLLIASALCTSDVAAATNADLRTALARADHQKTLFWLPDHFSPCAASLRFDLDESVFILDALAQATRSETPVEVLAQQTHGLASTLTRWAHYNALIRAFVPEASHRCGGQSANVEPRILVPITHNASYVVTHSPLPRGIGYKLTGVDVRRPLFLTYLTATCEGSTRDIESKRLVRTQNQRDLGLVGAVFMRYTPAGEVMSVLLVDTDNTQQQIAAGPTEGAPSVFSSDVPSTALLLFPNGTVIHLLAFDTQPVAAIAPGFLAASALGVVMITAALAGILKVLRTSVPFFWRRE,MGILGWVGLIAVGVLCVRGGLPSTEYVIRSRVAREVGDILKVPCVPLPSDDLDWRYETPSAINYALIDGIFLRYHCPGLDTVLWDRHAQKAYWVNPFLFVAGFLEDLSYPAFPANTQETETRLALYKEIRQALDSRKQAASHTPVKAGCVNFDYSRTRRCVGRQDLGPTNGTSGRTPVLPPDDEAGLQPKPLTTPPPIIATSDPTPRRDAATKSRRRRPHSRRL
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
[Repeated 1 time(s)]AlphaFold prediction finished
Results in /Users/kellykeisen/Downloads/ChimeraX/AlphaFold/prediction_58
> open
> /Users/kellykeisen/Downloads/ChimeraX/AlphaFold/prediction_58/best_model.pdb
Chain information for best_model.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
Computing secondary structure
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models #3,1,0,0,-41.543,0,1,0,49.712,0,0,1,-3.3465
> view matrix models #3,1,0,0,-41.649,0,1,0,49.681,0,0,1,-3.4298
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.55457,-0.72096,0.41552,-34.394,-0.29726,-0.63804,-0.71031,39.066,0.77723,0.2704,-0.56816,-29.284
> view matrix models
> #3,0.14611,-0.98311,0.11025,-38.745,-0.80453,-0.18294,-0.56504,41.834,0.57566,-0.006143,-0.81766,-32.971
> select clear
> select #3/B
6388 atoms, 6568 bonds, 838 residues, 1 model selected
> select #3/A
2045 atoms, 2106 bonds, 262 residues, 1 model selected
> view matrix models
> #3,0.53595,-0.83929,-0.091401,-42.411,-0.82197,-0.54344,0.17041,53.629,-0.1927,-0.016204,-0.98112,-34.725
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.53595,-0.83929,-0.091401,41.217,-0.82197,-0.54344,0.17041,16.537,-0.1927,-0.016204,-0.98112,35.444
> view matrix models
> #3,0.53595,-0.83929,-0.091401,91.101,-0.82197,-0.54344,0.17041,-0.42672,-0.1927,-0.016204,-0.98112,10.21
> view matrix models
> #3,0.53595,-0.83929,-0.091401,91.124,-0.82197,-0.54344,0.17041,-3.257,-0.1927,-0.016204,-0.98112,7.8002
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.64183,-0.66349,-0.38448,86.308,-0.73789,-0.67083,-0.07416,-7.2116,-0.20872,0.3313,-0.92015,8.712
> view matrix models
> #3,0.53873,0.3179,-0.7802,79.914,0.52122,-0.85333,0.012202,-7.1797,-0.66189,-0.41323,-0.62542,14.059
> select clear
> ui mousemode right "translate selected models"
Drag select of 6 residues
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> select clear
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.53873,0.3179,-0.7802,35.957,0.52122,-0.85333,0.012202,-2.9352,-0.66189,-0.41323,-0.62542,48.488
> view matrix models
> #3,0.53873,0.3179,-0.7802,43.546,0.52122,-0.85333,0.012202,-30.241,-0.66189,-0.41323,-0.62542,78.597
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.43168,0.23908,-0.86977,42.256,0.016313,-0.96615,-0.25748,-33.952,-0.90188,0.096958,-0.42096,82.001
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.43168,0.23908,-0.86977,35.858,0.016313,-0.96615,-0.25748,-12.62,-0.90188,0.096958,-0.42096,57.494
> view matrix models
> #3,0.43168,0.23908,-0.86977,39.048,0.016313,-0.96615,-0.25748,-13.227,-0.90188,0.096958,-0.42096,57.517
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8222,0.1065,-0.55914,43.59,0.2507,-0.94968,0.18776,-6.4057,-0.51101,-0.29455,-0.80753,51.024
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.8222,0.1065,-0.55914,46.573,0.2507,-0.94968,0.18776,0.34056,-0.51101,-0.29455,-0.80753,41.66
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.87923,0.01041,-0.47629,47.849,0.20193,-0.91365,0.3528,3.0113,-0.43149,-0.40637,-0.80541,41.63
> view matrix models
> #3,0.89359,0.11257,-0.43454,48.476,0.27246,-0.90535,0.32574,2.5017,-0.35674,-0.40947,-0.83969,41.004
> view matrix models
> #3,0.85893,0.25674,-0.44309,48.346,0.40677,-0.86769,0.28576,1.7103,-0.31109,-0.42568,-0.84971,40.798
> view matrix models
> #3,0.91576,0.054481,-0.39802,49.045,0.22472,-0.89072,0.39512,3.6545,-0.333,-0.45128,-0.82793,41.174
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91576,0.054481,-0.39802,49.021,0.22472,-0.89072,0.39512,6.8004,-0.333,-0.45128,-0.82793,35.46
> view matrix models
> #3,0.91576,0.054481,-0.39802,47.762,0.22472,-0.89072,0.39512,6.4551,-0.333,-0.45128,-0.82793,42.066
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.77891,0.06274,-0.62399,44.317,0.43556,-0.76998,0.46629,7.3294,-0.4512,-0.63498,-0.62707,45.431
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.77891,0.06274,-0.62399,45.123,0.43556,-0.76998,0.46629,7.7678,-0.4512,-0.63498,-0.62707,42.465
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.77891,0.06274,-0.62399,41.496,0.43556,-0.76998,0.46629,10.109,-0.4512,-0.63498,-0.62707,43.416
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.84181,0.073037,-0.53482,42.843,0.36601,-0.80547,0.46611,10.19,-0.39674,-0.58812,-0.70478,42.11
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.84181,0.073037,-0.53482,44.765,0.36601,-0.80547,0.46611,13.528,-0.39674,-0.58812,-0.70478,41.02
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.76917,0.40655,-0.49305,45.436,0.57174,-0.78245,0.24676,9.8089,-0.28546,-0.47169,-0.83428,38.812
> view matrix models
> #3,0.80012,0.26671,-0.53729,44.729,0.49357,-0.80175,0.33703,11.335,-0.34088,-0.53485,-0.77313,39.86
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.80012,0.26671,-0.53729,52.012,0.49357,-0.80175,0.33703,9.6074,-0.34088,-0.53485,-0.77313,35.927
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.75209,0.29245,-0.59062,51.211,0.63021,-0.58136,0.51464,12.234,-0.19286,-0.75927,-0.62154,38.225
> view matrix models
> #3,0.92471,0.055503,-0.3766,54.477,0.31355,-0.67204,0.67085,15.086,-0.21586,-0.73843,-0.63885,37.97
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.92471,0.055503,-0.3766,46.019,0.31355,-0.67204,0.67085,-18.75,-0.21586,-0.73843,-0.63885,53.875
> view matrix models
> #3,0.92471,0.055503,-0.3766,45.624,0.31355,-0.67204,0.67085,-19.702,-0.21586,-0.73843,-0.63885,53.071
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96813,0.15969,-0.19295,48.474,0.24834,-0.71205,0.65674,-19.846,-0.032512,-0.68373,-0.72901,51.424
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96813,0.15969,-0.19295,59.104,0.24834,-0.71205,0.65674,23.436,-0.032512,-0.68373,-0.72901,29.57
> select clear
Drag select of 35 residues
> cartoon hide sel
Drag select of 16 residues
> cartoon hide sel
> hide #2 models
Drag select of 34 residues
> cartoon hide sel
Drag select of 40 residues
> cartoon hide sel
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #3/A
2045 atoms, 2106 bonds, 262 residues, 1 model selected
> color sel cornflower blue
> color sel purple
> select clear
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.96813,0.15969,-0.19295,41.132,0.24834,-0.71205,0.65674,11.413,-0.032512,-0.68373,-0.72901,6.8106
> select clear
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.96813,0.15969,-0.19295,50.149,0.24834,-0.71205,0.65674,28.649,-0.032512,-0.68373,-0.72901,30.596
> view matrix models
> #3,0.96813,0.15969,-0.19295,57.513,0.24834,-0.71205,0.65674,23.241,-0.032512,-0.68373,-0.72901,28.902
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97905,0.14652,-0.14137,58.129,0.20217,-0.61732,0.76029,23.515,0.024126,-0.77295,-0.63401,30.551
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97905,0.14652,-0.14137,60.627,0.20217,-0.61732,0.76029,29.828,0.024126,-0.77295,-0.63401,34.458
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97304,-0.051312,-0.22484,60.238,0.14668,-0.61463,0.77506,29.395,-0.17796,-0.78715,-0.59053,32.839
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97304,-0.051312,-0.22484,52.329,0.14668,-0.61463,0.77506,30.502,-0.17796,-0.78715,-0.59053,35.899
> select clear
> ui mousemode right "rotate selected models"
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.97099,-0.096031,-0.219,52.462,0.12035,-0.59511,0.79458,30.371,-0.20663,-0.79788,-0.56629,35.855
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97099,-0.096031,-0.219,52.63,0.12035,-0.59511,0.79458,29.293,-0.20663,-0.79788,-0.56629,37.905
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97636,-0.090173,-0.19646,52.88,0.11987,-0.53043,0.83921,29.555,-0.17988,-0.84292,-0.50708,38.822
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.97636,-0.090173,-0.19646,53.242,0.11987,-0.53043,0.83921,32.87,-0.17988,-0.84292,-0.50708,36.816
> select clear
> ui mousemode right "rotate selected models"
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.91105,0.022777,-0.41166,50.343,0.36947,-0.48821,0.79066,34.861,-0.18297,-0.87243,-0.4532,37.347
> select clear
> ui mousemode right "translate selected models"
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.91105,0.022777,-0.41166,48.413,0.36947,-0.48821,0.79066,35.469,-0.18297,-0.87243,-0.4532,38.53
> select clear
> select #3/B
6388 atoms, 6568 bonds, 838 residues, 1 model selected
> ui tool show "Color Actions"
> color sel hot pink
> select clear
> hide #!1 models
> show #2 models
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV_gD_Nec1_compare.cxs"
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91148,0.022772,-0.41072,48.426,0.36898,-0.48662,0.79187,35.472,-0.18183,-0.87332,-0.45194,38.555
> select clear
[Repeated 1 time(s)]
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> select clear
> select add #3
10191 atoms, 10479 bonds, 1324 residues, 1 model selected
> view matrix models
> #3,0.90818,0.022854,-0.41795,48.325,0.37266,-0.49885,0.78248,35.45,-0.19061,-0.86639,-0.46156,38.362
