Wrong orientation for defined axis

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-12.6.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
define axis gives wrong orientations on moved/reoriented model

open attached file 6idf.pdb (used this one from the "orientations of proteins in membranes" database because it has the atoms defining the plane of the membrane)

then:
open 6lqg
mm #2 to #1
define axis #2 perhelix t

...you can see all the axes are parallel to each other although they do seem to be centered on the helices in #2

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6idf

6idf title:  
Cryo-EM structure of γ secretase in complex with a Notch fragment [more
info...]  
  
Chain information for 6idf #1  
---  
Chain | Description | UniProt  
A | Nicastrin | NICA_HUMAN  
B | Presenilin-1 | PSN1_HUMAN  
C | Gamma-secretase subunit APH-1A | APH1A_HUMAN  
D | Gamma-secretase subunit PEN-2 | PEN2_HUMAN  
E | Notch1 |  
  
Non-standard residues in 6idf #1  
---  
BMA — beta-D-mannopyranose  
CLR — cholesterol  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
  

> hide

> cartoon

> open 6lqg

6lqg title:  
Human gamma-secretase in complex with small molecule Avagacestat [more
info...]  
  
Chain information for 6lqg #2  
---  
Chain | Description | UniProt  
A | Nicastrin | NICA_HUMAN  
B | Presenilin-1 | PSN1_HUMAN  
C | Gamma-secretase subunit APH-1A | APH1A_HUMAN  
D | Gamma-secretase subunit PEN-2 | PEN2_HUMAN  
  
Non-standard residues in 6lqg #2  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CLR — cholesterol  
EN9 —
(2R)-2-[(4-chlorophenyl)sulfonyl-[[2-fluoranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]methyl]amino]-5,5,5-tris(fluoranyl)pentanamide  
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)  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
  

> close session

> open 6idf.pdb

6idf.pdb title:  
Cryo-em structure of γ secretase In complex with A notch fragment [more
info...]  
  
Chain information for 6idf.pdb #1  
---  
Chain | Description | UniProt  
A | No description available | NICA_HUMAN  
B | No description available | PSN1_HUMAN  
C | No description available | APH1A_HUMAN  
D | No description available | PEN2_HUMAN  
E | No description available |  
  
Non-standard residues in 6idf.pdb #1  
---  
BMA — β-D-mannose  
CLR — cholesterol  
DUM — (DUM)  
NAG — N-acetyl-D-glucosamine  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
  

> hide protein

> cartoon

> open 1lqg

Summary of feedback from opening 1lqg fetched from pdb  
---  
note | Fetching compressed mmCIF 1lqg from
http://files.rcsb.org/download/1lqg.cif  
  
1lqg title:  
Escherichia coli uracil-DNA glycosylase complex with uracil-DNA glycosylase
inhibitor protein [more info...]  
  
Chain information for 1lqg #2  
---  
Chain | Description | UniProt  
A B | URACIL-DNA GLYCOSYLASE | UNG_ECOLI  
C D | URACIL-DNA GLYCOSYLASE INHIBITOR | UNGI_BPPB2  
  
1lqg mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| software_defined_assembly  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6idf.pdb, chain A (#1) with 1lqg, chain B (#2), sequence alignment
score = 104.7  
RMSD between 6 pruned atom pairs is 1.361 angstroms; (across all 204 pairs:
21.503)  
  

> close #2

> open 6lqg

6lqg title:  
Human gamma-secretase in complex with small molecule Avagacestat [more
info...]  
  
