The following bug report has been submitted:
Platform: macOS-12.6.8-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 UTC)
Description
When inputing the following commands, the erros messages are displayed swapaa D#1:203.a
Missing or invalid "residues" argument: only initial part "D" of atom specifier valid
swapaa D#1:203.A
Missing or invalid "residues" argument: only initial part "D" of atom specifier valid
swapaa D #1:203.A
No amino acid residues specified for swapping
list residues
Unknown command: list residues
swapaa asp #1:203.a
Missing or invalid "residues" argument: invalid residues specifier
swapaa asp #1:203.A
Missing or invalid "residues" argument: invalid residues specifier
swapaa Glu #1:203.a
Missing or invalid "residues" argument: invalid residues specifier
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open /Users/iMacSofi/Downloads/4ib3.pdb
4ib3.pdb title:
Structure of camp dependent protein kinase A In complex with adp,
phosphorylated peptide PSP20, and No metal [more info...]
Chain information for 4ib3.pdb #1
---
Chain | Description | UniProt
A | PKA C-α | KAPCA_MOUSE 1-350
S | phosphorylated pseudo-substrate peptide PSP20 |
Non-standard residues in 4ib3.pdb #1
---
ADP — adenosine-5'-diphosphate
> set bgColor white
> select :ADP
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel hot pink
> select /A:12-350
2804 atoms, 2875 bonds, 339 residues, 1 model selected
> color sel light sea green
> select /S:605-624
159 atoms, 161 bonds, 20 residues, 1 model selected
> color sel forest green
> color sel orange
> color sel dim gray
> color sel lime
> color sel orange red
> select :ADP
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel magenta
> color sel light sea green
> select /A:12-350
2804 atoms, 2875 bonds, 339 residues, 1 model selected
> color sel dark gray
> select :ADP
27 atoms, 29 bonds, 1 residue, 1 model selected
> select /S:605-624
159 atoms, 161 bonds, 20 residues, 1 model selected
> color sel hot pink
> select ::name="GLU"
225 atoms, 203 bonds, 25 residues, 1 model selected
> show sel target ab
> select ::name="ARG"
198 atoms, 182 bonds, 18 residues, 1 model selected
> show sel target ab
> select ::name="GLU"
225 atoms, 203 bonds, 25 residues, 1 model selected
> select /A:12-350
2804 atoms, 2875 bonds, 339 residues, 1 model selected
> color sel light sea green
> select /S:605-624
159 atoms, 161 bonds, 20 residues, 1 model selected
> select :ADP
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select ::name="GLU"
225 atoms, 203 bonds, 25 residues, 1 model selected
> ui tool show H-Bonds
> hbonds color #fa4a64 reveal true
1002 hydrogen bonds found
> select /S:605-624
159 atoms, 161 bonds, 8 pseudobonds, 20 residues, 2 models selected
> color (#!1 & sel) byelement
> select ::name="GLU"
225 atoms, 203 bonds, 4 pseudobonds, 25 residues, 2 models selected
> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"
> ui tool show Distances
> select subtract /A:203@OE1
224 atoms, 202 bonds, 3 pseudobonds, 25 residues, 2 models selected
> select add /A:203@OE1
225 atoms, 202 bonds, 3 pseudobonds, 25 residues, 2 models selected
> select add /S:615@NH1
226 atoms, 202 bonds, 3 pseudobonds, 26 residues, 2 models selected
Exactly two atoms must be selected!
[Repeated 2 time(s)]
> select subtract /S:615@NH1
225 atoms, 202 bonds, 3 pseudobonds, 25 residues, 2 models selected
> select add /S:615@NH1
226 atoms, 202 bonds, 3 pseudobonds, 26 residues, 2 models selected
Exactly two atoms must be selected!
> select subtract /A:203@OE1
225 atoms, 202 bonds, 3 pseudobonds, 26 residues, 2 models selected
> select add /A:203@OE1
226 atoms, 202 bonds, 3 pseudobonds, 26 residues, 2 models selected
Exactly two atoms must be selected!
> select add /S:615@NE
227 atoms, 202 bonds, 3 pseudobonds, 26 residues, 2 models selected
> select subtract /A:203@OE2
226 atoms, 201 bonds, 3 pseudobonds, 26 residues, 2 models selected
> select add /A:203@OE2
227 atoms, 201 bonds, 3 pseudobonds, 26 residues, 2 models selected
Exactly two atoms must be selected!
