Opened 13 months ago

Closed 13 months ago

Last modified 13 months ago

#16222 closed defect (fixed)

Similar Structures: key error from clicking Traces

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Comparison Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.7-arm64-arm-64bit
ChimeraX Version: 1.9.dev202410300405 (2024-10-30 04:05:08 UTC)
Description
using Similar Structures tool

Not sure of the series of events that causes this but I opened a previously saved mmseqs2 search from a .sms file.  Then I clicked Ligands, which fetched structures and showed ligands successfully.
Then I clicked Traces, which again started to fetch structures but then ran into this error.

Another possibly unintended observation is that when I open an sms file it makes another identical sms file.  I'll attach one of them

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; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  
UCSF ChimeraX version: 1.9.dev202410300405 (2024-10-30)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/meng/Desktop/startup.cxc format cmd

> 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; ui dockable false "Help Viewer"

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html; ui dockable false "Help Viewer"

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

> alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-
> channel.html; ui dockable false "Help Viewer"; windowsize 600 800

executed startup.cxc  

> open /Users/meng/Downloads/ChimeraX/Foldseek/1hxz_foldseek_pdb_1_2.sms
> format sms

No such file/path:
/Users/meng/Downloads/ChimeraX/Foldseek/1hxz_foldseek_pdb_1_2.sms  

> open /Users/meng/Downloads/ChimeraX/MMseqs2/1hxz_mmseqs2_pdb.sms format sms

Summary of feedback from opening
/Users/meng/Downloads/ChimeraX/MMseqs2/1hxz_mmseqs2_pdb.sms  
---  
notes | > open /Users/meng/Downloads/ChimeraX/PDB/1hxz.cif1hxz.cif title:  
Miniprotein MP-2 complex with streptavidin [more info...]  
  
  
  
  
| Chain information for 1hxz.cif #1  
  
---  
  
  
Chain  
| Description  
| UniProt  
  
  
  
  
  
A B  
| STREPTAVIDIN  
| SAV_STRAV 11-139  
  
  
  
C D  
| MP-2  
|  
  
  
  
  
  
1hxz.cif mmCIF Assemblies  
  
---  
1| author_and_software_defined_assembly  
  
  
Found 9 similar structures to 1hxz.cif #1/D in pdb database using mmseqs2,
name mm1  
  
Read 9 similar structures to 1hxz.cif #1/D in pdb database using mmseqs2, name
mm1  

> close session

> open /Users/meng/Downloads/ChimeraX/Foldseek/2gbp_foldseek_pdb.sms format
> sms

Summary of feedback from opening
/Users/meng/Downloads/ChimeraX/Foldseek/2gbp_foldseek_pdb.sms  
---  
notes | > open /Users/meng/Downloads/ChimeraX/PDB/2gbp.cif2gbp.cif title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
  
  
  
| Chain information for 2gbp.cif #1  
  
---  
  
  
Chain  
| Description  
| UniProt  
  
  
  
  
  
A  
| D-GALACTOSE/D-GLUCOSE BINDING PROTEIN  
| DGAL_ECOLI 1-309  
  
  
  
  
  
  
  
Non-standard residues in 2gbp.cif #1  
  
---  
  
  
  
  
BGC — β-D-glucose  
  
  
  
CA — calcium ion  
  
  
  
  
Found 727 similar structures to 2gbp.cif #1/A in pdb database using foldseek,
name fs1  
  
Read 727 similar structures to 2gbp.cif #1/A in pdb database using foldseek,
name fs1  