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.90818,0.022854,-0.41795,48.525,0.37266,-0.49885,0.78248,34.947,-0.19061,-0.86639,-0.46156,39.048
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.91086,0.022779,-0.41209,48.606,0.36969,-0.48893,0.79011,34.965,-0.18348,-0.87203,-0.45377,39.205
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.91086,0.022779,-0.41209,48.227,0.36969,-0.48893,0.79011,36.055,-0.18348,-0.87203,-0.45377,37.827
> select clear
> select #3/C
1758 atoms, 1805 bonds, 224 residues, 1 model selected
> color sel white
> select clear
> show #!1 models
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> view matrix models
> #1,0.97757,-0.15039,-0.14742,20.484,-0.12783,-0.98006,0.15215,58.627,-0.16737,-0.12989,-0.9773,179.55
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #1/A:278
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:278-307
229 atoms, 238 bonds, 30 residues, 1 model selected
> show sel target ab
> cartoon hide sel
> style sel sphere
Changed 229 atom styles
> select clear
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-34
87 atoms, 89 bonds, 12 residues, 1 model selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-51
228 atoms, 237 bonds, 29 residues, 1 model selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-43
164 atoms, 168 bonds, 21 residues, 1 model selected
> show sel target ab
> style sel sphere
Changed 164 atom styles
> cartoon hide sel
> ui tool show "Color Actions"
> color sel sky blue
> color #1 #76d6ffff
> select #1/A:278
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:278-307
229 atoms, 238 bonds, 30 residues, 1 model selected
> color #1 #7a81ffff
> select #1/A:278
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:278-280
25 atoms, 24 bonds, 3 residues, 1 model selected
> select clear
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-43
164 atoms, 168 bonds, 21 residues, 1 model selected
> color #1 #76d6ffff
> select #1/A:23-24
14 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/A:23-43
164 atoms, 168 bonds, 21 residues, 1 model selected
> color sel cornflower blue
> select clear
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV_gD_Nec1_compare.cxs"
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV_gD_Nec1_gHgL_compare.png" width 2000 height 1670
> supersample 3
> select clear
> select #2/B:335
9 atoms, 8 bonds, 1 residue, 1 model selected
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV_gD_Nec1_compare.cxs"
> alphafold predict
> SPGRTITVGPRGNASNAAPSASPRNASAPRTTPTPPQPRKATKSKASTAKPAPPPKTGPPKTSSEPVRCNRHDPLARYGSRVQIRCRFPNSTRTESRLQIWRYATATDAEIGTAPSLEEVMVNVSAPPGGQLVYDSAPNRTDPHVIWAEGAGPGASPRLYSVVGPLGRQRLIIEELTLETQGMYYWVWGRTDRPSAYGTWVRVRVFRPPSLTIHPHAVLEGQPFKATCTAATYYPGNRAEFVWFEDGRRVFDPAQIHTQTQENPDGFSTVSTVTSAAVGGQGPPRTFTCQLTWHRDSVSFSRRNASGTASVLPRPTITMEFTGDHAVCTAGCVPEGVTFAWFLGDDSSPAEKVAVASQTSCGRPGTATIRSTLPVSYEQTEYICRLAGYPDGIPVLEHHGSHQPPPRDPTERQVIRAVEG,QVHDWTEQTDPWFLDGLGMDRMYWRDTNTGRLWLPNTPDPQKPPRGFLAPPDELNLTTASLPLLRWYEERFCFVLVTTAEFPRDPGQLLYIPKTYLLGRPPNASLPAPTTVEPTAQPPPAVAPLKGLLHNPTASVLLRSRAWVTFSAVPDPEALTFPRGDNVATASHPSGPRDTPPPRPPVGARRHPTTELDITHLHNASTTWLATRGLLRSPGRYVYFSPSASTWPVGIWTTGELVLGCDAALVRARYGREFMGLVISMHDSPPAEVMVVPAGQTLDRVGDPADENPPGALPGPPGGPRYRVFVLGSLTRADNGSALDALRRVGGYPEEGTNYAQFLSRAYAEFFSGDAGAEQGPRPPLFWRLTGLLATSGFAFVNAAHANGAVCLSDLLGFLAHSRALAGLAARGAAGCAADSVFFNVSVLDPTARLQLEARLQHLVAEILEREQSLALHALGYQLAFVLDSPSAYDAVAPSAAHLIDALYAEFLGGRVLTTPVVHRALFYASAVLRQPFLAGVPSAVQRERARRSLLIASALCTSDVAAATNADLRTALARADHQKTLFWLPDHFSPCAASLRFDLDESVFILDALAQATRSETPVEVLAQQTHGLASTLTRWAHYNALIRAFVPEASHRCGGQSANVEPRILVPITHNASYVVTHSPLPRGIGYKLTGVDVRRPLFLTYLTATCEGSTRDIESKRLVRTQNQRDLGLVGAVFMRYTPAGEVMSVLLVDTDNTQQQIAAGPTEGAPSVFSSDVPSTALLLFPNGTVIHLLAFDTQPVAAIAP,STEYVIRSRVAREVGDILKVPCVPLPSDDLDWRYETPSAINYALIDGIFLRYHCPGLDTVLWDRHAQKAYWVNPFLFVAGFLEDLSHPAFPANTQETETRLALYKEIRQALDSRKQAASHTPVKAGCVNFDYSRTRRCVGRQDLGPTNGTSGRTPVLPPDDEAGLQPKPLTTPPPIIATSDPTPRRDAATKSRRRRPHSRRL
Running AlphaFold prediction
> select clear
> select #2/A:23-96
578 atoms, 594 bonds, 74 residues, 1 model selected
> select clear
> select #2/A:91-253
1287 atoms, 1328 bonds, 163 residues, 1 model selected
> select #1/A:268-307
301 atoms, 312 bonds, 40 residues, 1 model selected
> select #1/A:122-307
1365 atoms, 1409 bonds, 1 pseudobond, 175 residues, 2 models selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-307
2141 atoms, 2211 bonds, 1 pseudobond, 274 residues, 2 models selected
> select clear
> select #2/A:23-196
1383 atoms, 1425 bonds, 174 residues, 1 model selected
> select #1/A:307
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:23-307
2141 atoms, 2211 bonds, 1 pseudobond, 274 residues, 2 models selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-307
2141 atoms, 2211 bonds, 1 pseudobond, 274 residues, 2 models selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-307
2141 atoms, 2211 bonds, 1 pseudobond, 274 residues, 2 models selected
> select clear
> select #2/A
1814 atoms, 1871 bonds, 231 residues, 1 model selected
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/fold_2026_06_06_09_58/fold_2026_06_06_09_58_model_0.cif"
Chain information for fold_2026_06_06_09_58_model_0.cif #4
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select add #4
12294 atoms, 12653 bonds, 1587 residues, 2 models selected
> view matrix models
> #2,0.36377,0.23781,0.90062,43.872,0.2102,0.92097,-0.32808,89.241,-0.90746,0.30866,0.28503,190.55,#4,1,0,0,-16.289,0,1,0,50.225,0,0,1,98.495
> undo
> select add #2
14644 atoms, 15058 bonds, 1887 residues, 2 models selected
> select subtract #2
10480 atoms, 10782 bonds, 1356 residues, 1 model selected
> view matrix models #4,1,0,0,4.4485,0,1,0,35.576,0,0,1,102.19
> ui mousemode right "rotate selected models"
> select #4/A
2884 atoms, 2973 bonds, 369 residues, 1 model selected
> color sel orange
> color sel light sea green
> view matrix models
> #4,0.24289,-0.93407,-0.26177,8.3102,0.05334,-0.25658,0.96505,59.188,-0.96859,-0.24836,-0.012497,90.03
> view matrix models
> #4,0.09999,-0.88225,-0.46003,4.9602,0.17378,-0.43976,0.88114,63.534,-0.9797,-0.16805,0.10934,88.937
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.09999,-0.88225,-0.46003,47.871,0.17378,-0.43976,0.88114,54.91,-0.9797,-0.16805,0.10934,14.194
> view matrix models
> #4,0.09999,-0.88225,-0.46003,80.494,0.17378,-0.43976,0.88114,-8.3546,-0.9797,-0.16805,0.10934,38.841
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.158,-0.8774,-0.453,76.904,0.54173,-0.46058,0.70313,-3.4897,-0.82557,-0.1343,0.54809,41.657
> hide #3 models
> hide #2 models
> show #2 models
> hide #!1 models
> view matrix models
> #4,0.26861,-0.89597,0.35366,85.334,0.68363,0.43598,0.58529,-16.251,-0.6786,0.084561,0.72963,40.677
> view matrix models
> #4,0.92297,0.38397,0.026251,72.848,-0.33111,0.82696,-0.45442,-39.363,-0.19619,0.41073,0.8904,42.511
> view matrix models
> #4,0.92637,0.24512,0.28592,75.858,-0.076039,0.8653,-0.49545,-36.602,-0.36885,0.43723,0.82023,39.523
> view matrix models
> #4,0.84986,-0.07462,0.5217,80.605,0.11277,0.99275,-0.041704,-34.771,-0.5148,0.094273,0.85211,43.112
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.84986,-0.07462,0.5217,91.361,0.11277,0.99275,-0.041704,28.059,-0.5148,0.094273,0.85211,27.063
> view matrix models
> #4,0.84986,-0.07462,0.5217,81.009,0.11277,0.99275,-0.041704,28.768,-0.5148,0.094273,0.85211,21.746
> view matrix models
> #4,0.84986,-0.07462,0.5217,83.359,0.11277,0.99275,-0.041704,32.806,-0.5148,0.094273,0.85211,19.148
> view matrix models
> #4,0.84986,-0.07462,0.5217,82.301,0.11277,0.99275,-0.041704,30.312,-0.5148,0.094273,0.85211,18.515
> view matrix models
> #4,0.84986,-0.07462,0.5217,132.63,0.11277,0.99275,-0.041704,27.48,-0.5148,0.094273,0.85211,19.643
> view matrix models
> #4,0.84986,-0.07462,0.5217,132.65,0.11277,0.99275,-0.041704,27.479,-0.5148,0.094273,0.85211,19.653
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.87465,0.12462,-0.46847,126.98,-0.21551,-0.76567,-0.60605,49.563,-0.43422,0.63104,-0.64284,7.9052
> view matrix models
> #4,0.59262,0.74952,0.295,115.28,-0.33184,0.56089,-0.75848,26.277,-0.73396,0.35159,0.58111,11.759
> view matrix models
> #4,-0.29776,0.93666,-0.18441,98.727,-0.19714,-0.24933,-0.94814,40.567,-0.93407,-0.24596,0.25889,17.681
> view matrix models
> #4,-0.90533,0.41545,0.088159,99.538,-0.18398,-0.19655,-0.96308,39.859,-0.38278,-0.88813,0.25438,35.506
> view matrix models
> #4,-0.90476,0.41564,0.093077,99.557,-0.20036,-0.22248,-0.95413,40.076,-0.37586,-0.8819,0.28457,35.587
> view matrix models
> #4,-0.92106,0.32908,0.20823,101.05,-0.32088,-0.9443,0.073019,52.913,0.22066,0.00043717,0.97535,31.575
> view matrix models
> #4,-0.83131,0.34233,0.43786,102.72,0.5102,0.1575,0.84551,48.827,0.22048,0.92628,-0.30559,13.094
> view matrix models
> #4,-0.90008,0.29772,0.31817,102.15,0.4014,0.2824,0.87128,45.409,0.16954,0.91193,-0.37368,12.434
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.90008,0.29772,0.31817,10.009,0.4014,0.2824,0.87128,47.439,0.16954,0.91193,-0.37368,95.116
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.48538,0.87152,-0.069686,5.387,0.35499,0.26929,0.89525,47.082,0.799,0.40979,-0.44009,111.59
> view matrix models
> #4,-0.49014,0.87138,-0.021454,5.4612,0.21625,0.14541,0.96545,47.368,0.84439,0.46856,-0.25971,111.78
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.49014,0.87138,-0.021454,39.582,0.21625,0.14541,0.96545,44.586,0.84439,0.46856,-0.25971,135.73
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.567,0.81911,-0.087008,39.181,0.17054,0.22007,0.96046,42.749,0.80587,0.52974,-0.26447,134.2
