id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3221 Chain mix up using ISOLDE Tristan Croll Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-05-09) Description Just had a *really* weird glitch (that I can't replicate). Opened 6yyt and its map (EMD 11007), associated with Clipper, added hydrogens, started ISOLDE and tried to simulate... at which point somehow chain P had been reassigned as chain Q. Since there was already another chain Q (identical in sequence to P) ISOLDE refused to start a simulation. After working out what was going on I closed the model, which caused a segmentation fault (unfortunately I didn't have core dumps enabled, so didn't catch it for analysis). Reopened everything, and this time it all works fine. Log: UCSF ChimeraX version: 1.0rc202005090702 (2020-05-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6yyt 6yyt title: Structure of replicating SARS-CoV-2 polymerase [more info...] Chain information for 6yyt #1 --- Chain | Description A | nsp12 B D | nsp8 C | nsp7 P Q T U | RNA product Non-standard residues in 6yyt #1 --- ZN — zinc ion > open 11007 fromDatabase emdb Opened emd_11007.map, grid size 240,240,240, pixel 0.834, shown at level 3.34, step 1, values float32 > select /P 298 atoms, 332 bonds, 1 model selected > select /Q 298 atoms, 332 bonds, 1 model selected > clipper associate #2 toModel #1 6yyt title: Structure of replicating SARS-CoV-2 polymerase [more info...] Chain information for 6yyt --- Chain | Description 1.2/A | nsp12 1.2/B 1.2/D | nsp8 1.2/C | nsp7 1.2/P 1.2/Q 1.2/T 1.2/U | RNA product Non-standard residues in 6yyt #1.2 --- ZN — zinc ion > select /P 298 atoms, 332 bonds, 1 model selected > select /Q 298 atoms, 332 bonds, 1 model selected > select /P:5@OP2 1 atom, 1 model selected > preset custom ""make bond"" > open /home/tic20/chimerax_presets/make_bond.py executed make_bond.py Preset implemented in Python; no expansion to individual ChimeraX commands available. > select clear > select /P 298 atoms, 332 bonds, 1 model selected > select /Q 298 atoms, 332 bonds, 1 model selected > addh Summary of feedback from adding hydrogens to 6yyt #1.2 --- warnings | Not adding hydrogens to /B PHE 6 CB because it is missing heavy- atom bond partners Not adding hydrogens to /B SER 7 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B SER 8 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B SER 11 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B TYR 12 CB because it is missing heavy-atom bond partners 23 messages similar to the above omitted Unknown hybridization for atom (P) of residue type C; not adding hydrogens to it notes | Termini for 6yyt (#1.2) chain A determined from SEQRES records Termini for 6yyt (#1.2) chain B determined from SEQRES records Termini for 6yyt (#1.2) chain C determined from SEQRES records Termini for 6yyt (#1.2) chain D determined from SEQRES records Termini for 6yyt (#1.2) chain P determined from SEQRES records 3 messages similar to the above omitted Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A VAL 31, /A PHE 77, /A ARG 118, /B PHE 6, /C SER 1, /D PHE 6, /P C 5, /Q C 5, /T U 7, /U C 5 Chain-final residues that are actual C termini: /P G 18, /Q G 18, /T G 18, /U G 18 Chain-final residues that are not actual C termini: /A LYS 50, /A ALA 97, /A THR 929, /B ALA 191, /C GLU 73, /D ALA 191 1178 hydrogen bonds Adding 'H' to /A VAL 31 Adding 'H' to /A PHE 77 Adding 'H' to /A ARG 118 Adding 'H' to /B PHE 6 Adding 'H' to /C SER 1 1 messages similar to the above omitted /A LYS 50 is not terminus, removing H atom from 'C' /A ALA 97 is not terminus, removing H atom from 'C' /A THR 929 is not terminus, removing H atom from 'C' /B ALA 191 is not terminus, removing H atom from 'C' /C GLU 73 is not terminus, removing H atom from 'C' 1 messages similar to the above omitted 10617 hydrogens added > hide HC > select /P 451 atoms, 485 bonds, 1 model selected > select /Q 450 atoms, 484 bonds, 1 model selected > select /T 387 atoms, 416 bonds, 1 model selected > select /U 451 atoms, 485 bonds, 1 model selected > delete nucleic&@H > delete nucleic&@HP1 > toolshed show Shell /opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226: UserWarning: IPython History requires SQLite, your history will not be saved warn(""IPython History requires SQLite, your history will not be saved"") > select #1 21988 atoms, 22327 bonds, 72 pseudobonds, 10 models selected > isolde start > set selectionWidth 4 Done loading forcefield > select clear > select #1 21988 atoms, 22327 bonds, 72 pseudobonds, 15 models selected > select clear OpenGL version: 3.3.0 NVIDIA 440.33.01 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 6.4G 46G 227M 10G 55G 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 }}} " defect closed normal Third Party can't reproduce Eric Pettersen all ChimeraX