> select subtract /A:203@OE1
226 atoms, 201 bonds, 3 pseudobonds, 26 residues, 2 models selected
> select /S:615@NH1
1 atom, 1 residue, 1 model selected
> select /S:615@NH1
1 atom, 1 residue, 1 model selected
> select /S:615@NH1
1 atom, 1 residue, 1 model selected
> select add /A:203@OE1
2 atoms, 2 residues, 1 model selected
> distance /S:615@NH1 /A:203@OE1
Distance between /S ARG 615 NH1 and /A GLU 203 OE1: 2.889Å
> select add /A:203@OE2
3 atoms, 2 residues, 1 model selected
> select add /S:615@NE
4 atoms, 2 residues, 1 model selected
Exactly two atoms must be selected!
> distance style color #faaadf
[Repeated 2 time(s)]
> distance style color #faa9de
[Repeated 2 time(s)]
> distance style color #faa8dd
[Repeated 2 time(s)]
> distance style color #faa6da
[Repeated 2 time(s)]
> distance style color #faa4d7
[Repeated 2 time(s)]
> distance style color #faa3d7
[Repeated 2 time(s)]
> distance style color #faa3d6
[Repeated 2 time(s)]
> distance style color #faa2d6
[Repeated 2 time(s)]
> distance style color #fa98d2
[Repeated 2 time(s)]
> distance style color #fa8ccc
[Repeated 2 time(s)]
> distance style color #fa6db5
[Repeated 2 time(s)]
> distance style color #fa57a2
[Repeated 2 time(s)]
> distance style color #fa509b
[Repeated 2 time(s)]
> distance style color #fa5099
[Repeated 2 time(s)]
> distance style color #fa4e96
[Repeated 2 time(s)]
> distance style color #fa4d94
[Repeated 2 time(s)]
> distance style color #fa498c
[Repeated 2 time(s)]
> distance style color #fa417f
[Repeated 2 time(s)]
> distance style color #fa346a
[Repeated 2 time(s)]
> distance style color #fa2958
[Repeated 2 time(s)]
> distance style color #fa1f47
[Repeated 2 time(s)]
> distance style color #fa162f
[Repeated 2 time(s)]
> distance style color #fa131e
[Repeated 2 time(s)]
> distance style color #fa1319
[Repeated 2 time(s)]
> distance style color #fa1418
[Repeated 2 time(s)]
> distance style color #fa1417
[Repeated 2 time(s)]
> distance style color #fa1516
[Repeated 2 time(s)]
> distance style color #fa1a17
[Repeated 2 time(s)]
> distance style color #fa2319
[Repeated 2 time(s)]
> distance style color #fa2b1b
[Repeated 2 time(s)]
> distance style color #fa321c
[Repeated 2 time(s)]
> distance style color #fa391c
[Repeated 2 time(s)]
> distance style color #fa431b
[Repeated 2 time(s)]
> distance style color #fa4a1b
[Repeated 2 time(s)]
> distance style color #fa4c1a
[Repeated 2 time(s)]
> distance style color #fa5418
[Repeated 2 time(s)]
> distance style color #fa5c16
[Repeated 2 time(s)]
> distance style color #fa6015
[Repeated 2 time(s)]
> distance style color #fa6a13
[Repeated 2 time(s)]
> distance style color #fa7014
[Repeated 2 time(s)]
> distance style color #fa7615
[Repeated 2 time(s)]
> distance style color #fa8317
[Repeated 2 time(s)]
> distance style color #fa9a1e
[Repeated 2 time(s)]
> distance style color #faab24
[Repeated 2 time(s)]
> distance style color #fabc2a
[Repeated 2 time(s)]
> distance style color #fad839
[Repeated 2 time(s)]
> distance style color #fae13d
[Repeated 2 time(s)]
> distance style color #faf147
[Repeated 2 time(s)]
> distance style color #ecfa53
[Repeated 2 time(s)]
> distance style color #cafa5f
[Repeated 2 time(s)]
> distance style color #c1fa61
[Repeated 2 time(s)]
> distance style color #bcfa64
[Repeated 2 time(s)]
> distance style color #b8fa68
[Repeated 2 time(s)]
> distance style color #aefa71
[Repeated 2 time(s)]
> distance style color #a5fa7a
[Repeated 2 time(s)]
> distance style color #a2fa7d
[Repeated 2 time(s)]
> distance style color #9ffa80
[Repeated 2 time(s)]
> distance style color #9bfa84
[Repeated 2 time(s)]
> distance style color #9afa86
[Repeated 2 time(s)]
> distance style color #97fa8a
[Repeated 2 time(s)]
> distance style color #97fa8b
[Repeated 2 time(s)]
> distance style color #95fa8c
[Repeated 2 time(s)]
> distance style color #8efa8f
[Repeated 2 time(s)]
> distance style color #8ffa93
[Repeated 2 time(s)]
> distance style color #8ffa95
[Repeated 2 time(s)]
> distance style color #8ffa99
[Repeated 2 time(s)]
> distance style color #8ffa9c
[Repeated 2 time(s)]
> distance style color #90fa9d
[Repeated 2 time(s)]
> distance style color #8ffa9d