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.567,0.81911,-0.087008,21.464,0.17054,0.22007,0.96046,0.76061,0.80587,0.52974,-0.26447,129.82
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.567,0.81911,-0.087008,34.731,0.17054,0.22007,0.96046,1.7477,0.80587,0.52974,-0.26447,129.65
> view matrix models
> #4,-0.567,0.81911,-0.087008,33.774,0.17054,0.22007,0.96046,1.3656,0.80587,0.52974,-0.26447,128.44
> view matrix models
> #4,-0.567,0.81911,-0.087008,32.654,0.17054,0.22007,0.96046,-2.0226,0.80587,0.52974,-0.26447,124.77
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.65841,0.75266,0.0011663,32.718,0.20605,0.17876,0.96207,-0.86972,0.72391,0.63368,-0.27278,121.96
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.65841,0.75266,0.0011663,24.194,0.20605,0.17876,0.96207,-1.7231,0.72391,0.63368,-0.27278,124.46
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #4
10480 atoms, 10782 bonds, 1356 residues, 1 model selected
> view matrix models
> #4,-0.65841,0.75266,0.0011663,23.598,0.20605,0.17876,0.96207,-1.2638,0.72391,0.63368,-0.27278,122.05
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.66221,0.74929,0.0055796,23.613,0.19732,0.16719,0.96598,-1.1869,0.72287,0.64078,-0.25856,121.96
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1-21
165 atoms, 167 bonds, 21 residues, 1 model selected
> select #4/A:328-369
357 atoms, 368 bonds, 42 residues, 1 model selected
> select #4/A:282-369
684 atoms, 709 bonds, 88 residues, 1 model selected
> select #4/A:326-369
373 atoms, 384 bonds, 44 residues, 1 model selected
> select #4/A
2884 atoms, 2973 bonds, 369 residues, 1 model selected
> color sel hot pink
> select #4/A:324-369
383 atoms, 394 bonds, 46 residues, 1 model selected
> select #4/A:316-369
428 atoms, 439 bonds, 54 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #4/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #4/A:258-369
863 atoms, 892 bonds, 112 residues, 1 model selected
> color sel magenta
> select #4/A:282
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:282-284
18 atoms, 18 bonds, 3 residues, 1 model selected
> color sel yellow
> select clear
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:742-785
311 atoms, 320 bonds, 44 residues, 1 model selected
> select #4/B:604-785
1384 atoms, 1415 bonds, 182 residues, 1 model selected
> select #4/B:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/B:1-100
835 atoms, 867 bonds, 100 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C
Alignment identifier is 4/C
> select #4/C:158-202
354 atoms, 364 bonds, 45 residues, 1 model selected
> select #4/C:158-202
354 atoms, 364 bonds, 45 residues, 1 model selected
> select #4/C:202
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/C:153-202
394 atoms, 405 bonds, 50 residues, 1 model selected
> cartoon hide sel
> select #4/A:281
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:281-294
105 atoms, 110 bonds, 14 residues, 1 model selected
> select #4/A:339
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:315-339
171 atoms, 173 bonds, 25 residues, 1 model selected
> select #4/A:315
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/A:315-369
436 atoms, 447 bonds, 55 residues, 1 model selected
> color sel light gray
> color sel dim gray
> select #4/C
1606 atoms, 1650 bonds, 202 residues, 1 model selected
> color sel cornflower blue
> color sel medium blue
> select clear
> hide #2 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #2 models
> hide #2 models
> show #!1 models
> show #2 models
> select add #1
4912 atoms, 4549 bonds, 6 pseudobonds, 1070 residues, 4 models selected
> cartoon (#!1 & sel)
> hide (#!1 & sel) target a
> select #1/B
2378 atoms, 2211 bonds, 1 pseudobond, 511 residues, 2 models selected
> cartoon hide (#!1 & sel)
> view #1 clip false
[Repeated 1 time(s)]
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select #4/A:369
13 atoms, 13 bonds, 1 residue, 1 model selected
> select #4/A:318-369
416 atoms, 427 bonds, 52 residues, 1 model selected
> select #2/A:239
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:236-239
30 atoms, 29 bonds, 4 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> show #1-2,4 target ab
> hide #1-2,4 target a
> select #2/A:253
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #2/A:104
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/A:104-197
752 atoms, 773 bonds, 94 residues, 1 model selected
> select #2/A:253
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:253
5 atoms, 4 bonds, 1 residue, 1 model selected
> cartoon sel
> select #2/A:253
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/A:239-253
110 atoms, 115 bonds, 15 residues, 1 model selected
> select #2/A:226
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A:226-253
216 atoms, 222 bonds, 28 residues, 1 model selected
> select #1/A:307
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #1/A:282
7 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 5 residues
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
> select #1/A:273-307
264 atoms, 274 bonds, 35 residues, 1 model selected
> select #1/A:280-307
213 atoms, 222 bonds, 28 residues, 1 model selected
> select #1/A:280-307
213 atoms, 222 bonds, 28 residues, 1 model selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-43
164 atoms, 168 bonds, 21 residues, 1 model selected
> select #4/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:1-16
122 atoms, 123 bonds, 16 residues, 1 model selected
> select #2/B:117
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:144
5 atoms, 4 bonds, 1 residue, 1 model selected
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/fold_2026_06_06_11_31/fold_2026_06_06_11_31_model_0.cif"
Chain information for fold_2026_06_06_11_31_model_0.cif #5
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> select add #5
11388 atoms, 11707 bonds, 1472 residues, 2 models selected
> view matrix models
> #2,0.60127,0.541,0.58804,56.627,-0.22726,0.82132,-0.52325,37.621,-0.76605,0.18098,0.61678,94.07,#5,0.87698,0.43171,-0.21104,6.4502,-0.35861,0.8803,0.31059,-3.7435,0.31986,-0.1967,0.92682,-2.8187
> undo
> select add #2
15547 atoms, 15979 bonds, 2002 residues, 2 models selected
> select subtract #2
11383 atoms, 11703 bonds, 1471 residues, 1 model selected
> view matrix models
> #5,0.39144,0.79983,-0.45503,-11.607,0.62821,0.12906,0.76727,13.516,0.67241,-0.58619,-0.45194,2.7463
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.39144,0.79983,-0.45503,-16.038,0.62821,0.12906,0.76727,37.934,0.67241,-0.58619,-0.45194,95.438
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.49733,0.71903,-0.48545,-14.933,0.66739,0.040443,0.74361,38.788,0.55431,-0.6938,-0.45976,95.704
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.49733,0.71903,-0.48545,15.886,0.66739,0.040443,0.74361,16.129,0.55431,-0.6938,-0.45976,111.04
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.56948,0.58711,-0.57532,17.016,0.62545,0.14467,0.76673,15.128,0.53339,-0.79647,-0.28482,112.47
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.56948,0.58711,-0.57532,23.335,0.62545,0.14467,0.76673,10.826,0.53339,-0.79647,-0.28482,113.86
> select clear
> ui mousemode right "rotate selected models"
> select add #5
11383 atoms, 11703 bonds, 1471 residues, 1 model selected
> view matrix models
> #5,0.66759,0.57551,-0.47235,24.337,0.53326,0.073133,0.84278,11.247,0.51957,-0.81452,-0.25808,114.04
> view matrix models
> #5,0.68621,0.53318,-0.49481,24.701,0.5415,0.079758,0.83691,11.211,0.48569,-0.84223,-0.23399,114.19
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.68621,0.53318,-0.49481,22.27,0.5415,0.079758,0.83691,11.107,0.48569,-0.84223,-0.23399,114.6
> select clear
> ui tool show Match→Align
> msa3d #4/A#5/A cutoffDistance 10 maxIterations none minStretch 1 refChain
> #4/A
Match→Align cutoff: 10.0, in column if within cutoff of: any
259 residue pairs aligned
369 fully populated columns
Matching fold_2026_06_06_11_31_model_0.cif chain A onto
fold_2026_06_06_09_58_model_0.cif chain A
RMSD between 369 atom pairs is 20.298 angstroms
221 residue pairs aligned
Iteration 1: 369 fully populated columns
Pairwise RMSDs across all fully populated columns
---
Model | 4 | 5
4 | 0.000 | 20.298
5 | 20.298 | 0.000
Overall RMSD: 20.298
Sequence lengths: 369 369
SDM (cutoff 10.0): -2.981
Q-score: 0.021
Alignment identifier is MA-1
Showing conservation header ("seq_conservation" residue attribute) for
alignment MA-1
Chains used in RMSD evaluation for alignment MA-1:
fold_2026_06_06_09_58_model_0.cif #4/A, fold_2026_06_06_11_31_model_0.cif #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment MA-1
> undo
[Repeated 2 time(s)]
> select clear
> select add #5
11383 atoms, 11703 bonds, 1471 residues, 1 model selected
> view matrix models
> #5,0.68621,0.53318,-0.49481,24.908,0.5415,0.079758,0.83691,10.756,0.48569,-0.84223,-0.23399,114.18
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.59825,0.52338,-0.60677,24.103,0.63826,0.14658,0.75574,10.378,0.48448,-0.8394,-0.24637,114.11
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.59825,0.52338,-0.60677,24.822,0.63826,0.14658,0.75574,9.4171,0.48448,-0.8394,-0.24637,114.11
> select clear
> ui mousemode right "rotate selected models"
> select add #5
11383 atoms, 11703 bonds, 1471 residues, 1 model selected
> view matrix models
> #5,0.49141,0.60491,-0.62658,23.511,0.59595,0.29108,0.74841,7.9584,0.6351,-0.74119,-0.21746,114.17
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.49141,0.60491,-0.62658,22.495,0.59595,0.29108,0.74841,4.0592,0.6351,-0.74119,-0.21746,108.96
