Error in AddH error message :-)

[tic20@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.5.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-03-25)
Description
Trying to help a colleague debug a bad PDB file, and this traceback comes up when I attempt to run `addh hbond true` on it. I'm afraid I can't share the file itself.

Log:
UCSF ChimeraX version: 0.9 (2019-03-25)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open work3.pdb

Chain information for work3.pdb #1  
---  
Chain | Description  
C D | No description available  
H I | No description available  
L M | No description available  
  

> show selAtoms ribbons

> hide selAtoms

> addh hbond true

Summary of feedback from adding hydrogens to work3.pdb #1  
---  
notes | No usable SEQRES records for work3.pdb (#1) chain C; guessing termini
instead  
No usable SEQRES records for work3.pdb (#1) chain D; guessing termini instead  
No usable SEQRES records for work3.pdb (#1) chain H; guessing termini instead  
No usable SEQRES records for work3.pdb (#1) chain I; guessing termini instead  
No usable SEQRES records for work3.pdb (#1) chain L; guessing termini instead  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /C MET 46, /D MET 46, /H GLN
1, /I GLN 1, /L GLN 1, /M GLN 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /L CYS 214, /M CYS 214  
Chain-final residues that are not actual C termini: /C GLY 210, /D GLY 210, /H
PRO 213, /I PRO 213  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 790, in _find_acceptors  
acc_func, args = acc_info[atom.num_bonds]  
IndexError: list index out of range  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 253, in execute  
cmd.run(cmd_text)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2616, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 58, in cmd_addh  
add_h_func(session, structures, in_isolation=in_isolation, **prot_schemes)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/cmd.py", line 166, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/addh/hbond.py", line 243, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 489, in find_hbonds  
limited_acceptors, generic_acc_info)  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 792, in _find_acceptors  
session.logger.warning("%d has bad number of bonds (%d)" % (atom,
atom.num_bonds))  
NameError: name 'session' is not defined  
  
NameError: name 'session' is not defined  
  
File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-
packages/chimerax/atomic/hbonds/hbond.py", line 792, in _find_acceptors  
session.logger.warning("%d has bad number of bonds (%d)" % (atom,
atom.num_bonds))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 415.27
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[tic20@…]

Replacing line 792 with the following gives a nice clean message:

                     structure.session.logger.warning('Atom {} in {} {}{} 
has bad number of bonds ({})'.format(
                         atom.name, atom.residue.name, 
atom.residue.chain_id, atom.residue.number,
                         atom.num_bonds
                     ))


On 2019-03-26 14:08, ChimeraX wrote: