XMAS: parse_sequence_dbs: list index out of range

[rsouzaamado777@…]

The following bug report has been submitted:
Platform:        macOS-10.15.6-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Hey guys, I came up with this problem. I am generating my crosslinking data from SIM-XL (http://patternlabforproteomics.org/sim-xl/index.html).
But I am still able to generate a .mzid file. I don't know if it some incompatibility issue with my evidence file.  However I believe .mzid files should be standarized files for proteomics.

Being getting the following bug:
"
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-packages/chimerax/xmas/mzidentml.py", line 104, in parse_sequence_dbs
sq.ProteinDescription = cv_param[0].getAttribute("value")
"
Best,
R.

(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show XMAS

> open "/Users/rodolphocarvalho/Desktop/Ycf1/Xplex XL-
> MS/SIMXL_results/AF-P39109-F1-model_v2.pdb" format pdb

AF-P39109-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for metal resistance protein YCF1 (P39109)
[more info...]  
  
Chain information for AF-P39109-F1-model_v2.pdb #1  
---  
Chain | Description | UniProt  
A | metal resistance protein YCF1 | YCFI_YEAST  
  
Traceback (most recent call last):  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 285, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s,  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 443, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/tool.py", line 456, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 37, in __init__  
evidence = cls(evidence_file)  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/read_evidence.py", line 51, in __init__  
self.peptide_pairs = parse_xl_peptides(evidence_file)  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/mzidentml.py", line 166, in parse_xl_peptides  
dbs = parse_sequence_dbs(mzidentfile)  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/mzidentml.py", line 104, in parse_sequence_dbs  
sq.ProteinDescription = cv_param[0].getAttribute("value")  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/Users/rodolphocarvalho/Library/Application Support/ChimeraX/1.3/site-
packages/chimerax/xmas/mzidentml.py", line 104, in parse_sequence_dbs  
sq.ProteinDescription = cv_param[0].getAttribute("value")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel HD Graphics 5000 OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir6,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 4 GB
      Boot ROM Version: 122.0.0.0.0
      SMC Version (system): 2.13f15

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G73)
      Kernel Version: Darwin 19.6.0
      Time since boot: 23:42

Graphics/Displays:

    Intel HD Graphics 5000:

      Chipset Model: Intel HD Graphics 5000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a26
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          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
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    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
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    ChimeraX-ChemGroup: 2.0
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    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
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    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
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    ChimeraX-HKCage: 1.3
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[pett]

Reported by Rodolpho Souza Amado de Carvalho

[pett]

Fixed with newest release of XMAS (1.1.3)