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:
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/G614_close_fab_J175_real_space_refined_000.pdb

Chain information for G614_close_fab_J175_real_space_refined_000.pdb #1  
---  
Chain | Description  
A B C | No description available  
D F H | No description available  
E G I | No description available  
  

> open2
> /Users/zhangjun/Desktop/cryosparc_P24_J175_006_volume_map_sharp_righthand.mrc

Opened cryosparc_P24_J175_006_volume_map_sharp_righthand.mrc, grid size
480,480,480, pixel 0.83, shown at level 0.0708, step 2, values float32  

> clipper associate #2 toModel #1

Chain information for G614_close_fab_J175_real_space_refined_000.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | No description available  
1.2/D 1.2/F 1.2/H | No description available  
1.2/E 1.2/G 1.2/I | No description available  
  

> volume #1.1.1.1 level 0.1565

> set bgColor white

> isolde start

> set selectionWidth 4

Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to
G614_close_fab_J175_real_space_refined_000.pdb #1.2  
---  
warnings | Not adding hydrogens to /F LYS 217 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /G LYS 125 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /G LYS 168 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D LYS 217 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E LYS 125 CB because it is missing heavy-atom bond
partners  
4 messages similar to the above omitted  
notes | No usable SEQRES records for
G614_close_fab_J175_real_space_refined_000.pdb (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for G614_close_fab_J175_real_space_refined_000.pdb
(#1.2) chain B; guessing termini instead  
No usable SEQRES records for G614_close_fab_J175_real_space_refined_000.pdb
(#1.2) chain C; guessing termini instead  
No usable SEQRES records for G614_close_fab_J175_real_space_refined_000.pdb
(#1.2) chain D; guessing termini instead  
No usable SEQRES records for G614_close_fab_J175_real_space_refined_000.pdb
(#1.2) chain E; guessing termini instead  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A GLN 14, /B GLN 14, /C GLN
14, /D GLN 1, /E ASP 1, /F GLN 1, /G ASP 1, /H GLN 1, /I ASP 1  
Chain-initial residues that are not actual N termini: /A LYS 77, /A SER 254,
/A SER 689, /B LYS 77, /B SER 254, /B SER 689, /C LYS 77, /C SER 254, /C SER
689  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A PRO 1162, /A HIS 69, /A
LEU 244, /A THR 676, /B PRO 1162, /B HIS 69, /B LEU 244, /B THR 676, /C PRO
1162, /C HIS 69, /C LEU 244, /C THR 676, /D LYS 225, /E GLU 212, /F LYS 225,
/G GLU 212, /H LYS 225, /I GLU 212  
3645 hydrogen bonds  
Adding 'H' to /A LYS 77  
Adding 'H' to /A SER 254  
Adding 'H' to /A SER 689  
Adding 'H' to /B LYS 77  
Adding 'H' to /B SER 254  
4 messages similar to the above omitted  
/A PRO 1162 is not terminus, removing H atom from 'C'  
/A HIS 69 is not terminus, removing H atom from 'C'  
/A LEU 244 is not terminus, removing H atom from 'C'  
/A THR 676 is not terminus, removing H atom from 'C'  
/B PRO 1162 is not terminus, removing H atom from 'C'  
13 messages similar to the above omitted  
36789 hydrogens added  
  

> hide HC

> isolde restrain ligands #1

> select #1

74679 atoms, 75693 bonds, 18 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]

Ancient version of ISOLDE. Traceback is long-since fixed (problem is incorrect bonding between sugar residues - ISOLDE now communicates that clearly).