AddH: 5ky0: list index out of range while finding roomiest

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2019-12-24)
Description
Protonation issue.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.92 (2019-12-24)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5ky0 fromDatabase pdbe_updated

Summary of feedback from opening 5ky0 fetched from pdbe_updated  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 7845  
notes | Fetching compressed mmCIF 5ky0 from http://www.ebi.ac.uk/pdbe/entry-
files/download/5ky0_updated.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
  
5ky0 title:  
mouse POFUT1 in complex with mouse Notch1 EGF12(D464G) and GDP [more info...]  
  
Chain information for 5ky0 #1  
---  
Chain | Description  
A | GDP-fucose protein O-fucosyltransferase 1  
B | Neurogenic locus notch homolog protein 1  
  
Non-standard residues in 5ky0 #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
NAG — N-acetyl-D-glucosamine  
  
  

> addh hbond true

Summary of feedback from adding hydrogens to 5ky0 #1  
---  
warnings | Not adding hydrogens to /A LYS 142 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /A LYS 143 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ARG 277 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 329 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A ASP 330 CB because it is missing heavy-atom bond
partners  
3 messages similar to the above omitted  
notes | Termini for 5ky0 (#1) chain A determined from SEQRES records  
Termini for 5ky0 (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A ALA 31, /A GLY 263,
/B ASN 454  
Chain-final residues that are actual C termini: /A ASP 384, /B THR 491  
Chain-final residues that are not actual C termini: /A LEU 257  
1606 hydrogen bonds  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 63, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 171, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 667, in add_hydrogens  
rooms = roomiest(remaining, a, _room_dist, bonding_info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 804, in roomiest  
return list(zip(*pos_info))[1]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 804, in roomiest  
return list(zip(*pos_info))[1]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Fix available in next daily build.