The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
When showing atom alternate locations of 2fwz I cannot run matchmaker to align it to 8u1m probably because matchmaker is trying to match the altloc models as well.
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 2fwz format mmcif fromDatabase pdb
2fwz title:
Structure of human Hsp90-alpha bound to the potent water soluble inhibitor
PU-H71 [more info...]
Chain information for 2fwz #1
---
Chain | Description
A | Heat shock protein HSP 90-alpha
Non-standard residues in 2fwz #1
---
H71 —
8-[(6-iodo-1,3-benzodioxol-5-yl)thio]-9-[3-(isopropylamino)propyl]-9H-purin-6-amine
110 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> log metadata #1
Metadata for 2fwz #1
---
Title | Structure of human Hsp90-alpha bound to the potent water soluble inhibitor PU-H71
Citation | Immormino, R.M., Kang, Y., Chiosis, G., Gewirth, D.T. (2006). Structural and quantum chemical studies of 8-aryl-sulfanyl adenine class Hsp90 inhibitors. J.Med.Chem., 49, 4953-4960. PMID: 16884307. DOI: 10.1021/jm060297x
Non-standard residue | H71 — 8-[(6-iodo-1,3-benzodioxol-5-yl)thio]-9-[3-(isopropylamino)propyl]-9H-purin-6-amine
Gene source | Homo sapiens (human)
Experimental method | X-ray diffraction
Resolution | 2.1Å
> open 2fwz fromDatabase eds
Summary of feedback from opening 2fwz fetched from eds
---
note | Fetching map 2fwz from http://www.ebi.ac.uk/pdbe/coordinates/files/2fwz.ccp4
Opened eds 2fwz as #2, grid size 96,132,144, pixel 0.695,0.692,0.685, shown at
level 0.886, step 1, values float32
> usage vol cover
volume cover volumes [atomBox an atoms specifier] [pad a number] [box box
bounds] [x 2 floats] [y 2 floats] [z 2 floats] [fBox box bounds] [fx 2 floats]
[fy 2 floats] [fz 2 floats] [iBox box bounds] [ix 2 floats] [iy 2 floats] [iz
2 floats] [useSymmetry true or false] [cellSize cellSize] [step map step]
[modelId modelId]
— Use symmetry to extend a map to cover a region
cellSize: 3-tuple of integers
modelId: a model id
> volume cover #2 atomBox #1
Extended map eds 2fwz to box of size (75, 74, 77),
cell size (96, 132, 144) grid points, 8 symmetry operations,
0 points not covered by any symmetry,
maximum value difference where symmetric map copies overlap = 2.2799e-06
Opened eds 2fwz extended as #3, grid size 75,74,77, pixel 0.695,0.692,0.685,
shown at step 1, values float32
> hide cartoons
> show atoms
> volume #3 level 0.5347
> select :H71
28 atoms, 31 bonds, 1 residue, 1 model selected
> volume zone #3 nearAtoms sel & #1 range 4.17
> hide solvent
> select sel @< 5
117 atoms, 84 bonds, 40 residues, 1 model selected
> undo
> select sel :< 5
189 atoms, 162 bonds, 40 residues, 1 model selected
> select ~sel & ##selected
1792 atoms, 1526 bonds, 491 residues, 1 model selected
> hide sel atoms
> select /A:1001@C96
1 atom, 1 residue, 1 model selected
> select up
28 atoms, 31 bonds, 1 residue, 1 model selected
> color sel orange
> color sel pink
> color sel orange
> color sel byhetero
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms sel distance 4.34
> surface zone #3 nearAtoms sel distance 8
> volume #3 level 0.3208
> surface zone #3 nearAtoms sel distance 8.53
> surface zone #3 nearAtoms sel distance 3.25
> volume #3 level 0.436
> surface zone #3 nearAtoms sel distance 3.42
> surface zone #3 nearAtoms sel distance 4.56
> surface zone #3 nearAtoms sel distance 3.25
> surface zone #3 nearAtoms sel distance 3.1
> surface zone #3 nearAtoms sel distance 5.44
> help help:user/tools/altlocexplorer.html
> ui tool show "Altloc Explorer"
> volume #2 level 0.8863
> close #2
> altlocs change A
Changed 2 residues to alternate location A (11 residues were already A)
> altlocs change B
Changed 12 residues to alternate location B (1 residue were already B)
> altlocs change A
Changed 12 residues to alternate location A (1 residue were already A)
> altlocs change B
Changed 12 residues to alternate location B (1 residue were already B)
> select @@altloc='A'
Nothing selected
> select @@altloc=A
Nothing selected
> select @@altloc2=A
Nothing selected
> select @@alt_loc=A
Nothing selected
> help altlocs
> altlocs show #1
> show #1
> hide solvent
> volume region all imageMode "full region"
> volume unzone
> mousemode rightMode "crop volume"
> volume #3 style surface
> volume #3 style mesh
Volume zone shortcut requires 1 displayed atomic model and 1 map, got 27
atomic models, 1 maps.