> view matrix models
> #5,0.49141,0.60491,-0.62658,22.411,0.59595,0.29108,0.74841,0.39798,0.6351,-0.74119,-0.21746,112.34
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.4967,0.69485,-0.52006,22.096,0.61931,0.13606,0.77327,1.9154,0.60807,-0.70616,-0.36275,111.34
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.4967,0.69485,-0.52006,15.153,0.61931,0.13606,0.77327,12.115,0.60807,-0.70616,-0.36275,110.22
> view matrix models
> #5,0.4967,0.69485,-0.52006,10.651,0.61931,0.13606,0.77327,5.6616,0.60807,-0.70616,-0.36275,111.25
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.53085,0.65082,-0.5428,11.108,0.62316,0.13431,0.77048,5.6853,0.57434,-0.74726,-0.33426,111.53
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.53085,0.65082,-0.5428,20.176,0.62316,0.13431,0.77048,6.334,0.57434,-0.74726,-0.33426,112.41
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.58227,0.57349,-0.57626,20.96,0.6293,0.13083,0.76607,6.3776,0.51473,-0.8087,-0.28471,112.81
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.58227,0.57349,-0.57626,22.667,0.6293,0.13083,0.76607,6.5039,0.51473,-0.8087,-0.28471,112.86
> select clear
> hide #2 models
> hide #!1 models
> show #!1 models
> hide #4 models
> hide #!1 models
> show #2 models
> select add #5
11383 atoms, 11703 bonds, 1471 residues, 1 model selected
> view matrix models
> #5,0.58227,0.57349,-0.57626,22.769,0.6293,0.13083,0.76607,6.5182,0.51473,-0.8087,-0.28471,113.77
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.58243,0.57315,-0.57643,22.772,0.6297,0.1303,0.76583,6.5238,0.51405,-0.80902,-0.28502,113.77
> view matrix models
> #5,0.5885,0.55998,-0.58318,22.887,0.64521,0.10938,0.75613,6.7416,0.48721,-0.82126,-0.29693,113.69
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.5885,0.55998,-0.58318,23.374,0.64521,0.10938,0.75613,7.3675,0.48721,-0.82126,-0.29693,114.95
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.576,0.586,-0.56993,23.142,0.61372,0.15054,0.77504,6.9335,0.53997,-0.79621,-0.27293,115.1
> view matrix models
> #5,0.60318,0.53227,-0.59402,23.64,0.61475,0.16427,0.77142,6.8096,0.50819,-0.83048,-0.22813,115.4
> select clear
Drag select of 20 residues
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> select #5/A:328-369
357 atoms, 368 bonds, 42 residues, 1 model selected
> select #5/A:369
13 atoms, 13 bonds, 1 residue, 1 model selected
> select #5/A:318-369
416 atoms, 427 bonds, 52 residues, 1 model selected
> cartoon hide sel
Drag select of 25 residues
> cartoon hide sel
> select clear
[Repeated 1 time(s)]
> select #5/A:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:253-322
515 atoms, 534 bonds, 70 residues, 1 model selected
> select #5/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:250-322
536 atoms, 555 bonds, 73 residues, 1 model selected
> select #5/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:250-305
416 atoms, 430 bonds, 56 residues, 1 model selected
> select #5/A:250
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:250-297
361 atoms, 374 bonds, 48 residues, 1 model selected
> color sel magenta
[Repeated 1 time(s)]
> select clear
> select #5/A:247
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:246-247
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/A:246-247
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #5/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:1-22
173 atoms, 175 bonds, 22 residues, 1 model selected
> color sel red
> select clear
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-87
500 atoms, 514 bonds, 65 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-86
492 atoms, 506 bonds, 64 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #2/A:114-164
408 atoms, 422 bonds, 51 residues, 1 model selected
> select #2/A:114-253
1107 atoms, 1141 bonds, 140 residues, 1 model selected
> select clear
> select #2/A:23-25
22 atoms, 22 bonds, 3 residues, 1 model selected
> cartoon sel
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-39
138 atoms, 142 bonds, 17 residues, 1 model selected
> select #1/A:73-74
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:73-74
12 atoms, 12 bonds, 2 residues, 1 model selected
> select #1/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:23-37
116 atoms, 118 bonds, 15 residues, 1 model selected
> select #1/A:270-307
288 atoms, 299 bonds, 38 residues, 1 model selected
> select #1/A:271-307
281 atoms, 291 bonds, 37 residues, 1 model selected
> select #1/A:286-307
171 atoms, 179 bonds, 22 residues, 1 model selected
> cartoon #2,5
> cartoon hide #2,5
> undo
Drag select of 25 residues
Drag select of 22 residues
Drag select of 25 residues
> cartoon hide sel
> select clear
[Repeated 2 time(s)]
> select #5/B:14
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:334
4 atoms, 3 bonds, 1 residue, 1 model selected
Drag select of 59 residues
> select #5/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:1-58
456 atoms, 470 bonds, 58 residues, 1 model selected
> hide #2 models
Drag select of 10 residues
> select #5/A:336-369
306 atoms, 317 bonds, 34 residues, 1 model selected
> select #5/A:291-369
623 atoms, 646 bonds, 79 residues, 1 model selected
> select #5/A:283
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:283-369
677 atoms, 701 bonds, 87 residues, 1 model selected
> select #5/A:271
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:271-369
769 atoms, 795 bonds, 99 residues, 1 model selected
> select #5/A:298
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:298-369
562 atoms, 579 bonds, 72 residues, 1 model selected
> cartoon hide sel
Drag select of 13 residues
> cartoon hide sel
> select #5/A:258
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:258-297
301 atoms, 312 bonds, 40 residues, 1 model selected
> select #5/A:245-246
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/A:245-297
401 atoms, 416 bonds, 53 residues, 1 model selected
> color sel magenta
> select clear
> select #5/A:23
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:23-244
1748 atoms, 1800 bonds, 222 residues, 1 model selected
> color sel white
> select clear
> select #5/C
1606 atoms, 1650 bonds, 202 residues, 1 model selected
> color sel medium purple
> select clear
> select #5/B
5990 atoms, 6159 bonds, 785 residues, 1 model selected
> color sel dark magenta
> color sel sky blue
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> ui tool show "Basic Actions"
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV_gD_Nec1_gH-
> gL_AF3.cxs"
Drag select of 1361 residues
> show sel target ab
> surface sel
> select clear
> select #5/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:1-25
195 atoms, 198 bonds, 25 residues, 1 model selected
> select #5/A:22
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:1-22
173 atoms, 175 bonds, 22 residues, 1 model selected
> color sel orange red
> select #5/A:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:245-297
401 atoms, 416 bonds, 53 residues, 1 model selected
> color sel medium orchid
> select clear
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV_gD_Nec1_gH-
> gL_AF3.cxs"
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/fold_2026_06_06_11_31/fold_2026_06_06_11_31_model_2.cif"
Chain information for fold_2026_06_06_11_31_model_2.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> close #6
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/fold_2026_06_06_11_31_next/fold_2026_06_06_11_31_model_0.cif"
Chain information for fold_2026_06_06_11_31_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
> select #6/A
2323 atoms, 2394 bonds, 297 residues, 1 model selected
> color sel orange red
> color sel hot pink
> select clear
> select #6/A:1
9 atoms, 8 bonds, 1 residue, 1 model selected
> open "/Users/kellykeisen/Documents/Current Projects/APEC-x/gD_gH-
> gL_fold_2026_06_06_11_31/fold_2026_06_06_11_31_model_1.cif"
Chain information for fold_2026_06_06_11_31_model_1.cif #7
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select add #7
9671 atoms, 9947 bonds, 1253 residues, 2 models selected
> select add #6
20484 atoms, 21063 bonds, 2651 residues, 2 models selected
> select subtract #6
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> hide #6 models
> view matrix models
> #7,-0.37165,0.92319,0.097987,14.294,-0.88316,-0.31905,-0.34385,-8.9083,-0.28618,-0.21433,0.9339,-0.8697
> view matrix models
> #7,-0.49008,0.72506,0.48385,16.632,-0.84493,-0.25867,-0.46817,-9.6884,-0.2143,-0.63826,0.73939,-6.1101
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.49008,0.72506,0.48385,50.421,-0.84493,-0.25867,-0.46817,-25.748,-0.2143,-0.63826,0.73939,108.73
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.26732,0.87771,-0.3977,40.515,-0.89538,0.37878,0.23411,-14.631,0.35612,0.29351,0.88715,114.46
> view matrix models
> #7,0.24624,0.31663,-0.91603,31.89,-0.60105,0.79133,0.11196,-13.894,0.76033,0.52301,0.38517,110.03
> view matrix models
> #7,0.16891,0.35004,-0.92138,32.46,-0.58657,0.78695,0.19143,-13.315,0.79209,0.50812,0.33825,109.37
> view matrix models
> #7,0.16243,0.34637,-0.92393,32.44,-0.5947,0.78155,0.18844,-13.344,0.78737,0.51885,0.33293,109.43
> view matrix models
> #7,-0.03624,0.43061,-0.90181,34.2,-0.52638,0.75885,0.3835,-12.168,0.84948,0.48859,0.19916,107.76
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.03624,0.43061,-0.90181,18.013,-0.52638,0.75885,0.3835,-3.8286,0.84948,0.48859,0.19916,111.09
> view matrix models
> #7,-0.03624,0.43061,-0.90181,18.377,-0.52638,0.75885,0.3835,-4.4115,0.84948,0.48859,0.19916,111.26
> select clear