[Repeated 2 time(s)]
> distance style color #90fa9d
[Repeated 2 time(s)]
> distance style color #8ffa9d
[Repeated 2 time(s)]
> distance style color #8ffa9e
[Repeated 2 time(s)]
> distance style color #8ffa9f
[Repeated 2 time(s)]
> distance style color #8ffaa0
[Repeated 2 time(s)]
> distance style color #8efaa3
[Repeated 2 time(s)]
> distance style color #8bfaa8
[Repeated 2 time(s)]
> distance style color #89faac
[Repeated 2 time(s)]
> distance style color #87faaf
[Repeated 2 time(s)]
> distance style color #83fab5
[Repeated 2 time(s)]
> distance style color #83fab6
[Repeated 2 time(s)]
> distance style color #83fab7
[Repeated 2 time(s)]
> distance style color #83fabb
[Repeated 2 time(s)]
> distance style color #83fabc
[Repeated 2 time(s)]
> distance style color #83fabe
[Repeated 2 time(s)]
> distance style color #83fabf
[Repeated 2 time(s)]
> distance style color #84fabf
[Repeated 2 time(s)]
> distance style color #85fabf
[Repeated 2 time(s)]
> distance style color #88fabe
[Repeated 2 time(s)]
> distance style color #89fabe
[Repeated 2 time(s)]
> distance style color #8ffabf
[Repeated 2 time(s)]
> distance style color #98fabe
[Repeated 2 time(s)]
> distance style color #9efabd
[Repeated 2 time(s)]
> distance style color #9ffabd
[Repeated 2 time(s)]
> distance style color #9ffabc
[Repeated 2 time(s)]
> distance style color #a0fabb
[Repeated 2 time(s)]
> distance style color #a3fab7
[Repeated 2 time(s)]
> distance style color #a4fab3
[Repeated 2 time(s)]
> distance style color #a6faad
[Repeated 2 time(s)]
> distance style color #a7faa9
[Repeated 2 time(s)]
> distance style color #aefaa9
[Repeated 2 time(s)]
> distance style color #b3faa9
[Repeated 2 time(s)]
> distance style color #b5faa9
[Repeated 2 time(s)]
> distance style color #bcfaab
[Repeated 2 time(s)]
> distance style color #befaab
[Repeated 2 time(s)]
> distance style color #bffaab
[Repeated 2 time(s)]
> distance style color #c0faab
[Repeated 2 time(s)]
> distance style color #c2faac
[Repeated 2 time(s)]
> distance style color #cdfaaf
[Repeated 2 time(s)]
> distance style color #d5faaf
[Repeated 2 time(s)]
> distance style color #d6faaf
[Repeated 2 time(s)]
> distance style color #d7faaf
[Repeated 2 time(s)]
> distance style color #d8faaf
[Repeated 2 time(s)]
> distance style color #dafaaf
[Repeated 2 time(s)]
> distance style color #defaaf
[Repeated 2 time(s)]
> distance style color #e4faae
[Repeated 2 time(s)]
> distance style color #e6faae
[Repeated 2 time(s)]
> distance style color #e7faad
[Repeated 2 time(s)]
> distance style color #e8faae
[Repeated 2 time(s)]
> distance style color #eefaba
[Repeated 2 time(s)]
> distance style color #f4fac5
[Repeated 2 time(s)]
> distance style color #f9face
[Repeated 2 time(s)]
> distance style color #faf7d5
[Repeated 2 time(s)]
> distance style color #faf6d5
[Repeated 2 time(s)]
> distance style color #fae7dd
[Repeated 2 time(s)]
> distance style color #fad9db
[Repeated 2 time(s)]
> distance style color #fac9dc
[Repeated 2 time(s)]
> distance style color #fac1db
[Repeated 2 time(s)]
> distance style color #fac1da
[Repeated 2 time(s)]
> distance style color #fac1d0
[Repeated 2 time(s)]
> distance style color #fac1cb
[Repeated 2 time(s)]
> distance style color #fac0c4
[Repeated 2 time(s)]
> distance style color #fac0c2
[Repeated 2 time(s)]
> distance style color #fac0c1
[Repeated 2 time(s)]
> distance style color #fabfc1
[Repeated 2 time(s)]
> distance style color #fac3c0
[Repeated 2 time(s)]
> distance style color #fac7c0
[Repeated 2 time(s)]
> distance style color #fad0bf
[Repeated 2 time(s)]
> distance style color #fadabd
[Repeated 2 time(s)]
> distance style color #fadebb
[Repeated 2 time(s)]
> distance style color #fae1ba
[Repeated 2 time(s)]
> distance style color #fae3b8
[Repeated 2 time(s)]
> distance style color #fae6b4
[Repeated 2 time(s)]
> distance style color #fae8b2
[Repeated 2 time(s)]
> distance style color #faefa8
[Repeated 2 time(s)]
> distance style color #faf2a3
[Repeated 2 time(s)]
> distance style color #faf59f
[Repeated 2 time(s)]
> distance style color #faf69e
[Repeated 2 time(s)]
> distance style color #faf69d
[Repeated 2 time(s)]