Chain information for 6lqg #2  
---  
Chain | Description | UniProt  
A | Nicastrin | NICA_HUMAN  
B | Presenilin-1 | PSN1_HUMAN  
C | Gamma-secretase subunit APH-1A | APH1A_HUMAN  
D | Gamma-secretase subunit PEN-2 | PEN2_HUMAN  
  
Non-standard residues in 6lqg #2  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CLR — cholesterol  
EN9 —
(2R)-2-[(4-chlorophenyl)sulfonyl-[[2-fluoranyl-4-(1,2,4-oxadiazol-3-yl)phenyl]methyl]amino]-5,5,5-tris(fluoranyl)pentanamide  
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)  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6idf.pdb, chain A (#1) with 6lqg, chain A (#2), sequence alignment
score = 3357.9  
RMSD between 666 pruned atom pairs is 0.386 angstroms; (across all 667 pairs:
0.394)  
  

> define axis #2 perHelix true

Axis '6lqg #2/helix axes/chain A helix 1' centered at [-9.00853104 0.53642014
22.97481276] with direction [ 0.00281514 -0.57060459 0.82122011], radius
1.80581, and length 9.93519  
Axis '6lqg #2/helix axes/chain A helix 2' centered at [-11.99964727
-23.34625921 43.71446459] with direction [-0.02207195 0.47852839 0.87779463],
radius 1.91725, and length 14.9933  
Axis '6lqg #2/helix axes/chain A helix 3' centered at [-1.48674352e-02
-2.57651479e+01 4.38672617e+01] with direction [-0.2163561 -0.43070081
-0.87617741], radius 1.88393, and length 16.3818  
Axis '6lqg #2/helix axes/chain A helix 4' centered at [-10.77814306 -4.6222266
39.87837168] with direction [-0.79846283 -0.46454936 -0.38295038], radius
1.9963, and length 22.88  
Axis '6lqg #2/helix axes/chain A helix 5' centered at [ 26.26114145
-20.30883173 23.89296105] with direction [ 0.35806217 0.43761947 -0.82479129],
radius 1.97137, and length 21.7224  
Axis '6lqg #2/helix axes/chain A helix 6' centered at [29.48940855 1.30585714
59.90156976] with direction [0.75718215 0.5602377 0.33587038], radius 1.82982,
and length 27.2752  
Axis '6lqg #2/helix axes/chain A helix 7' centered at [ 37.49577548
-14.52663814 45.75829761] with direction [ 0.99280589 -0.04007761 -0.1128284
], radius 1.96112, and length 19.8155  
Axis '6lqg #2/helix axes/chain A helix 8' centered at [ 47.04880362
-13.04546343 52.24609754] with direction [-0.21489583 0.63963401 -0.73802989],
radius 1.12468, and length 6.22546  
Axis '6lqg #2/helix axes/chain A helix 9' centered at [ 39.20105408
-26.67144884 64.9829857 ] with direction [ 0.78318867 -0.15951926 0.60097347],
radius 1.43217, and length 7.58471  
Axis '6lqg #2/helix axes/chain A helix 10' centered at [ 38.80704108
-13.02347334 72.26794417] with direction [-0.47478967 0.80647946 0.35237147],
radius 1.87517, and length 32.1481  
Axis '6lqg #2/helix axes/chain A helix 11' centered at [ 34.42830037
-17.9637371 54.46574794] with direction [ 0.7947361 -0.60472829 -0.05194444],
radius 1.62724, and length 10.5502  
Axis '6lqg #2/helix axes/chain A helix 12' centered at [10.84728281
-2.40670131 59.31068672] with direction [-0.09253705 -0.21193256 -0.97289336],
radius 1.73472, and length 9.60028  
Axis '6lqg #2/helix axes/chain A helix 13' centered at [13.19035825
15.00668234 57.21157215] with direction [ 0.83564841 -0.49616715 0.23560539],
radius 1.69247, and length 9.77305  
Axis '6lqg #2/helix axes/chain A helix 14' centered at [30.69368396
-0.53967022 67.56886947] with direction [ 0.9695062 -0.24472788 0.0128839 ],
radius 1.88977, and length 30.9173  
Axis '6lqg #2/helix axes/chain A helix 15' centered at [20.66342703 6.97544669
58.71365282] with direction [-0.59292161 -0.28287903 -0.75393861], radius
