id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3564 mmcif.find_template_residue() sometimes mistakenly claims template does not exist Tristan Croll Greg Couch "{{{ 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 }}} " defect closed normal Input/Output fixed all ChimeraX