> distance style color #faf69c
[Repeated 2 time(s)]
> distance style color #faf79b
[Repeated 2 time(s)]
> distance style color #faf79a
[Repeated 2 time(s)]
> distance style color #faf89a
[Repeated 2 time(s)]
> distance style color #f7fa93
[Repeated 2 time(s)]
> distance style color #f4fa8f
[Repeated 2 time(s)]
> distance style color #ecfa84
[Repeated 2 time(s)]
> distance style color #e8fa7f
[Repeated 2 time(s)]
> distance style color #e5fa7c
[Repeated 2 time(s)]
> distance style color #e4fa7a
[Repeated 2 time(s)]
> distance style color #e3fa79
[Repeated 2 time(s)]
> distance style color #e1fa76
[Repeated 2 time(s)]
> distance style color #dffa72
[Repeated 2 time(s)]
> distance style color #dffa71
[Repeated 2 time(s)]
> distance style color #ddfa6e
[Repeated 2 time(s)]
> distance style color #dbfa6b
[Repeated 2 time(s)]
> distance style color #d8fa67
[Repeated 2 time(s)]
> distance style color #d6fa63
[Repeated 2 time(s)]
> distance style color #d4fa61
[Repeated 2 time(s)]
> distance style color #d1fa5d
[Repeated 2 time(s)]
> distance style color #d0fa5c
[Repeated 2 time(s)]
> distance style color #d0fa5b
[Repeated 2 time(s)]
> distance style color #d0fa5a
[Repeated 2 time(s)]
> distance style color #d0fa59
[Repeated 2 time(s)]
> distance style color #d0fa58
[Repeated 2 time(s)]
> distance style color #d0fa57
[Repeated 2 time(s)]
> select /A:203@OE2
1 atom, 1 residue, 1 model selected
> select add /S:615@NE
2 atoms, 2 residues, 1 model selected
> distance /A:203@OE2 /S:615@NE
Distance between /A GLU 203 OE2 and /S ARG 615 NE: 2.732Å
> select /A:203@OE1
1 atom, 1 residue, 1 model selected
> select add /S:615@NE
2 atoms, 2 residues, 1 model selected
> distance /A:203@OE1 /S:615@NE
Distance between /A GLU 203 OE1 and /S ARG 615 NE: 3.410Å
> color #2 #70fa92ff models
> color #2 #8ffa98ff models
> color #2 #8efa98ff models
> color #2 #85fa96ff models
> select subtract /A:203
1 atom, 1 residue, 1 model selected
> select /A:203
9 atoms, 8 bonds, 1 pseudobond, 1 residue, 2 models selected
> select subtract /A:203
Nothing selected
> select /A:203
9 atoms, 8 bonds, 1 pseudobond, 1 residue, 2 models selected
> color (#!1 & sel) byhetero
> select subtract /A:203
Nothing selected
> select add /A:203
9 atoms, 8 bonds, 1 pseudobond, 1 residue, 2 models selected
> color (#!1 & sel) byelement
> color #2 #f58db6ff models
> color #2 black models
> swapaa D#1:203.a
Missing or invalid "residues" argument: only initial part "D" of atom
specifier valid
> swapaa D#1:203.A
Missing or invalid "residues" argument: only initial part "D" of atom
specifier valid
> swapaa D #1:203.A
No amino acid residues specified for swapping
> list residues
Unknown command: list residues
> swapaa asp #1:203.a
Missing or invalid "residues" argument: invalid residues specifier
> swapaa asp #1:203.A
Missing or invalid "residues" argument: invalid residues specifier
> swapaa Glu #1:203.a
Missing or invalid "residues" argument: invalid residues specifier
OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M395X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac17,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3,3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 24 GB
System Firmware Version: 512.0.0.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.34f3
Software:
System Software Overview:
System Version: macOS 12.6.8 (21G725)
Kernel Version: Darwin 21.6.0
Time since boot: 1 day 10 minutes
Graphics/Displays:
AMD Radeon R9 M395X:
Chipset Model: AMD Radeon R9 M395X
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x6920
Revision ID: 0x0000
ROM Revision: 113-C905AA-799
VBIOS Version: 113-C905A0-007
EFI Driver Version: 01.00.799
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-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: 1.8rc202405282004
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.13
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.2
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.52.4
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.45
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.0
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Sofia,
--Eric