Drag select of fold_2026_06_06_11_31_model_0.cif_A SES surface, 312529 of
431760 triangles, fold_2026_06_06_11_31_model_0.cif_B SES surface,
fold_2026_06_06_11_31_model_0.cif_C SES surface, 202221 of 273838 triangles,
fold_2026_06_06_11_31_model_0.cif_D SES surface, 6469 atoms, 2613 residues,
5492 bonds
> surface hidePatches (#7#!5 & sel)
> hide (#7#!5 & sel) target a
> select clear
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> view matrix models
> #7,-0.03624,0.43061,-0.90181,15.557,-0.52638,0.75885,0.3835,15.118,0.84948,0.48859,0.19916,112.43
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.29172,0.31483,-0.9032,13.13,-0.66721,0.74359,0.043702,12.751,0.68537,0.58987,0.42698,115.92
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.29172,0.31483,-0.9032,24.063,-0.66721,0.74359,0.043702,-6.6984,0.68537,0.58987,0.42698,111.91
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.021049,0.90148,-0.43231,34.035,-0.94112,0.12807,0.31287,-7.8249,0.33741,0.41344,0.84571,115.76
> view matrix models
> #7,-0.018417,0.89076,-0.4541,33.754,-0.92834,0.15342,0.33859,-7.4707,0.37127,0.4278,0.8241,115.53
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.018417,0.89076,-0.4541,22.137,-0.92834,0.15342,0.33859,8.6756,0.37127,0.4278,0.8241,120.49
> view matrix models
> #7,-0.018417,0.89076,-0.4541,22.41,-0.92834,0.15342,0.33859,8.6019,0.37127,0.4278,0.8241,119.93
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.0071594,0.85236,-0.5229,21.476,-0.94867,0.15956,0.27308,8.1832,0.3162,0.49802,0.80746,120.59
> select clear
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> view matrix models
> #7,0.033477,0.83989,-0.54173,21.03,-0.96542,0.16739,0.19985,7.6948,0.25853,0.51631,0.81645,121.07
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.033477,0.83989,-0.54173,21.715,-0.96542,0.16739,0.19985,4.5361,0.25853,0.51631,0.81645,119.47
> select clear
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> view matrix models
> #7,0.033477,0.83989,-0.54173,23.864,-0.96542,0.16739,0.19985,3.4836,0.25853,0.51631,0.81645,120.1
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.02309,0.84981,-0.52658,24.118,-0.95736,0.17051,0.2332,3.7552,0.28797,0.49874,0.81752,119.83
> select clear
> ui mousemode right "rotate selected models"
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> view matrix models
> #7,0.021059,0.87617,-0.48155,24.714,-0.94572,0.17369,0.27468,4.08,0.3243,0.44962,0.83226,119.41
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.021059,0.87617,-0.48155,23.88,-0.94572,0.17369,0.27468,3.2054,0.3243,0.44962,0.83226,118.85
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.011908,0.86597,-0.49996,23.798,-0.94381,0.15542,0.29168,3.2021,0.33028,0.47534,0.81545,118.88
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.011908,0.86597,-0.49996,22.031,-0.94381,0.15542,0.29168,3.9104,0.33028,0.47534,0.81545,118.43
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.028592,0.86035,-0.5089,21.99,-0.94252,0.14635,0.30038,3.9095,0.33291,0.48824,0.80672,118.44
> select clear
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> view matrix models
> #7,-0.077408,0.88628,-0.45664,22.863,-0.93984,0.087985,0.33008,3.7048,0.33272,0.45472,0.82615,118.35
> view matrix models
> #7,-0.11006,0.90064,-0.4204,23.435,-0.93634,0.047927,0.34781,3.5338,0.3334,0.43192,0.83803,118.28
> view matrix models
> #7,-0.10671,0.90214,-0.41804,23.451,-0.93693,0.049509,0.34601,3.5332,0.33284,0.42859,0.83996,118.27
> view matrix models
> #7,-0.12052,0.90067,-0.41746,23.509,-0.94972,0.017806,0.31259,3.0647,0.28898,0.43415,0.85324,118.63
> select clear
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.12052,0.90067,-0.41746,24.083,-0.94972,0.017806,0.31259,4.4375,0.28898,0.43415,0.85324,119.87
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.11597,0.89022,-0.44053,23.784,-0.95942,0.014374,0.28161,4.1914,0.25702,0.45531,0.85243,120.18
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.11597,0.89022,-0.44053,23.325,-0.95942,0.014374,0.28161,3.065,0.25702,0.45531,0.85243,119.13
> view matrix models
> #7,-0.11597,0.89022,-0.44053,21.028,-0.95942,0.014374,0.28161,4.6432,0.25702,0.45531,0.85243,118.17
> select clear
> select add #7
9662 atoms, 9939 bonds, 1252 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.10202,0.89402,-0.43626,21.029,-0.96186,0.023234,0.27255,4.6448,0.2538,0.44742,0.85755,118.17
> select clear
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> select add #6
10822 atoms, 11124 bonds, 1399 residues, 1 model selected
> view matrix models
> #6,0.93553,-0.0082116,0.35316,2.9825,0.35248,-0.044396,-0.93477,-16.866,0.023355,0.99898,-0.038639,-0.56802
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.93553,-0.0082116,0.35316,27.112,0.35248,-0.044396,-0.93477,-21.452,0.023355,0.99898,-0.038639,64.552
> view matrix models
> #6,0.93553,-0.0082116,0.35316,43.344,0.35248,-0.044396,-0.93477,-23.427,0.023355,0.99898,-0.038639,100.59
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.10541,-0.21123,-0.97174,38.307,-0.84961,-0.48867,0.19839,-10.827,-0.51677,0.84651,-0.12795,102.11
> view matrix models
> #6,-0.8849,-0.46233,0.056544,48.95,0.3494,-0.57861,0.73697,-14.813,-0.30801,0.6719,0.67356,105.55
> view matrix models
> #6,0.18166,-0.65227,0.7359,46.095,0.91865,-0.15442,-0.36364,-23.432,0.35082,0.7421,0.57115,101.26
> view matrix models
> #6,-0.12679,-0.99193,0.0011837,39.979,0.71899,-0.092723,-0.68881,-24.189,0.68336,-0.086481,0.72495,94.264
> view matrix models
> #6,-0.84048,-0.48177,-0.24796,46.251,0.24695,-0.74794,0.61612,-16.338,-0.48229,0.45661,0.7476,105.59
> view matrix models
> #6,-0.38691,-0.5212,-0.76069,39.333,-0.51198,-0.56468,0.64731,-10.095,-0.76693,0.63991,-0.048361,102.72
> view matrix models
> #6,-0.58746,-0.24734,-0.77053,42.508,-0.58012,-0.53514,0.61408,-9.7082,-0.56422,0.80774,0.17088,104.36
> view matrix models
> #6,-0.56706,-0.19925,-0.79921,42.523,-0.52136,-0.66436,0.53555,-11.61,-0.63767,0.72037,0.27285,104.93
> view matrix models
> #6,-0.57817,-0.22013,-0.78566,42.538,-0.5335,-0.62656,0.56815,-11.012,-0.61733,0.74764,0.24482,104.8
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.57817,-0.22013,-0.78566,35.455,-0.5335,-0.62656,0.56815,1.4812,-0.61733,0.74764,0.24482,115.01
> view matrix models
> #6,-0.57817,-0.22013,-0.78566,33.698,-0.5335,-0.62656,0.56815,-4.3849,-0.61733,0.74764,0.24482,112.69
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.56545,-0.22014,-0.79486,33.55,-0.52882,-0.6428,0.55422,-4.6377,-0.63294,0.73372,0.24705,112.7
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view matrix models
> #6,-0.67978,-0.72381,0.1183,37.386,0.73136,-0.65692,0.18321,-15.259,-0.054892,0.21106,0.97593,110.76
> view matrix models
> #6,0.2422,-0.96408,-0.10906,28.252,-0.11293,0.083633,-0.99008,-13.414,0.96363,0.25211,-0.088618,96.831
> view matrix models
> #6,0.091044,-0.37264,-0.9235,27.433,-0.99108,0.056717,-0.12059,-1.7041,0.097316,0.92624,-0.36416,105.05
> view matrix models
> #6,-0.58739,-0.21042,-0.78147,33.857,-0.59734,-0.53877,0.59406,-3.152,-0.54604,0.81575,0.19078,112.35
> select subtract #6
Nothing selected
> select add #6
10822 atoms, 11124 bonds, 1399 residues, 1 model selected
> hide #6 models
> select subtract #6
Nothing selected
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/fold_2026_06_06_11_31_next/fold_2026_06_06_11_31_model_0.cif"
Chain information for fold_2026_06_06_11_31_model_0.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
Computing secondary structure
Drag select of 18 residues
Drag select of 14 residues
Drag select of 6 residues
Drag select of 27 residues
Drag select of 30 residues
> cartoon hide sel
> select add #8
10822 atoms, 11124 bonds, 1399 residues, 1 model selected
> view matrix models
> #8,0.69932,-0.71189,-0.064444,-3.0499,0.47016,0.52601,-0.7087,-2.531,0.53842,0.46531,0.70256,1.7383
> view matrix models
> #8,0.73125,-0.31499,-0.60503,2.6137,0.56783,0.77257,0.28408,-6.7037,0.37795,-0.55128,0.7438,-4.9912
> view matrix models
> #8,0.72136,-0.52108,-0.45619,0.34763,0.68979,0.59942,0.40607,-9.3906,0.06185,-0.60759,0.79184,-3.7265
> view matrix models
> #8,0.90492,0.089204,-0.41613,3.5002,0.41554,0.025973,0.9092,-14.664,0.091913,-0.99567,-0.013564,-2.3979
> view matrix models
> #8,-0.42464,0.53857,-0.72776,16.665,0.88456,0.41814,-0.20669,-8.5952,0.19299,-0.73151,-0.65395,2.4049
> view matrix models
> #8,-0.50149,0.25775,0.82588,6.6325,-0.20771,0.8908,-0.40414,2.6646,-0.83986,-0.37422,-0.39319,9.962
> view matrix models
> #8,-0.34676,0.023827,0.93765,3.3522,-0.12008,0.99032,-0.069571,1.0435,-0.93024,-0.13671,-0.34054,11.981
> view matrix models
> #8,-0.45084,0.23199,0.86193,5.936,0.0091839,0.96679,-0.25541,1.0856,-0.89256,-0.10724,-0.438,12.496
> view matrix models
> #8,-0.19374,0.98067,-0.02757,14.703,-0.93155,-0.1927,-0.30834,-1.3958,-0.30769,-0.034054,0.95088,1.9046
> view matrix models
> #8,-0.36705,0.081332,-0.92664,14.022,-0.48524,-0.86663,0.11614,-11.406,-0.79361,0.49227,0.35756,11.987
> view matrix models
> #8,-0.41441,0.014889,-0.90997,13.733,-0.46939,-0.86011,0.19969,-11.909,-0.7797,0.50989,0.36343,11.999
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.41441,0.014889,-0.90997,44.699,-0.46939,-0.86011,0.19969,-22.993,-0.7797,0.50989,0.36343,109.73
> view matrix models
> #8,-0.41441,0.014889,-0.90997,18.014,-0.46939,-0.86011,0.19969,15.95,-0.7797,0.50989,0.36343,113.04
> view matrix models
> #8,-0.41441,0.014889,-0.90997,18.084,-0.46939,-0.86011,0.19969,15.806,-0.7797,0.50989,0.36343,113.04
> view matrix models
