ISOLDE: KeyError in find_glycan_template_name_and_link

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open2
> /Users/zhangjun/Desktop/omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb

Chain information for
omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb #1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  

> open2
> /Users/zhangjun/Desktop/omicron_polishopendeepemhancer_J127resample.mrc

Opened omicron_polishopendeepemhancer_J127resample.mrc, grid size 480,480,480,
pixel 0.83, shown at level 0.0364, step 2, values float32  

> volume #2 step 1

> clipper associate #2 toModel #1

Chain information for
omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B 1.2/C | No description available  
  

> set bgColor white

> isolde start

> set selectionWidth 4

Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to
omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb #1.2  
---  
notes | No usable SEQRES records for
omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb (#1.2)
chain A; guessing termini instead  
No usable SEQRES records for
omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb (#1.2)
chain B; guessing termini instead  
No usable SEQRES records for
omicron_opendeepemhancer_chimerax20220103_real_space_refined_000.pdb (#1.2)
chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLN 14, /B GLN 14, /C GLN
14  
Chain-initial residues that are not actual N termini: /A LYS 77, /A ALA 260,
/A TRP 633, /A VAL 687, /B LYS 77, /B ALA 260, /B VAL 687, /C LYS 77, /C ALA
260, /C VAL 687  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PRO 1162, /A ILE 68, /A
LEU 244, /A ALA 626, /A LYS 679, /B PRO 1162, /B ILE 68, /B LEU 244, /B SER
680, /C PRO 1162, /C ILE 68, /C LEU 244, /C SER 680  
2579 hydrogen bonds  
Adding 'H' to /A LYS 77  
Adding 'H' to /A ALA 260  
Adding 'H' to /A TRP 633  
Adding 'H' to /A VAL 687  
Adding 'H' to /B LYS 77  
5 messages similar to the above omitted  
/A PRO 1162 is not terminus, removing H atom from 'C'  
/A ILE 68 is not terminus, removing H atom from 'C'  
/A LEU 244 is not terminus, removing H atom from 'C'  
/A ALA 626 is not terminus, removing H atom from 'C'  
/A LYS 679 is not terminus, removing H atom from 'C'  
8 messages similar to the above omitted  
27140 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> select #1

54837 atoms, 55579 bonds, 20 pseudobonds, 15 models selected  

QWidget::repaint: Recursive repaint detected  

Traceback (most recent call last):  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2679, in _start_sim_or_toggle_pause  
self.start_sim()  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/isolde.py", line 2699, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 609, in __init__  
raise e  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1319, in __init__  
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3044, in
find_residue_templates  
tname, prot_res = find_glycan_template_name_and_link(sugar)  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 133, in
find_glycan_template_name_and_link  
return ('GLYCAM_'+_glycam_prefix[bonded_atom_numbers]+core_name, link_res)  
KeyError: (4, 7)  
  
KeyError: (4, 7)  
  
File "/Users/zhangjun/Library/Application Support/ChimeraX/0.93/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 133, in
find_glycan_template_name_and_link  
return ('GLYCAM_'+_glycam_prefix[bonded_atom_numbers]+core_name, link_res)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.

[Tristan Croll]

Long-since fixed. Upshot is that the user has an almost-certainly-incorrect combination of bonds between sugar residues, for which there is no matching template in the GLYCAM force field. More recent ISOLDE versions will catch this error and describe the problem clearly to the user.