Sequence-Viewer-generated 'select' command bad if blank chain ID

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202108040454 (2021-08-04 04:54:51 UTC)
Description
selecting columns to select structure with blank chain causes error

session blankchain.cxs attached

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

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

executed startup.cxc  
UCSF ChimeraX version: 1.3.dev202108040454 (2021-08-04)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6ir5 format mmcif fromDatabase pdb

6ir5 title:  
P domain of GII.3-TV24 [more info...]  
  
Chain information for 6ir5 #1  
---  
Chain | Description | UniProt  
A B C D | VP1 Capsid protein | Q66296_9CALI  
  

> open G*a.pdb

Chain information for GII3a.pdb #2  
---  
Chain | Description  
? | No description available  
  

> mmaker #2 to #1/A show true

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 6ir5, chain A (#1) with GII3a.pdb, chain (blank) (#2), sequence
alignment score = 1586.9  
Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Hiding conservation header for alignment 1  
Chains used in RMSD evaluation for alignment 1: 6ir5 #1/A, GII3a.pdb #2/?  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 301 pruned atom pairs is 0.217 angstroms; (across all 301 pairs:
0.217)  
  

> select #1/A:289

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:289 #2/ :73

Expected a keyword  

> save blankchain.cxs




OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 427.140.8.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1323)
      Kernel Version: Darwin 19.6.0
      Time since boot: 3:42

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
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    certifi: 2021.5.30
    cftime: 1.5.0
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    ChimeraX-AddCharge: 1.1.4
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    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
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    ChimeraX-AtomicLibrary: 4.1
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    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
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    ChimeraX-BugReporter: 1.0
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    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
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    ChimeraX-Core: 1.3.dev202108040454
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    ChimeraX-Crystal: 1.0
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    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-MapEraser: 1.0
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    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
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    ChimeraX-MatchMaker: 1.2.1
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    ChimeraX-Nucleotides: 2.0.2
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    ChimeraX-PDB: 2.5.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
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    ChimeraX-PubChem: 2.1
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    ChimeraX-Registration: 1.1
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    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
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    ChimeraX-SaveCommand: 1.5
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File attachment: blankchain.cxs

blankchain.cxs​

[Elaine Meng]

Added by email2trac

[pett]

"concise_residue_spec" routine wasn't handling blank chain IDs correctly