swapaa failure for non-rotameric side chains

[Tristan Croll]

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

[Eric Pettersen]

Logic to check for no rotamers was no longer correct due to changes to handle altlocs.