> sequence search /A

Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2,
name mm1  

> similarstructures fetchcoords

Fetching compressed mmCIF 1glg from http://files.rcsb.org/download/1glg.cif  
Fetching compressed mmCIF 2fvy from http://files.rcsb.org/download/2fvy.cif  
Fetching CCD CO2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/CO2/CO2.cif  
Fetching compressed mmCIF 2hph from http://files.rcsb.org/download/2hph.cif  
Fetching compressed mmCIF 2qw1 from http://files.rcsb.org/download/2qw1.cif  
Fetching CCD 3MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/3MG/3MG.cif  
Fetching compressed mmCIF 2ipn from http://files.rcsb.org/download/2ipn.cif  
Fetching compressed mmCIF 2ipm from http://files.rcsb.org/download/2ipm.cif  
Fetching compressed mmCIF 2ipl from http://files.rcsb.org/download/2ipl.cif  
Fetching compressed mmCIF 8fxt from http://files.rcsb.org/download/8fxt.cif  
Fetching CCD YDM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/YDM/YDM.cif  
Fetching compressed mmCIF 1gca from http://files.rcsb.org/download/1gca.cif  
Fetching compressed mmCIF 3ga5 from http://files.rcsb.org/download/3ga5.cif  
Fetching CCD RGG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/RGG/RGG.cif  
Fetching CCD SCN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/SCN/SCN.cif  
Fetching compressed mmCIF 5kws from http://files.rcsb.org/download/5kws.cif  
Fetching compressed mmCIF 4z0n from http://files.rcsb.org/download/4z0n.cif  
Fetching compressed mmCIF 8fxu from http://files.rcsb.org/download/8fxu.cif  
Fetching CCD YDQ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/YDQ/YDQ.cif  
Fetching compressed mmCIF 4yo7 from http://files.rcsb.org/download/4yo7.cif  
Fetching CCD INS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/INS/INS.cif  
Fetching compressed mmCIF 5jx2 from http://files.rcsb.org/download/5jx2.cif  
Fetching CCD ALY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ALY/ALY.cif  
Fetching CCD BTB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/BTB/BTB.cif  
Fetching compressed mmCIF 6bgc from http://files.rcsb.org/download/6bgc.cif  
Fetching compressed mmCIF 6bgd from http://files.rcsb.org/download/6bgd.cif  
Fetching compressed mmCIF 4rsm from http://files.rcsb.org/download/4rsm.cif  
Fetching CCD 3VB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/3VB/3VB.cif  
Fetching compressed mmCIF 4rs3 from http://files.rcsb.org/download/4rs3.cif  
Fetching CCD XYL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/XYL/XYL.cif  
Fetching compressed mmCIF 5hko from http://files.rcsb.org/download/5hko.cif  
Fetching CCD 62W from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/W/62W/62W.cif  
Fetching compressed mmCIF 2ioy from http://files.rcsb.org/download/2ioy.cif  
Fetching CCD RIP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/RIP/RIP.cif  
Fetching compressed mmCIF 7e7m from http://files.rcsb.org/download/7e7m.cif  
Fetching compressed mmCIF 2gx6 from http://files.rcsb.org/download/2gx6.cif  
Fetching compressed mmCIF 3urm from http://files.rcsb.org/download/3urm.cif  
Fetching compressed mmCIF 3uug from http://files.rcsb.org/download/3uug.cif  
Fetching CCD BDP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/BDP/BDP.cif  
Fetching compressed mmCIF 1urp from http://files.rcsb.org/download/1urp.cif  
Fetching compressed mmCIF 2dri from http://files.rcsb.org/download/2dri.cif  
