id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2287 Swapaa: template atom is None tic20@… 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 (2019-07-27) Description Trying to mutate a GLY to GLU raises an error Log: UCSF ChimeraX version: 0.91 (2019-07-27) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open working_through_401.pdb Chain information for working_through_401.pdb #1 --- Chain | Description A | No description available > select :GLY 336 atoms, 291 bonds, 1 model selected > select /A:353 7 atoms, 6 bonds, 1 model selected > swapaa sel GLU Using Dunbrack library /A GLY 353: phi -175.8, psi 173.2 trans 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 2655, 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 53, in swap_aa rots = get_rotamers(session, res, res_type=r_type, lib=lib, log=log) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 222, in get_rotamers array([ta.scene_coord for ta in res_match_atoms])) File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 222, in array([ta.scene_coord for ta in res_match_atoms])) AttributeError: 'NoneType' object has no attribute 'scene_coord' AttributeError: 'NoneType' object has no attribute 'scene_coord' File ""/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/atomic/rotamers/command/swap_res.py"", line 222, in array([ta.scene_coord for ta in res_match_atoms])) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 415.27 OpenGL renderer: TITAN Xp/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Structure Editing duplicate all ChimeraX