ISOLDE: KeyError in find_glycan_template_name_and_link

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-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  

> open
> /Users/zhangjun/Documents/RealSpaceRefine_20/test_real_space_refined.pdb
> format PDB

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

> open2 /Users/zhangjun/Desktop/perfushion_class001polish_righthand.mrc

Opened perfushion_class001polish_righthand.mrc, grid size 480,480,480, pixel
0.825, shown at level 0.00535, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.01624

> clipper associate #2 toModel #1

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

> isolde start

> set selectionWidth 4

Done loading forcefield  

> set bgColor white

> select #1

27531 atoms, 28289 bonds, 18 pseudobonds, 13 models selected  
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: (5,)  
  
KeyError: (5,)  
  
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-14.5.22
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.

[Tristan Croll]

When I get my next builds of ISOLDE out there will be a more informative error message for this, but the issue here is that one of your sugars has an incorrect link to another residue (it's bonded on the O5 oxygen, which is impossible - that's the oxygen closing the sugar ring. See ​http://ligand-expo.rcsb.org/reports/N/NAG/NAG_D3L3.gif). You'll need to find and delete that bond, and replace it with the correct one. My guess is that some other package's automatic ligand linking has misfired, and this is what should actually be the bond between C1 and Asn.

[Tristan Croll]

Arg! Didn't notice that this was an anonymous report. Sigh. Closing as fixed...