Fetching compressed mmCIF 4yv7 from http://files.rcsb.org/download/4yv7.cif  
Fetching compressed mmCIF 1drj from http://files.rcsb.org/download/1drj.cif  
Fetching compressed mmCIF 1drk from http://files.rcsb.org/download/1drk.cif  
Fetching compressed mmCIF 4zjp from http://files.rcsb.org/download/4zjp.cif  
Fetching compressed mmCIF 1dbp from http://files.rcsb.org/download/1dbp.cif  
Fetching compressed mmCIF 4ry0 from http://files.rcsb.org/download/4ry0.cif  
Fetching compressed mmCIF 5ibq from http://files.rcsb.org/download/5ibq.cif  
Fetching CCD XXM from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/XXM/XXM.cif  
Fetching compressed mmCIF 1ba2 from http://files.rcsb.org/download/1ba2.cif  
Fetching compressed mmCIF 4ry9 from http://files.rcsb.org/download/4ry9.cif  
Fetching CCD TLZ from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/TLZ/TLZ.cif  
Fetching compressed mmCIF 4ys6 from http://files.rcsb.org/download/4ys6.cif  
Fetching compressed mmCIF 4irx from http://files.rcsb.org/download/4irx.cif  
Fetching compressed mmCIF 4ywh from http://files.rcsb.org/download/4ywh.cif  
Fetching CCD XYP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/XYP/XYP.cif  
Fetching compressed mmCIF 4wwh from http://files.rcsb.org/download/4wwh.cif  
Fetching compressed mmCIF 5dte from http://files.rcsb.org/download/5dte.cif  
Fetching CCD ALL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/ALL/ALL.cif  
Fetching compressed mmCIF 6hb0 from http://files.rcsb.org/download/6hb0.cif  
Fetching compressed mmCIF 6hbd from http://files.rcsb.org/download/6hbd.cif  
Fetching compressed mmCIF 6hbm from http://files.rcsb.org/download/6hbm.cif  
Fetching CCD AHR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/AHR/AHR.cif  
Fetching compressed mmCIF 6hyh from http://files.rcsb.org/download/6hyh.cif  
Fetching CCD GYE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/GYE/GYE.cif  
Fetching compressed mmCIF 4rxm from http://files.rcsb.org/download/4rxm.cif  
Fetching compressed mmCIF 3m9w from http://files.rcsb.org/download/3m9w.cif  
Fetching compressed mmCIF 3m9x from http://files.rcsb.org/download/3m9x.cif  
Fetching compressed mmCIF 3ma0 from http://files.rcsb.org/download/3ma0.cif  
Fetching compressed mmCIF 1gub from http://files.rcsb.org/download/1gub.cif  
Fetching compressed mmCIF 1gud from http://files.rcsb.org/download/1gud.cif  
Fetching compressed mmCIF 1rpj from http://files.rcsb.org/download/1rpj.cif  
Fetching compressed mmCIF 2rjo from http://files.rcsb.org/download/2rjo.cif  
Fetching compressed mmCIF 5ocp from http://files.rcsb.org/download/5ocp.cif  
Fetching CCD FUB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/FUB/FUB.cif  
Fetching compressed mmCIF 4yle from http://files.rcsb.org/download/4yle.cif  
Fetching compressed mmCIF 8wl5 from http://files.rcsb.org/download/8wl5.cif  
Fetching compressed mmCIF 8wl7 from http://files.rcsb.org/download/8wl7.cif  
Fetching compressed mmCIF 8wl9 from http://files.rcsb.org/download/8wl9.cif  
Fetching compressed mmCIF 8wlb from http://files.rcsb.org/download/8wlb.cif  
Fetching CCD WEB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/WEB/WEB.cif  
Fetching compressed mmCIF 3l6u from http://files.rcsb.org/download/3l6u.cif  
Fetching compressed mmCIF 3rot from http://files.rcsb.org/download/3rot.cif  
Fetched coordinates for 99 hits, time 0:35  
Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2,
name mm1  