> #8,-0.41441,0.014889,-0.90997,22.04,-0.46939,-0.86011,0.19969,9.6918,-0.7797,0.50989,0.36343,112.68
> view matrix models
> #8,-0.41441,0.014889,-0.90997,24.839,-0.46939,-0.86011,0.19969,10.438,-0.7797,0.50989,0.36343,117.37
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.48056,0.21122,-0.85115,26.372,-0.71162,-0.66113,0.23772,13.185,-0.51251,0.71993,0.46801,116.7
> view matrix models
> #8,-0.46514,0.14929,-0.87256,25.937,-0.66525,-0.70924,0.23328,12.57,-0.58403,0.68898,0.42921,117.13
> select clear
> select add #8
10822 atoms, 11124 bonds, 1399 residues, 1 model selected
> view matrix models
> #8,-0.55822,-0.16087,-0.81395,23.905,-0.63771,-0.54439,0.54494,11.924,-0.53077,0.82326,0.2013,119.03
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.55822,-0.16087,-0.81395,31.029,-0.63771,-0.54439,0.54494,8.45,-0.53077,0.82326,0.2013,115.76
> view matrix models
> #8,-0.55822,-0.16087,-0.81395,9.091,-0.63771,-0.54439,0.54494,38.885,-0.53077,0.82326,0.2013,127.27
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.60948,-0.40945,-0.67889,-0.64199,-0.79279,-0.30993,-0.52481,47.373,0.0044793,0.85807,-0.51351,128.12
> view matrix models
> #8,0.77623,-0.11868,-0.61918,0.15273,-0.54742,-0.61405,-0.56857,43.863,-0.31273,0.78029,-0.54162,129.65
> view matrix models
> #8,-0.0032409,0.089726,-0.99596,8.5188,-0.86219,-0.50479,-0.042671,43.745,-0.50658,0.85857,0.078996,128.04
> view matrix models
> #8,-0.14095,-0.12872,-0.98161,7.6768,-0.93342,-0.31317,0.1751,44.412,-0.32995,0.94093,-0.076003,128.41
> view matrix models
> #8,-0.26125,-0.15244,-0.95316,8.0859,-0.88043,-0.36717,0.30004,43.011,-0.39571,0.91758,-0.038287,128.43
> select clear
> select #7/A
2323 atoms, 2394 bonds, 297 residues, 1 model selected
> select #8/A
2323 atoms, 2394 bonds, 297 residues, 1 model selected
> color sel orange
> color sel light sea green
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.26125,-0.15244,-0.95316,18.154,-0.88043,-0.36717,0.30004,5.3774,-0.39571,0.91758,-0.038287,112.83
> view matrix models
> #8,-0.26125,-0.15244,-0.95316,20.466,-0.88043,-0.36717,0.30004,7.3574,-0.39571,0.91758,-0.038287,111.76
> view matrix models
> #8,-0.26125,-0.15244,-0.95316,22.11,-0.88043,-0.36717,0.30004,5.6271,-0.39571,0.91758,-0.038287,112.44
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.2132,-0.049604,-0.97575,22.696,-0.8845,-0.4144,0.21433,5.7695,-0.41498,0.90874,0.044473,112.04
> view matrix models
> #8,-0.18685,-0.071355,-0.97979,22.396,-0.87726,-0.43677,0.1991,5.6429,-0.44215,0.89674,0.019011,112.26
> view matrix models
> #8,-0.22416,-0.053859,-0.97306,22.717,-0.85809,-0.46242,0.22326,5.205,-0.46199,0.88502,0.057439,112.08
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.22416,-0.053859,-0.97306,23.982,-0.85809,-0.46242,0.22326,6.28,-0.46199,0.88502,0.057439,112.42
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.23691,-0.037376,-0.97081,24.17,-0.86927,-0.43811,0.22899,6.4966,-0.43388,0.89815,0.071301,112.27
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.23691,-0.037376,-0.97081,23.752,-0.86927,-0.43811,0.22899,6.1758,-0.43388,0.89815,0.071301,113.42
> select clear
> hide #!5 models
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/fold_2026_06_06_11_31_next/HSV1_gD_HVEM_1JMA.cif"
HSV1_gD_HVEM_1JMA.cif title:
Crystal structure of the herpes simplex virus glycoprotein D bound to the
cellular receptor hvea/hvem [more info...]
Chain information for HSV1_gD_HVEM_1JMA.cif #9
---
Chain | Description | UniProt
A | GLYCOPROTEIN D | VGLD_HSV1P 1-285
B | HERPESVIRUS ENTRY MEDIATOR | TR14_HUMAN 1-161
Non-standard residues in HSV1_gD_HVEM_1JMA.cif #9
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SO4 — sulfate ion
18 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #9
2867 atoms, 2899 bonds, 1 pseudobond, 415 residues, 3 models selected
> view matrix models #9,1,0,0,39.187,0,1,0,-27.043,0,0,1,34.551
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.78849,0.53347,-0.30609,0.84553,-0.0080469,0.50657,0.86216,12.989,0.61499,-0.67734,0.40372,75.461
> view matrix models
> #9,-0.85692,0.35099,0.37748,-12.107,-0.047932,0.6749,-0.73635,-21.105,-0.51321,-0.64909,-0.56151,36.589
> hide #!9 models
> show #!9 models
> hide #8 models
> show #7 models
> view matrix models
> #9,-0.25811,0.70118,-0.66463,-34.975,0.93685,0.34969,0.0050843,27.911,0.23598,-0.62135,-0.74716,47.428
> view matrix models
> #9,0.98249,-0.014387,0.18573,42.415,-0.16796,-0.49968,0.84977,65.153,0.080581,-0.86609,-0.49335,61.613
> view matrix models
> #9,0.43625,-0.62316,-0.64912,52.462,0.025691,-0.71247,0.70123,78.596,-0.89946,-0.32259,-0.2948,14.741
> view matrix models
> #9,0.65543,-0.41474,-0.63119,45.653,0.15593,-0.74342,0.6504,82.178,-0.73899,-0.52471,-0.42259,27.235
> view matrix models
> #9,0.6633,-0.35966,-0.65626,42.393,0.14859,-0.79618,0.58653,83.985,-0.73346,-0.48656,-0.47466,24.458
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.6633,-0.35966,-0.65626,95.076,0.14859,-0.79618,0.58653,70.837,-0.73346,-0.48656,-0.47466,97.88
> view matrix models
> #9,0.6633,-0.35966,-0.65626,92.032,0.14859,-0.79618,0.58653,77.654,-0.73346,-0.48656,-0.47466,99.061
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.70977,-0.57654,-0.40476,108.73,-0.33387,-0.78128,0.52739,66.182,-0.62028,-0.23919,-0.74702,83.598
> view matrix models
> #9,-0.089097,-0.96055,-0.26345,115.9,-0.60695,-0.15736,0.77901,29.968,-0.78973,0.22931,-0.56898,56.962
> view matrix models
> #9,0.24235,-0.89043,-0.38524,116.9,-0.73237,-0.42833,0.52931,38.652,-0.63632,0.15386,-0.75592,61.429
> view matrix models
> #9,0.052043,-0.9041,-0.42415,113.22,-0.67863,-0.34361,0.64915,36.857,-0.73263,0.25406,-0.63143,55.813
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.052043,-0.9041,-0.42415,68.338,-0.67863,-0.34361,0.64915,30.947,-0.73263,0.25406,-0.63143,45.747
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.95545,-0.11584,0.27146,53.512,0.11522,-0.70039,-0.7044,46.404,0.27173,0.7043,-0.65584,40.83
> view matrix models
> #9,-0.74261,0.56405,0.36109,-17.055,0.26209,-0.25141,0.93172,49.128,0.61632,0.78654,0.038867,53.685
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.74261,0.56405,0.36109,10.003,0.26209,-0.25141,0.93172,52.176,0.61632,0.78654,0.038867,35.729
> view matrix models
> #9,-0.74261,0.56405,0.36109,9.8542,0.26209,-0.25141,0.93172,51.406,0.61632,0.78654,0.038867,41.884
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.78386,0.55471,0.27904,8.3041,0.19481,-0.20701,0.95875,47.998,0.58959,0.80588,0.054205,40.505
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.78386,0.55471,0.27904,5.9439,0.19481,-0.20701,0.95875,46.562,0.58959,0.80588,0.054205,40.145
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.79285,0.50523,0.34077,9.4213,0.27074,-0.20894,0.9397,47.92,0.54597,0.83731,0.028873,37.146
> view matrix models
> #9,-0.62554,0.67902,0.38423,3.8588,0.40007,-0.14363,0.90516,46.41,0.6698,0.71994,-0.18181,42.974
> view matrix models
> #9,-0.65712,0.67089,0.34367,3.0604,0.33794,-0.14534,0.92988,45.619,0.67379,0.72718,-0.13121,43.414
> view matrix models
> #9,-0.62335,0.67981,0.38639,3.892,0.13524,-0.39297,0.90955,54.891,0.77016,0.61922,0.15302,55.592
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.62335,0.67981,0.38639,0.26649,0.13524,-0.39297,0.90955,52.079,0.77016,0.61922,0.15302,52.874
> view matrix models
> #9,-0.62335,0.67981,0.38639,0.562,0.13524,-0.39297,0.90955,55.253,0.77016,0.61922,0.15302,54.263
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.53356,0.62287,0.57214,8.3114,0.23504,-0.54063,0.80776,63.901,0.81244,0.56547,0.14206,57.923
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.53356,0.62287,0.57214,9.3496,0.23504,-0.54063,0.80776,71.744,0.81244,0.56547,0.14206,57.286
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.48005,0.36583,0.79732,28.01,0.22994,-0.82464,0.51681,82.963,0.84657,0.43143,0.31175,67.927
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.48005,0.36583,0.79732,25.919,0.22994,-0.82464,0.51681,84.08,0.84657,0.43143,0.31175,66.591
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.55855,0.31475,0.76743,26.704,0.27271,-0.80409,0.52827,83.983,0.78336,0.50435,0.36329,62.058
> view matrix models
> #9,-0.54569,0.2542,0.7985,30.775,0.25659,-0.85643,0.44799,85.343,0.79774,0.44935,0.40212,65.97
> view matrix models
> #9,-0.4919,0.23706,0.83776,33.399,0.30439,-0.85467,0.42058,85.801,0.81571,0.46188,0.34825,64.833
> view matrix models
> #9,-0.46587,0.2758,0.84077,31.831,0.26859,-0.86128,0.43135,85.604,0.84311,0.42677,0.32716,67.01
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.46587,0.2758,0.84077,29.335,0.26859,-0.86128,0.43135,87.72,0.84311,0.42677,0.32716,66.523
> view matrix models
> #9,-0.46587,0.2758,0.84077,28.066,0.26859,-0.86128,0.43135,87.973,0.84311,0.42677,0.32716,67.614
> view matrix models
> #9,-0.46587,0.2758,0.84077,29.397,0.26859,-0.86128,0.43135,88.12,0.84311,0.42677,0.32716,65.846
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.39419,0.35662,0.84702,26.477,0.20128,-0.86576,0.45819,87.409,0.89672,0.3511,0.26949,70.245
> view matrix models
> #9,-0.53919,0.4673,0.70064,15.233,-0.025828,-0.84072,0.54085,82.671,0.84179,0.27353,0.46538,76.359
> view matrix models
> #9,-0.58622,0.41938,0.69316,16.816,0.0095628,-0.85195,0.52353,83.748,0.8101,0.31353,0.49542,73.959
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.58622,0.41938,0.69316,19.262,0.0095628,-0.85195,0.52353,83.919,0.8101,0.31353,0.49542,72.531
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.63591,0.36162,0.6818,21.276,0.051244,-0.8617,0.50483,85.02,0.77006,0.35596,0.52943,69.888
