id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3286 ISOLDE: KeyError in find_glycan_template_name_and_link chimerax-bug-report@… Tristan Croll "{{{ 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. }}} " defect closed normal Third Party fixed all ChimeraX