> sequence search /A

Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2,
name mm2  

> similarstructures traces

> foldseek /A

Found 727 similar structures to 2gbp.cif #1/A in pdb database using foldseek,
name fs1  

> open /Users/meng/Downloads/ChimeraX/mmseqs2/2gbp*sms

Summary of feedback from opening
/Users/meng/Downloads/ChimeraX/mmseqs2/2gbp_mmseqs2_pdb.sms  
---  
note | Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm1  
  
Summary of feedback from opening
/Users/meng/Downloads/ChimeraX/mmseqs2/2gbp_mmseqs2_pdb_1.sms  
---  
note | Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2, name mm2  
  
Read 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2,
name mm1  
Read 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2,
name mm2  

> similarstructures ligands

Found 8973 ligands in 99 hits: 3MG, 62W, ACT, AHR, ALL, ASP, BGC, BTB, CA,
CIT, CL, CO2, EDO, FUB, GAL, GLC, GOL, GYE, GZL, HOH, INS, MG, MLA, NA, PO4,
RGG, RIP, SO4, TRS, UNL, WEB, XYL, XYP, YDM, YDQ, ZN  

> similarstructures traces

Fetched coordinates for 99 hits, time 0:02  
Found 99 similar structures to 2gbp.cif #1/A in pdb database using mmseqs2,
name mm2  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/gui.py", line 333, in
_show_backbone_traces  
run(self.session, cmd)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/traces.py", line 80, in
similar_structures_traces  
hresname = [hitseq[i] for i in hi]  
^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/traces.py", line 80, in <listcomp>  
hresname = [hitseq[i] for i in hi]  
~~~~~~^^^  
KeyError: 0  
  
KeyError: 0  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/similarstructures/traces.py", line 80, in  
hresname = [hitseq[i] for i in hi]  
~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
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: MacBook Pro
      Model Identifier: MacBookPro18,1
      Model Number: MK1F3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.1.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7 (23H124)
      Kernel Version: Darwin 23.6.0
      Time since boot: 5 hours, 34 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.7.1
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    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: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.7
    ChimeraX-AtomicLibrary: 14.1.10
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.7
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13
    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-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.dev202410300405
    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-Dicom: 1.2.5
    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
    ChimeraX-Label: 1.1.11
    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-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    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: 1.5.17
    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-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-PhenixUI: 1.3
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.1
    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
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    ChimeraX-SchemeMgr: 1.0
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    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.2.2
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
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    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-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
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.0
    coverage: 7.6.4
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.7
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.54.1
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.12.1
    html2text: 2024.2.26
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
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    jedi: 0.19.1
    Jinja2: 3.1.4
    joblib: 1.4.2
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    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
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File attachment: 2gbp_mmseqs2_pdb.sms

2gbp_mmseqs2_pdb.sms​

Attachments (1)

2gbp_mmseqs2_pdb.sms​ (1.3 MB ) - added by Elaine Meng 13 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (7)

by Elaine Meng, 13 months ago

Attachment: 2gbp_mmseqs2_pdb.sms​ added

Added by email2trac

comment:1 by Elaine Meng, 13 months ago

Component: Unassigned → Structure Comparison
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Similar Structures: key error from clicking Traces

comment:2 by Tom Goddard, 13 months ago

Thanks. This is a bug in the new c-alpha traces code I wrote yesterday to replace the tubes. You are a pro at finding cases that break things which is great. I tried different searches using foldseek, mmseqs2, and blast and they all worked, but the error probably depends on the actual query protein.

The making a new .sms file is probably something I forgot to describe in my write-up. When you fetch coordinates mmseqs2 or blast search results it writes a new .sms file that includes those coordinates. Actually it is supposed to rewrite the old .sms file adding the C-alpha coordinates. So I am not sure why it is writing a new .sms. But I think I saw this when testing your 1hxz duplicates error and I planned to investigate that today.

comment:3 by Tom Goddard, 13 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The C-alpha traces code I added yesterday was not properly computing the amino acids to use for the trace residues. It used the wrong array index.

Please report the problem of the extra .sms files separately. I will look for what caused it.

comment:4 by Tom Goddard, 13 months ago

Actually I have not seen extra .sms files created as you describe "when I open an sms file it makes another identical sms file". Each search produces a new .sms file. And existing .sms files are rewritten when C-alpha coordinates are fetched. But there should be no new .sms file when you just open an existing .sms file. Let me know if you see this behavior and how you get it to happen.

I did just fix an error where a third search with the same structure and method produces a file 1xyz_foldseek_pdb_1_2.sms instead of the correct _2.sms suffix.

comment:5 by Elaine Meng, 13 months ago 

I may have been confused about the files.  I thought I hadn't done 2 searches with the same parameters, but perhaps I did!  So ignore that comment for now, unless I find a case I'm sure about.  Thanks!

comment:6 by Tom Goddard, 13 months ago

Ok. I noticed the file names when a search is done were like 1hxz_foldseek_pdb.sms without listing the chain. It is useful to know the chain, so I just changed the code so the file name will include the chain 1hxz_D_foldseek_pdb.sms. If there is only one chain in the query structure then it is omitted from the filename.

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