1.99863, and length 20.8182  
Axis '6lqg #2/helix axes/chain A helix 16' centered at [25.4199932 11.75609852
38.78052508] with direction [-0.89843897 -0.41616624 -0.14004672], radius
1.77758, and length 8.27393  
Axis '6lqg #2/helix axes/chain A helix 17' centered at [29.69210667 4.99796706
48.80540966] with direction [0.59762249 0.49195161 0.63311213], radius
1.98584, and length 22.7315  
Axis '6lqg #2/helix axes/chain A helix 18' centered at [41.64365677
17.84282325 38.4943711 ] with direction [-0.31339942 0.91036419 0.27021816],
radius 1.78758, and length 10.1876  
Axis '6lqg #2/helix axes/chain A helix 19' centered at [ 34.92690405
-18.69235995 35.43011218] with direction [ 0.26449904 -0.4238786 -0.86623737],
radius 1.81998, and length 9.23732  
Axis '6lqg #2/helix axes/chain A helix 20' centered at [-20.27363701
-13.90833793 1.8102781 ] with direction [-0.14353833 0.16461742 -0.9758575 ],
radius 1.8865, and length 42.2648  
Axis '6lqg #2/helix axes/chain A helix 21' centered at [-27.16889809
-6.91489261 -20.50941813] with direction [-0.58970334 0.78613506 -0.18504496],
radius 1.88083, and length 10.2901  
Axis '6lqg #2/helix axes/chain B helix 1' centered at [ 4.37262169 -3.26061417
-6.78509226] with direction [ 0.23518334 -0.22706441 0.94505585], radius
2.02021, and length 38.3592  
Axis '6lqg #2/helix axes/chain B helix 2' centered at [13.67617595 -3.99645542
12.38909573] with direction [0.41852085 0.88748991 0.19287809], radius
1.72566, and length 9.36971  
Axis '6lqg #2/helix axes/chain B helix 3' centered at [26.56866574 12.8399894
-2.34643467] with direction [ 0.34145017 -0.36222844 -0.86729599], radius
1.9255, and length 49.8467  
Axis '6lqg #2/helix axes/chain B helix 4' centered at [ 29.6911517 -6.35250047
-11.39026233] with direction [-0.50198377 -0.42670476 0.75228674], radius
1.90899, and length 28.1014  
Axis '6lqg #2/helix axes/chain B helix 5' centered at [ 16.69289235
-14.05391035 7.23242822] with direction [-0.67157236 -0.2677439 0.69087175],
radius 1.82062, and length 21.7055  
Axis '6lqg #2/helix axes/chain B helix 6' centered at [ 21.18186306
-20.01105461 -4.94764484] with direction [-0.01346634 0.46990421 -0.88261469],
radius 1.99575, and length 30.0867  
Axis '6lqg #2/helix axes/chain B helix 7' centered at [14.75315635 -6.39778514
-5.20434463] with direction [0.22322196 0.55640122 0.80036844], radius
1.89971, and length 34.6186  
Axis '6lqg #2/helix axes/chain B helix 8' centered at [17.25092877 14.4407663
-5.39342265] with direction [-0.12489168 -0.22993328 0.96515944], radius
2.00692, and length 31.7877  
Axis '6lqg #2/helix axes/chain B helix 9' centered at [ 24.49844707 8.66908055
-24.40811194] with direction [ 0.03329128 -0.58912847 -0.80735329], radius
1.95283, and length 18.9365  
Axis '6lqg #2/helix axes/chain B helix 10' centered at [10.63405142 3.35863272
-1.17349173] with direction [-0.41554258 0.11229574 0.90261511], radius
1.9578, and length 25.3909  
Axis '6lqg #2/helix axes/chain B helix 11' centered at [ 2.05132773 8.35422252
-9.93286121] with direction [ 0.25763144 0.22296703 -0.94016581], radius
1.94958, and length 38.3417  
Axis '6lqg #2/helix axes/chain B helix 12' centered at [ 3.54496559 13.6719919
-0.01549737] with direction [-0.4619759 0.09246264 0.88205948], radius
1.93928, and length 19.8823  
Axis '6lqg #2/helix axes/chain B helix 13' centered at [-9.54104975
11.83669425 12.60276218] with direction [-0.7228574 -0.48049779 0.4965874 ],
