Alt locs vs. coordinate sets

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
The attached PDB was created by saving a series of individual models (identical atoms, different coordinates) with "save trajectory_inbound.pdb #1-10". For some reason when I open it with "open trajectory_inbound.pdb coordset true" then the bisphosphoglycerate (residue name X15, /B:1420) is fixed in space across all frames. I've double-checked that the coordinates in the PDB file change between models, and you can see that for yourself if you open it with coordset false. I think it's *probably* because (only) that residue has all its atoms in altoc A (it shouldn't actually have an altloc - an oversight when copying the residue in from another model). 

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd "C:/Users/Tristan Croll/Documents/Structures/PGK1/2xe7"

Current working directory is: C:\Users\Tristan
Croll\Documents\Structures\PGK1\2xe7  

> open trajectory_inbound.pdb #1 coordsets true

'#1' has no suffix  

> open trajectory_inbound.pdb coordsets true

Chain information for trajectory_inbound.pdb #1  
---  
Chain | Description  
A | No description available  
  
trajectory_inbound.pdb has 144 coordinate sets  

> close

> open trajectory_inbound.pdb coordsets true

Chain information for trajectory_inbound.pdb #1  
---  
Chain | Description  
A | No description available  
  
trajectory_inbound.pdb has 99 coordinate sets  

> close

> open trajectory_inbound.pdb coordsets true

Chain information for trajectory_inbound.pdb #1  
---  
Chain | Description  
A | No description available  
  
trajectory_inbound.pdb has 10 coordinate sets  

> open trajectory_inbound.pdb

Chain information for trajectory_inbound.pdb  
---  
Chain | Description  
2.1/A | No description available  
2.2/A 2.3/A 2.4/A 2.5/A 2.6/A 2.7/A 2.8/A 2.9/A 2.10/A | No description
available  
  

> close #2

> ui tool show "Altloc Explorer"

> hbonds /B & @@num_alt_locs>1 interModel false reveal true name "altloc
> H-bonds" updateGroup true

Atom specifier selects no atoms  

> show /B:1420

> view /B:1420

> show /B:1420

> view /B:1420




OpenGL version: 3.3.0 NVIDIA 528.24
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 34,007,068,672
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-GB

Installed Packages:
    -himerax-isolde: 1.6.0
    -himerax-qscore: 1.0
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
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    beautifulsoup4: 4.11.2
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    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
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    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
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    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BugReporter: 1.0.1
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    ChimeraX-ChangeChains: 1.0.2
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    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
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    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
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    ChimeraX-PubChem: 2.1
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    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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File attachment: trajectory_inbound.pdb

trajectory_inbound.pdb​

[Tristan Croll]

Added by email2trac

[Eric Pettersen]

Hi Tristan,

In ChimeraX it's either alt locs or coordinate sets, but not both. If an atom has an alt loc, its xyz coordinate will come from looking in the atom's alt loc dictionary, not by indexing into the coordinate set.

--Eric