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Opened 5 years ago
Closed 5 years ago
#3564 closed defect (fixed)
mmcif.find_template_residue() sometimes mistakenly claims template does not exist
| Reported by: | Tristan Croll | Owned by: | Greg Couch |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-1127.13.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Every now and again, `mmcif.find_template_residue()` throws this error for a template that actually does exist (and downloads correctly on a repeat call). I guess the server's returning some error that's being misinterpreted? Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing /home/tic20/.cache/ChimeraX/1.0/installers/ChimeraX_ISOLDE-1.0rc1-cp37-cp37m-linux_x86_64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Arrays~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper~=0.13.0 in /home/tic20/.local/share/ChimeraX/1.0/site-packages (from ChimeraX- ISOLDE==1.0rc1) (0.13.0) Requirement already satisfied, skipping upgrade: ChimeraX- Core~=1.0rc202005052344 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Graphics~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Geometry~=1.0 in /opt/UCSF/ChimeraX/lib/python3.7/site-packages (from ChimeraX- Atomic>=1.0->ChimeraX-ISOLDE==1.0rc1) (1.0) Installing collected packages: ChimeraX-ISOLDE Attempting uninstall: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0rc1 Uninstalling ChimeraX-ISOLDE-1.0rc1: Successfully uninstalled ChimeraX-ISOLDE-1.0rc1 Successfully installed ChimeraX-ISOLDE-1.0rc1 Lock 140457846893328 acquired on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock Lock 140457846893328 released on /home/tic20/.cache/ChimeraX/1.0/toolshed/bundle_info.cache.lock WARNING: You are using pip version 20.1; however, version 20.2 is available. You should consider upgrading via the '/usr/bin/chimerax -m pip install --upgrade pip' command. > isolde demo crystal_intro > set selectionWidth 4 before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb #1 --- Chain | Description A | predicted microcompartment protein Done loading forcefield before.pdb title: Crystal structure of etub from clostridium kluyveri [more info...] Chain information for before.pdb --- Chain | Description 1.2/A | predicted microcompartment protein WARNING: multiple experimental reflection datasets found: (dataset) FOBS, SIGFOBS, (dataset) IOBS, SIGIOBS, (dataset) DANO, SIGDANO, (dataset) F(+), SIGF(+), F(-), SIGF(-), (dataset) I(+), SIGI(+), I(-), SIGI(-) Automatically choosing "(dataset) IOBS, SIGIOBS". Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Loaded crystallographic demo: PDB ID 3io0 > delete HC Fetching CCD THC from http://ligand-expo.rcsb.org/reports/T/THC/THC.cif > color sel bychain > color sel byhetero Fetching CCD AME from http://ligand-expo.rcsb.org/reports/A/AME/AME.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif Fetching CCD N7P from http://ligand-expo.rcsb.org/reports/N/N7P/N7P.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD NLG from http://ligand-expo.rcsb.org/reports/N/NLG/NLG.cif Fetching CCD CGU from http://ligand-expo.rcsb.org/reports/C/CGU/CGU.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD DAH from http://ligand-expo.rcsb.org/reports/D/DAH/DAH.cif Fetching CCD 5CR from http://ligand-expo.rcsb.org/reports/5/5CR/5CR.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD SER_LL_DHG from http://ligand- expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif Fetching CCD SER_LSN3_DHG from http://ligand- expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif Fetching CCD THR_LL_DHG1 from http://ligand- expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif Fetching CCD SER_LEO2_DHG from http://ligand- expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif Fetching CCD THR_LSN3_DHG1 from http://ligand- expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif Fetching CCD SER_LFZW_DHG from http://ligand- expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif Fetching CCD THR_LEO2_DHG1 from http://ligand- expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif Fetching CCD THR_LFZW_DHG1 from http://ligand- expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD SAC from http://ligand-expo.rcsb.org/reports/S/SAC/SAC.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD HIC from http://ligand-expo.rcsb.org/reports/H/HIC/HIC.cif Fetching CCD NMM from http://ligand-expo.rcsb.org/reports/N/NMM/NMM.cif Fetching CCD DA2 from http://ligand-expo.rcsb.org/reports/D/DA2/DA2.cif > color sel bychain > color sel byhetero Fetching CCD LYZ from http://ligand-expo.rcsb.org/reports/L/LYZ/LYZ.cif Fetching CCD MLZ from http://ligand-expo.rcsb.org/reports/M/MLZ/MLZ.cif > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero > color sel bychain > color sel byhetero Fetching CCD SC2 from http://ligand-expo.rcsb.org/reports/S/SC2/SC2.cif > color sel bychain > color sel byhetero Traceback (most recent call last): File "/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py", line 2514, in _show_selected_unparameterised_residue ccd_template, description = get_ccd_template_and_name(self.session, tname) File "/home/tic20/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py", line 2499, in get_ccd_template_and_name tmpl = mmcif.find_template_residue(session, ccd_name) File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 378, in find_template_residue return _mmcif.find_template_residue(name) ValueError: No template for residue type AAG ValueError: No template for residue type AAG File "/opt/UCSF/ChimeraX/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py", line 378, in find_template_residue return _mmcif.find_template_residue(name) See log for complete Python traceback. Fetching CCD AAG from http://ligand-expo.rcsb.org/reports/A/AAG/AAG.cif OpenGL version: 3.3.0 NVIDIA 450.51.05 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision T5600 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 5.4G 48G 167M 8.8G 56G Swap: 4.9G 0B 4.9G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1) Subsystem: NVIDIA Corporation Device [10de:11df] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → mmcif.find_template_residue() sometimes mistakenly claims template does not exist |
comment:2 by , 5 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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You should expect it to fail sometimes. If the network is slow, then fetching a CCD entry can timeout (it is probably too short at 15-seconds).
The daily build works around this problem by caching the failures. I've changed the code to use the default minute initial timeout, and then fail immediately for the next 10 minutes.