id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2369 swapaa failure for non-rotameric side chains Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core ChimeraX Version: 0.91 (2019-08-27) Description I *think* I may have reported this before, but a search isn't finding it. Anyway, the swapaa command is failing on non-rotameric sidechains. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.91 (2019-08-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 3oep format mmCIF fromDatabase pdb 3oep title: Crystal structure of TTHA0988 in space group P43212 [more info...] Chain information for 3oep #1 --- Chain | Description A | Putative uncharacterized protein TTHA0988 Non-standard residues in 3oep #1 --- GOL — glycerol (glycerin; propane-1,2,3-triol) SO4 — sulfate ion > select /A:287 11 atoms, 10 bonds, 1 model selected > toolshed show Shell /opt/UCSF/ChimeraX-daily/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"") > swapaa sel ALA Using Dunbrack library Swapping /A ARG 287 to ALA Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/cmd.py"", line 52, in swap_aa preserve=preserve, hbond_relax=relax, retain=retain) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 161, in swap_aa use_rotamer(session, res, rotamers[res], retain=retain, log=log) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 597, in use_rotamer swap_type = list(rots.values())[0].residues[0].name IndexError: list index out of range IndexError: list index out of range File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 597, in use_rotamer swap_type = list(rots.values())[0].residues[0].name See log for complete Python traceback. > ui mousemode rightMode swapaa > swapaa mousemode /A:287 ARG > swapaa sel GLY Using Dunbrack library Swapping /A ARG 287 to GLY Traceback (most recent call last): File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/cmd_line/tool.py"", line 254, in execute cmd.run(cmd_text) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2688, in run result = ci.function(session, **kw_args) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/cmd.py"", line 52, in swap_aa preserve=preserve, hbond_relax=relax, retain=retain) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 161, in swap_aa use_rotamer(session, res, rotamers[res], retain=retain, log=log) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 597, in use_rotamer swap_type = list(rots.values())[0].residues[0].name IndexError: list index out of range IndexError: list index out of range File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 597, in use_rotamer swap_type = list(rots.values())[0].residues[0].name See log for complete Python traceback. > swapaa mousemode /A:287 ARG OpenGL version: 3.3.0 NVIDIA 415.27 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Structure Editing fixed all ChimeraX