id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5977 ISOLDE: KeyError in find_glycan_template_name_and_link chimerax-bug-report@… Tristan Croll "{{{ 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. }}} " defect closed normal Third Party fixed all ChimeraX