> close #1.1
> volume zone #3 nearAtoms #1 range 4.17
> altlocs show #1
> volume #3 change image level -0.2599,0 level 0.8716,0.8 level 7.955,1
> volume #3 level 0.3204
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #1 distance 4.02
> surface zone #3 nearAtoms #1 distance 2.09
> volume #3 color #ffffb25d
> volume #3 level 0.2199
> close #3
> select ligand
28 atoms, 31 bonds, 1 residue, 1 model selected
> hide ligand :> 5
> hbonds sel reveal true
7 hydrogen bonds found
> select clear
> show surfaces
> lighting soft
> mlp
Map values for surface "2fwz_A SES surface": minimum -29.07, mean -5.325,
maximum 24.02
To also show corresponding color key, enter the above mlp command and add key
true
> lighting simple
> select ligand
28 atoms, 31 bonds, 1 residue, 1 model selected
> show sel surfaces
> mlp sel
mlp: no amino acids specified
> mlp sel
mlp: no amino acids specified
> hide #1.3 models
> style sel sphere
Changed 28 atom styles
> lighting soft
> surface hidePatches ligand :> 5
> style sel ball
Changed 28 atom styles
> select clear
> lighting simple
> transparency #2#1.1-2#!1 50
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
2fwz #!1/A GLU 16 OE2
2fwz #!1/A GLU 16 CD
2fwz #!1/A GLU 16 CG
2fwz #!1/A GLU 16 OE1
Using Amber 20 recommended default charges and atom types for standard
residues
Hydrogen copy of B #/A GLY 177 H (alt loc B) bonded to atom that should not
have hydrogens (copy of B #/A GLY 177 C (alt loc B))
> addh #1
Summary of feedback from adding hydrogens to multiple structures
---
warning | Not adding hydrogens to 2fwz #!1/A GLU 16 CB because it is missing heavy-atom bond partners
notes | Termini for 2fwz (#1) chain A determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: 2fwz #!1/A GLU 16
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: 2fwz #!1/A GLU 223
1187 hydrogen bonds
Adding 'H' to 2fwz #!1/A GLU 16
2fwz #!1/A GLU 223 is not terminus, removing H atom from 'C'
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
0 hydrogen bonds
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
2596 hydrogens added
> hide H
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
2fwz #!1/A GLU 16 OE2
2fwz #!1/A GLU 16 CD
2fwz #!1/A GLU 16 CG
2fwz #!1/A GLU 16 OE1
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 26 time(s)]Coulombic values for 2fwz_A SES surface #1.2: minimum,
-13.43, mean -1.13, maximum 14.64
Coulombic values for A_A SES surface #1.1.1.1.1: minimum, 0.65, mean 6.53,
maximum 9.76
Coulombic values for B_A SES surface #1.1.1.2.1: minimum, 0.25, mean 6.62,
maximum 10.71
Coulombic values for A_A SES surface #1.1.2.1.1: minimum, -3.82, mean 3.40,
maximum 7.77
Coulombic values for B_A SES surface #1.1.2.2.1: minimum, -1.77, mean 3.51,
maximum 9.22
Coulombic values for A_A SES surface #1.1.3.1.1: minimum, -1.42, mean 3.11,
maximum 7.18
Coulombic values for B_A SES surface #1.1.3.2.1: minimum, -1.52, mean 2.86,
maximum 7.25
Coulombic values for A_A SES surface #1.1.4.1.1: minimum, -8.82, mean -1.88,
maximum 4.13
Coulombic values for B_A SES surface #1.1.4.2.1: minimum, -8.60, mean -1.93,
maximum 3.59
Coulombic values for A_A SES surface #1.1.5.1.1: minimum, -9.31, mean -1.62,
maximum 3.26
Coulombic values for B_A SES surface #1.1.5.2.1: minimum, -8.89, mean -1.87,
maximum 2.37
Coulombic values for A_A SES surface #1.1.6.1.1: minimum, -1.35, mean 3.27,
maximum 8.90
Coulombic values for B_A SES surface #1.1.6.2.1: minimum, -1.33, mean 3.30,
maximum 9.25
Coulombic values for A_A SES surface #1.1.7.1.1: minimum, -1.02, mean 4.59,
maximum 7.49
Coulombic values for B_A SES surface #1.1.7.2.1: minimum, -1.41, mean 4.56,
maximum 7.20
Coulombic values for A_A SES surface #1.1.8.1.1: minimum, -1.28, mean 2.95,
maximum 7.59
Coulombic values for B_A SES surface #1.1.8.2.1: minimum, -1.34, mean 3.11,
maximum 7.59
Coulombic values for A_A SES surface #1.1.9.1.1: minimum, 0.32, mean 7.08,
maximum 9.85
Coulombic values for B_A SES surface #1.1.9.2.1: minimum, -0.05, mean 6.91,
maximum 9.74
Coulombic values for A_A SES surface #1.1.10.1.1: minimum, -8.90, mean -2.01,
maximum 2.46
Coulombic values for B_A SES surface #1.1.10.2.1: minimum, -9.20, mean -1.76,
maximum 3.68
Coulombic values for A_A SES surface #1.1.11.1.1: minimum, -0.51, mean 6.92,
maximum 12.01
Coulombic values for B_A SES surface #1.1.11.2.1: minimum, -0.53, mean 6.80,
maximum 9.89
Coulombic values for A_A SES surface #1.1.12.1.1: minimum, -0.34, mean 7.02,
maximum 10.46
Coulombic values for B_A SES surface #1.1.12.2.1: minimum, -0.59, mean 7.04,
maximum 9.99
Coulombic values for A_A SES surface #1.1.13.1.1: minimum, -2.56, mean 3.11,
maximum 7.96