radius 1.78526, and length 19.3897  
Axis '6lqg #2/helix axes/chain C helix 1' centered at [-13.23152575
-10.32421419 8.61254228] with direction [-0.46844561 0.53343226 -0.70427888],
radius 1.85235, and length 16.9118  
Axis '6lqg #2/helix axes/chain C helix 2' centered at [-14.95496113
-6.42871567 -6.35206208] with direction [ 0.20982737 0.01852265 -0.97756298],
radius 2.04886, and length 16.9767  
Axis '6lqg #2/helix axes/chain C helix 3' centered at [-8.58764589 14.28107887
-1.43220259] with direction [ 0.02256965 -0.63767256 -0.76997683], radius
1.94867, and length 50.4665  
Axis '6lqg #2/helix axes/chain C helix 4' centered at [-15.57645607 17.0557915
-4.45028626] with direction [ 0.14905927 -0.17836439 -0.9726086 ], radius
2.06303, and length 58.6475  
Axis '6lqg #2/helix axes/chain C helix 5' centered at [-13.59046308 3.26769368
-3.53220037] with direction [ 0.33050102 -0.1768285 0.92709264], radius
2.17791, and length 40.1031  
Axis '6lqg #2/helix axes/chain C helix 6' centered at [-21.94481157 4.07117638
-1.79364155] with direction [-0.1960994 0.47904045 -0.85560813], radius
2.10876, and length 45.5612  
Axis '6lqg #2/helix axes/chain C helix 7' centered at [-27.54843333
14.00360353 -0.77636154] with direction [ 0.23895834 -0.34655028 0.90708424],
radius 1.88204, and length 24.8846  
Axis '6lqg #2/helix axes/chain C helix 8' centered at [-30.71289026 2.53531983
-3.44930552] with direction [-0.02219294 0.04149612 -0.99889216], radius
1.90085, and length 28.8108  
Axis '6lqg #2/helix axes/chain C helix 9' centered at [-35.74507448
-8.71443792 -18.57883602] with direction [-0.32349192 0.91870133 0.22658516],
radius 1.85527, and length 13.5236  
Axis '6lqg #2/helix axes/chain D helix 1' centered at [ 20.48544252
-26.86720427 -23.16929121] with direction [ 0.27618811 -0.25963289
0.92537068], radius 1.83396, and length 20.4798  
Axis '6lqg #2/helix axes/chain D helix 2' centered at [ 24.1262905
-30.00061343 -10.71834484] with direction [0.69227006 0.08868249 0.71616868],
radius 1.16451, and length 5.88357  
Axis '6lqg #2/helix axes/chain D helix 3' centered at [ 11.4023139
-27.41395897 -17.55683952] with direction [-0.59223127 -0.12960985
-0.79527568], radius 2.18657, and length 27.8537  
Axis '6lqg #2/helix axes/chain D helix 4' centered at [ 14.33870856
-34.56959229 -8.1555397 ] with direction [-2.84542718e-02 9.35127833e-05
-9.99595091e-01], radius 1.94655, and length 50.401  
Axis '6lqg #2/helix axes/chain D helix 5' centered at [ 25.01843566
-28.44441671 17.6717989 ] with direction [-0.08197737 0.55023981 -0.83097284],
radius 1.75729, and length 10.3182  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 7:02

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
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    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
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    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
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    ChimeraX-ItemsInspection: 1.0.1
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    ChimeraX-ListInfo: 1.1.1
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    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.0.5
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0
File attachment: 6idf.pdb

6idf.pdb​

[Elaine Meng]

Added by email2trac

[Eric Pettersen]

fix: ​https://github.com/RBVI/ChimeraX/commit/c9e39d02f9cbf51a89dc252cc78069d82eea982f