AddH: list index out of range in roomiest()

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-01-15)
Description
Structure protonation

Log:
UCSF ChimeraX version: 0.9 (2019-01-15)  
How to cite UCSF ChimeraX  

> open 1rju fromDatabase pdbe_updated

Summary of feedback from opening 1rju fetched from pdbe_updated  
---  
notes | Fetching compressed mmCIF 1rju from http://www.ebi.ac.uk/pdbe/entry-
files/download/1rju_updated.cif  
Fetching CCD CU1 from http://ligand-expo.rcsb.org/reports/C/CU1/CU1.cif  
  
1rju title:  
Crystal structure of a truncated form of yeast copper thionein [more info...]  
  
Chain information for 1rju #1  
---  
Chain | Description  
V | Metallothionein  
  
Non-standard residues in 1rju #1  
---  
CU1 — copper (I) ion  
  
  

> addh hbond true

Summary of feedback from adding hydrogens to 1rju #1  
---  
notes | Termini for 1rju (#1) chain V determined from SEQRES records  
Chain-initial residues that are actual N termini: /V HIS 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /V ASN 36  
Chain-final residues that are not actual C termini:  
109 hydrogen bonds  
  
Traceback (most recent call last):  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 252, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2612, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 58, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 166, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/hbond.py", line 666, in add_hydrogens  
rooms = roomiest(remaining, a, _room_dist, bonding_info)  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 749, in roomiest  
return list(zip(*pos_info))[1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/private/var/folders/vq/c3s8rmy96xl28vqnlp31vv31fxhg53/T/AppTranslocation/A7D259F2-2586-4017-AD10-5B8DD476FE9C/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/addh/cmd.py", line 749, in roomiest  
return list(zip(*pos_info))[1]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.9
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Eric Pettersen]

Changed typing of sulfurs coordinating 3+ metals to S3-. Typing still being overridden by useCysName option, so need to revamp that.

[Eric Pettersen]

Fixed. AddH now treats CYS similarly to HIS (i.e. as "unspecified" rather than explicitly neutral).