Coulombic values for B_A SES surface #1.1.13.2.1: minimum, -1.46, mean 2.95,
maximum 5.29
To also show corresponding color key, enter the above coulombic command and
add key true
> surface hidePatches ligand :> 5
> select ligand
50 atoms, 53 bonds, 1 residue, 1 model selected
> show sel surfaces
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue H71 (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/jb/f14hkn9s19l691b68w_lvm0w0000gn/T/tmpea7dhfmz/ante.in.mol2 -fi
mol2 -o
/var/folders/jb/f14hkn9s19l691b68w_lvm0w0000gn/T/tmpea7dhfmz/ante.out.mol2 -fo
mol2 -c bcc -nc 1 -j 5 -s 2 -dr n
(H71) ``
(H71) `Welcome to antechamber 20.0: molecular input file processor.`
(H71) ``
(H71) `Info: Finished reading file
(/var/folders/jb/f14hkn9s19l691b68w_lvm0w0000gn/T/tmpea7dhfmz/ante.in.mol2);
atoms read (50), bonds read (53).`
(H71) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(H71) `Running:
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(H71) ``
(H71) ``
(H71) `Running:
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(H71) `Info: Total number of electrons: 256; net charge: 1`
(H71) ``
(H71) `Running:
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(H71) ``
(H71) `Running:
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(H71) ``
(H71) `Running:
/Users/goddard/Desktop/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -f
ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(H71) ``
Charges for residue H71 determined
Coulombic values for 2fwz_A SES surface #1.3: minimum, -0.38, mean 2.97,
maximum 7.57
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.2 models
> show #1.2 models
> hide #1.3 models
> show #1.3 models
> lighting soft
> hide #1.2 models
> lighting simple
> hide #1.3 models
> open 8u1m
Summary of feedback from opening 8u1m fetched from pdb
---
note | Fetching compressed mmCIF 8u1m from http://files.rcsb.org/download/8u1m.cif
8u1m title:
Cryo-EM structure of the HSP90 dimer (NTD-MD) in the semi-open state [more
info...]
Chain information for 8u1m #3
---
Chain | Description | UniProt
A B | Heat shock protein 83 | A0A7E5VSK5_TRINI 1-722
Non-standard residues in 8u1m #3
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> view
> mmaker #1 to #3/A
No matrix compatible with both reference structure and all match structures
> select #3/A:10-530
3789 atoms, 3856 bonds, 2 pseudobonds, 463 residues, 2 models selected
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac Studio
Model Identifier: Mac14,14
Model Number: Z1800003VLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 64 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 137 days, 21 hours, 13 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PHL 278B1:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
alphashape: 1.3.1
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.12.3
biopython: 1.83
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.23.0
ChimeraX-clix: 0.1.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepSSETracer: 1.1
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-maskChains: 1.1
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NIHPresets: 1.1.19
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-TetraScape: 0.2
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
click: 8.1.7
click-log: 0.4.0
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
fsspec: 2024.3.1
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib-metadata: 4.0.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.4
joblib: 1.4.2
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
llvmlite: 0.42.0
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numba: 0.59.1
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
platformdirs: 4.2.2
pooch: 1.8.2
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynndescent: 0.5.12
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyvista: 0.44.1
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
Rtree: 1.3.0
scikit-learn: 1.4.2
scipy: 1.14.0
scooby: 0.10.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
shapely: 2.0.6
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
sympy: 1.12
tables: 3.10.1
tcia_utils: 1.5.1
threadpoolctl: 3.5.0
tifffile: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
torch: 2.1.2
tornado: 6.4.2
tqdm: 4.66.4
traitlets: 5.14.3
trimesh: 4.4.7
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
umap-learn: 0.5.6
urllib3: 2.2.3
vtk: 9.3.1
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
zipp: 3.19.2
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Fix: https://github.com/RBVI/ChimeraX/commit/640e1ed422884eccfe0131851da64ad6356ce30b