> select clear
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> show #8 models
> select add #9
2867 atoms, 2899 bonds, 1 pseudobond, 415 residues, 3 models selected
> hide #8 models
> view matrix models
> #9,-0.64926,0.3325,0.68403,22.648,0.086576,-0.86122,0.50081,85.648,0.75562,0.38438,0.53037,68.04
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.64926,0.3325,0.68403,24.907,0.086576,-0.86122,0.50081,83.834,0.75562,0.38438,0.53037,67.226
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.65045,0.33249,0.68291,24.867,0.08514,-0.86152,0.50054,83.818,0.75476,0.38372,0.53207,67.27
> view matrix models
> #9,-0.67867,0.33254,0.65485,23.872,0.050359,-0.86846,0.4932,83.387,0.73272,0.3677,0.57265,68.318
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.67867,0.33254,0.65485,24.54,0.050359,-0.86846,0.4932,84.339,0.73272,0.3677,0.57265,69.135
> select clear
> ui mousemode right "rotate selected models"
> select add #9
2867 atoms, 2899 bonds, 1 pseudobond, 415 residues, 3 models selected
> view matrix models
> #9,-0.67726,0.34584,0.64939,23.752,0.027139,-0.87029,0.49179,83.949,0.73524,0.35069,0.58003,70.236
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.67726,0.34584,0.64939,23.836,0.027139,-0.87029,0.49179,85.152,0.73524,0.35069,0.58003,69.9
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.67974,0.34466,0.64743,23.822,0.027971,-0.86989,0.49245,85.157,0.73292,0.35285,0.58165,69.758
> view matrix models
> #9,-0.6894,0.35022,0.63409,23.119,0.012897,-0.86928,0.49414,84.844,0.72426,0.34884,0.59477,70.001
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.6894,0.35022,0.63409,23.21,0.012897,-0.86928,0.49414,84.541,0.72426,0.34884,0.59477,69.587
> select clear
> show #2 models
> hide #2 models
> show #!1 models
> hide #!9 models
> show #!9 models
> hide #7 models
> select #9/B
743 atoms, 759 bonds, 1 pseudobond, 106 residues, 2 models selected
> color (#!9 & sel) yellow
> select clear
> show #2 models
> hide #2 models
> hide #!1 models
> show #7 models
> hide #7 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV_gD_Nec1_HVEM_gH-gL_AF3.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #5/B
Alignment identifier is 5/B
> select #5/B:785
8 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/B:733-785
381 atoms, 390 bonds, 53 residues, 1 model selected
> select #5/B:779
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/B:779-784
37 atoms, 37 bonds, 6 residues, 1 model selected
> open "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV2_gD_gH-
> gL_fold_2026_06_06_11_31/fold_2026_06_06_11_31_model_0.cif"
Chain information for fold_2026_06_06_11_31_model_0.cif #10
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> select add #10
9798 atoms, 10073 bonds, 1273 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.68287,0.5097,-0.52335,26.781,0.52225,0.16033,0.83758,3.0155,0.51082,-0.84528,-0.15671,115.41,#10,0.99407,0.0998,0.043119,-2.3742,-0.097193,0.99353,-0.058825,5.3359,-0.048711,0.054285,0.99734,1.1021
> view matrix models
> #5,0.62303,0.48704,-0.61207,27.094,0.59243,0.21713,0.77581,3.5628,0.51075,-0.84596,-0.15326,115.43,#10,0.99862,-0.0091543,0.051765,-2.4245,0.012067,0.99834,-0.056239,2.9692,-0.051165,0.056786,0.99707,1.1866
> view matrix models
> #5,0.66507,0.50057,-0.55417,27.047,0.53971,0.19071,0.81997,2.3329,0.51614,-0.84443,-0.14333,115.5,#10,0.99679,0.063578,0.048683,-2.5678,-0.06003,0.99566,-0.071169,5.1849,-0.052996,0.068018,0.99628,1.3164
> select add #5
21144 atoms, 21739 bonds, 2738 residues, 3 models selected
> select subtract #5
9761 atoms, 10036 bonds, 1267 residues, 5 models selected
> view matrix models
> #10,0.29921,0.16952,-0.93901,-13.766,0.94219,0.10304,0.31883,18.389,0.1508,-0.98013,-0.12889,0.62612
> view matrix models
> #10,-0.20488,0.77023,-0.60397,-17.135,0.72202,-0.29769,-0.62456,12.928,-0.66084,-0.56403,-0.49513,-8.1154
> view matrix models
> #10,-0.069399,0.49853,-0.86409,-16.8,0.96765,-0.17697,-0.17981,16.459,-0.24256,-0.84862,-0.47012,-4.4381
> view matrix models
> #10,-0.34746,0.18005,-0.92025,-15.647,0.91015,0.3009,-0.28477,11.709,0.22563,-0.93651,-0.26842,-0.65279
> view matrix models
> #10,0.28362,-0.95007,-0.13006,1.6212,-0.50228,-0.031646,-0.86413,5.1586,0.81687,0.31042,-0.48618,-10.335
> view matrix models
> #10,0.036089,-0.92195,-0.38563,-1.4847,-0.81855,0.1941,-0.54064,5.1621,0.57329,0.33517,-0.74766,-13.452
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.036089,-0.92195,-0.38563,18.979,-0.81855,0.1941,-0.54064,24.511,0.57329,0.33517,-0.74766,113.28
> hide #!5 models
> show #!5 models
> hide #!9 models
> view matrix models
> #10,0.036089,-0.92195,-0.38563,26.764,-0.81855,0.1941,-0.54064,22.361,0.57329,0.33517,-0.74766,120.63
> view matrix models
> #10,0.036089,-0.92195,-0.38563,33.389,-0.81855,0.1941,-0.54064,-4.0947,0.57329,0.33517,-0.74766,123.11
> view matrix models
> #10,0.036089,-0.92195,-0.38563,34.544,-0.81855,0.1941,-0.54064,-6.1934,0.57329,0.33517,-0.74766,114.67
> view matrix models
> #10,0.036089,-0.92195,-0.38563,31.519,-0.81855,0.1941,-0.54064,-9.9676,0.57329,0.33517,-0.74766,116.27
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.023481,-0.97323,-0.22863,33.192,-0.9246,0.06584,-0.37522,-7.9115,0.38023,0.2202,-0.8983,115.32
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.023481,-0.97323,-0.22863,22.912,-0.9246,0.06584,-0.37522,-5.965,0.38023,0.2202,-0.8983,115.15
> view matrix models
> #10,0.023481,-0.97323,-0.22863,23.138,-0.9246,0.06584,-0.37522,-5.7039,0.38023,0.2202,-0.8983,115.13
> view matrix models
> #10,0.023481,-0.97323,-0.22863,25.08,-0.9246,0.06584,-0.37522,0.48076,0.38023,0.2202,-0.8983,121.07
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.032027,-0.96794,-0.24913,24.893,-0.91821,0.06996,-0.38987,0.3456,0.3948,0.24124,-0.88653,121.04
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.032027,-0.96794,-0.24913,22.89,-0.91821,0.06996,-0.38987,-1.0655,0.3948,0.24124,-0.88653,123.64
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.013366,-0.98991,-0.14104,23.909,-0.94385,0.034077,-0.32862,-0.35286,0.33011,0.13751,-0.93387,123.85
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.013366,-0.98991,-0.14104,23.462,-0.94385,0.034077,-0.32862,-0.9068,0.33011,0.13751,-0.93387,122.59
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.055173,-0.99743,-0.04575,24.444,-0.92232,-0.03336,-0.38498,-0.79153,0.38246,0.063437,-0.92179,123.42
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.055173,-0.99743,-0.04575,23.33,-0.92232,-0.03336,-0.38498,1.0679,0.38246,0.063437,-0.92179,120.72
> select clear
> select #10/A
2462 atoms, 2540 bonds, 314 residues, 1 model selected
> color sel white
> hide #!5 models
Drag select of 20 residues
> cartoon hide sel
> show #!5 models
> select add #10
9761 atoms, 10036 bonds, 1267 residues, 1 model selected
> view matrix models
> #10,0.055173,-0.99743,-0.04575,24.582,-0.92232,-0.03336,-0.38498,1.9329,0.38246,0.063437,-0.92179,120.97
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.064527,-0.9957,-0.066438,24.419,-0.91796,-0.033114,-0.39528,1.8573,0.39138,0.086494,-0.91616,120.79
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.064527,-0.9957,-0.066438,23.027,-0.91796,-0.033114,-0.39528,1.1857,0.39138,0.086494,-0.91616,120.37
> select clear
> select add #10
9761 atoms, 10036 bonds, 1267 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #10,0.088344,-0.99593,-0.017984,23.507,-0.89375,-0.071283,-0.44286,1.2719,0.43978,0.055197,-0.89641,121.02
> ui mousemode right "translate selected models"
> view matrix models
> #10,0.088344,-0.99593,-0.017984,22.678,-0.89375,-0.071283,-0.44286,0.80328,0.43978,0.055197,-0.89641,119.92
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #10 models
> show #10 models
> hide #10 models
> show #10 models
> select #10/C
1359 atoms, 1393 bonds, 170 residues, 1 model selected
> color sel light sea green
> hide #!5 models
> select clear
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV2_gD_gH-
> gL_AF3.cxs"
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV2_gD_gH-
> gL_AF3.png" width 2000 height 2902 supersample 3
> hide #10 models
> show #!9 models
> hide #!9 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!5 models
> hide #!5 models
> show #6 models
> hide #6 models
> show #7 models
> select #6/A
2323 atoms, 2394 bonds, 297 residues, 1 model selected
> select #7/A
2323 atoms, 2394 bonds, 297 residues, 1 model selected
> color sel white
> select #7/C
1349 atoms, 1386 bonds, 170 residues, 1 model selected
> color sel light sea green
> select #7/B
5990 atoms, 6159 bonds, 785 residues, 1 model selected
> color sel purple
> select clear
> select #7/A
2323 atoms, 2394 bonds, 297 residues, 1 model selected
> surface sel
> select clear
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV1_gD_gH-
> gL_AF3.png" width 1000 height 1451 supersample 3
> hide #!7 models
> show #10 models
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV2_gD_gH-
> gL_AF3.png" width 1000 height 1451 supersample 3
> hide #10 models
> show #!7 models
> surface hidePatches #7
> save "/Users/kellykeisen/Documents/Current Projects/APEC-x/HSV1_gD_gH-
> gL_AF3.png" width 1000 height 1451 supersample 3
> hide #!7 models
> show #!5 models
> hide #!5 models
> show #!1 models
> show #!5 models
> hide #!5 models
> open "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV1_gD_full_ecto_fold_2026_06_06_11_31/fold_2026_06_06_11_31_model_0.cif"
Chain information for fold_2026_06_06_11_31_model_0.cif #11
---
Chain | Description
A | .
Computing secondary structure
> select add #11
2449 atoms, 2526 bonds, 314 residues, 1 model selected
> view matrix models #11,1,0,0,28.647,0,1,0,13.715,0,0,1,36.673
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.9591,-0.26394,-0.10226,28.958,0.19264,0.87334,-0.44739,13.77,0.20739,0.4094,0.88847,36.126
> view matrix models
> #11,0.69321,0.65538,-0.2999,25.034,-0.079876,0.4834,0.87175,16.777,0.7163,-0.58035,0.38745,39.575
> view matrix models
> #11,0.68446,0.31627,0.65687,28.092,-0.62871,0.71222,0.3122,12.774,-0.36909,-0.62667,0.68633,36.202
> view matrix models
> #11,0.52505,0.49875,0.68961,27.067,-0.84751,0.38042,0.37013,12.947,-0.077739,-0.7788,0.62244,37.583
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.52505,0.49875,0.68961,51.924,-0.84751,0.38042,0.37013,25.668,-0.077739,-0.7788,0.62244,83.479
> view matrix models
> #11,0.52505,0.49875,0.68961,46.808,-0.84751,0.38042,0.37013,-4.0335,-0.077739,-0.7788,0.62244,111.31
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.79123,0.58721,0.17067,46.41,-0.61019,0.7398,0.28348,-4.2747,0.040199,-0.32844,0.94367,111.3
> view matrix models
> #11,-0.58072,-0.54667,-0.60326,42.374,0.30045,0.54478,-0.78291,-2.6877,0.75663,-0.6359,-0.15212,112.37
> view matrix models
> #11,-0.58777,-0.58606,-0.55773,42.556,0.33744,0.44896,-0.82738,-2.3918,0.73529,-0.67451,-0.066125,112.58
> view matrix models
> #11,-0.59396,-0.58082,-0.55666,42.521,0.32938,0.45571,-0.82694,-2.4398,0.73398,-0.67452,-0.079361,112.55
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.59396,-0.58082,-0.55666,54.444,0.32938,0.45571,-0.82694,28.184,0.73398,-0.67452,-0.079361,78.733
> view matrix models
> #11,-0.59396,-0.58082,-0.55666,53.833,0.32938,0.45571,-0.82694,30.797,0.73398,-0.67452,-0.079361,81.905
> view matrix models
> #11,-0.59396,-0.58082,-0.55666,54.106,0.32938,0.45571,-0.82694,30.303,0.73398,-0.67452,-0.079361,83.221
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.5582,-0.56856,-0.60429,54.102,0.37278,0.47881,-0.79485,30.482,0.74125,-0.66894,-0.055326,83.289
> ui mousemode right "translate selected models"
> select clear
> ui mousemode right "rotate selected models"
> select add #11
2449 atoms, 2526 bonds, 314 residues, 1 model selected
> view matrix models
> #11,-0.56329,-0.55758,-0.60976,54.041,0.35984,0.49876,-0.78851,30.394,0.74379,-0.66358,-0.080305,83.227
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.56329,-0.55758,-0.60976,54.169,0.35984,0.49876,-0.78851,29.602,0.74379,-0.66358,-0.080305,83.832
> ui mousemode right "rotate selected models"
> view matrix models
> #11,-0.59172,-0.51172,-0.6229,53.908,0.39058,0.49396,-0.77682,29.76,0.70521,-0.70295,-0.092418,83.76
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.59172,-0.51172,-0.6229,54.379,0.39058,0.49396,-0.77682,30.627,0.70521,-0.70295,-0.092418,81.276
> select clear
> hide #11 models
> show #!5 models
> show #11 models
> color #11 #ff40ffff
> select #5/A
2884 atoms, 2973 bonds, 369 residues, 1 model selected
> cartoon hide (#!5 & sel)
> hide #!1 models
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #11/A
Alignment identifier is 11/A
> select #11/A:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:245
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:269
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:269
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel sphere
Changed 5 atom styles
> color sel yellow
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel sphere
Changed 9 atom styles
> color sel yellow
> select #11/A:269
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:269
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide sel target a
> color sel hot pink
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> show sel target ab
> style sel sphere
Changed 5 atom styles
> color sel yellow
> select clear
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV1_gD_full_locking.cxs"
> select #11/A:31-32
14 atoms, 15 bonds, 2 residues, 1 model selected
> select #11/A:31-247
1707 atoms, 1759 bonds, 217 residues, 1 model selected
> color #11 white
> select #11/A:248
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #11/A:248-314
507 atoms, 527 bonds, 67 residues, 1 model selected
> ui tool show "Color Actions"
> color sel medium purple
> select #11/A:1-2
21 atoms, 21 bonds, 2 residues, 1 model selected
> select #11/A:1-31
242 atoms, 246 bonds, 31 residues, 1 model selected
> color sel dark violet
> select clear
> select #11/A:276-277
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #11/A:276-277
11 atoms, 10 bonds, 2 residues, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:277
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #11/A:190-191,277
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:190
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #11/A:190,277
14 atoms, 12 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV1_gD_full_locking.cxs"
> show #!5 models
> hide #!5 models
> select #11/A:314
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #11 models
> show #11 models
> show #!5 models
> hide #!5 models
> show #!1 models
> ui tool show Match→Align
> msa3d #11/A#1/A cutoffDistance 10 maxIterations none refChain #1/A
Match→Align cutoff: 10.0, in column if within cutoff of: any
261 residue pairs aligned
285 fully populated columns
285 fully populated columns in at least 3 column stetches
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align
run(self.session, "msa3d " + ' '.join(args))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 129, in make_alignment
ref_atoms = column_atoms(ref_seq, culled)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in column_atoms
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in <listcomp>
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'principal_atom'
AttributeError: 'NoneType' object has no attribute 'principal_atom'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 247, in
return Atoms([r.principal_atom for r in [residues[i] for i in seq_columns]])
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> save "/Users/kellykeisen/Documents/Current
> Projects/APEC-x/HSV1_gD_full_locking.cxs"
——— End of log from Sat Jun 6 16:29:38 2026 ———
> view name session-start
opened ChimeraX session
> ui tool show Match→Align
> msa3d #11/A#1/A maxIterations 3 refChain #1/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
240 residue pairs aligned
240 fully populated columns
223 fully populated columns in at least 3 column stetches
Matching fold_2026_06_06_11_31_model_0.cif, chain A onto 2c36, chain A
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align
run(self.session, "msa3d " + ' '.join(args))
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 131, in make_alignment
aligned = [copy(chain) for chain in ordered]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 131, in <listcomp>
aligned = [copy(chain) for chain in ordered]
^^^^
NameError: name 'copy' is not defined
NameError: name 'copy' is not defined
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 131, in
aligned = [copy(chain) for chain in ordered]
^^^^
See log for complete Python traceback.
> ui tool show Match→Align
> msa3d #11/A#1/A#2/A maxIterations none refChain #1/A
Match→Align cutoff: 5.0, in column if within cutoff of: any
211 fully populated columns
195 fully populated columns in at least 3 column stetches
Matching 3u82 chain A onto 2c36 chain A
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 199, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args, ma=self.match_align:
ma(apply=True))
^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/tool.py", line 259, in match_align
run(self.session, "msa3d " + ' '.join(args))
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 131, in make_alignment
aligned = [copy(chain) for chain in ordered]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 131, in <listcomp>
aligned = [copy(chain) for chain in ordered]
^^^^
NameError: name 'copy' is not defined
NameError: name 'copy' is not defined
File
"/Applications/ChimeraX-1.12-rc2026.06.06.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_align/cmd.py", line 131, in
aligned = [copy(chain) for chain in ordered]
^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac14,2
Model Number: Z1610005LLL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 12 days, 4 hours, 10 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
LG Ultra HD:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.2
bs4: 0.0.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202606060206
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.2.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.6
tqdm: 4.68.1
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
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