id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3601 _show_selected_unparameterised_residue: not enough values to unpack kartik.manne@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.9.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/home/kartikmanne/Documents/CH235 > structures/588AMS_CH235.12-M5-293/RealSpaceRefine_34/588AMS- > CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb"" Chain information for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb #1 --- Chain | Description A E I | No description available B F J | No description available C G K | No description available D H L | No description available > set bgColor white > addh Summary of feedback from adding hydrogens to 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb #1 --- notes | No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain A; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain B; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain C; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain D; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /A BMA 535, /B VAL 518, /C GLN 1, /D GLU 1, /E BMA 535, /F VAL 518, /G GLN 1, /H GLU 1, /I BMA 535, /J VAL 518, /K GLN 1, /L GLU 1 Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157, /A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY 312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I ASN 409, /J GLY 572, /K GLY 134 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU 62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K SER 128, /L GLY 212 2230 hydrogen bonds /A VAL 503 is not terminus, removing H atom from 'C' /A GLU 62 is not terminus, removing H atom from 'C' /A ASN 147 is not terminus, removing H atom from 'C' /A ILE 309 is not terminus, removing H atom from 'C' /A ASN 398 is not terminus, removing H atom from 'C' 25 messages similar to the above omitted 165 hydrogens added > open ""/home/kartikmanne/Documents/CH235 > structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"" Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size 320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32 > volume #2 step 1 > clipper associate #2 toModel #1 Chain information for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb --- Chain | Description 1.2/A 1.2/E 1.2/I | No description available 1.2/B 1.2/F 1.2/J | No description available 1.2/C 1.2/G 1.2/K | No description available 1.2/D 1.2/H 1.2/L | No description available > isolde start > set selectionWidth 4 Cached rota8000-val data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-leu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ile data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-pro data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-phe data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-tyr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-trp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-ser data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-thr data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-cys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-met data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-lys data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-his data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-arg data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asp data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-asn data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-gln data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Cached rota8000-glu data not found. Regenerating from text file. This is normal if running ISOLDE for the first time Done loading forcefield > clipper spotlight radius 32.00 > select #1 47724 atoms, 48273 bonds, 48 pseudobonds, 13 models selected Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 48, in _show_main_frame self._update_unparameterised_residues_list() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2735, in _start_sim_or_toggle_pause self.start_sim() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2755, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 612, in __init__ raise e File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1323, in __init__ template_dict = find_residue_templates(sim_construct.all_residues, ff, ligand_db=ligand_db, logger=session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2755, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 612, in __init__ raise e File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1344, in __init__ sim_params, residue_templates) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1426, in _create_openmm_system raise RuntimeError('Unparameterised residue detected') RuntimeError: Unparameterised residue detected During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2735, in _start_sim_or_toggle_pause self.start_sim() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2768, in start_sim self._unparam_mgr._sim_unparam_res_cb() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 204, in _sim_unparam_res_cb self._show_main_frame() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 48, in _show_main_frame self._update_unparameterised_residues_list() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. > delete H > addh Summary of feedback from adding hydrogens to 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb #1.2 --- notes | No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined.pdb (#1.2) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /A BMA 535, /B VAL 518, /C GLN 1, /D GLU 1, /E BMA 535, /F VAL 518, /G GLN 1, /H GLU 1, /I BMA 535, /J VAL 518, /K GLN 1, /L GLU 1 Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157, /A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY 312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I ASN 409, /J GLY 572, /K GLY 134 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU 62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K SER 128, /L GLY 212 2683 hydrogen bonds Adding 'H' to /A THR 71 Adding 'H' to /A CYS 157 Adding 'H' to /A GLY 312 Adding 'H' to /A ASN 409 Adding 'H' to /B GLY 572 13 messages similar to the above omitted /A VAL 503 is not terminus, removing H atom from 'C' /A GLU 62 is not terminus, removing H atom from 'C' /A ASN 147 is not terminus, removing H atom from 'C' /A ILE 309 is not terminus, removing H atom from 'C' /A ASN 398 is not terminus, removing H atom from 'C' 25 messages similar to the above omitted 23652 hydrogens added > isolde start > set selectionWidth 4 Done loading forcefield Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 48, in _show_main_frame self._update_unparameterised_residues_list() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. > ui tool show ISOLDE > set selectionWidth 4 Done loading forcefield Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2608, in _xtal_mask_to_selection self._xtal_mask_to_atoms(sel, focus) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/isolde.py"", line 2617, in _xtal_mask_to_atoms atoms, 0, context, cutoff, focus=focus) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/symmetry.py"", line 973, in isolate_and_cover_selection extra_padding=extra_padding) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/map_mgr.py"", line 358, in cover_atoms zm.set_symmetry_map(atoms, transforms, transform_indices) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 111, in set_symmetry_map self.structure = self._unique_structure(atoms) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') TypeError: All atoms for zone mask must be from a single model! TypeError: All atoms for zone mask must be from a single model! File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/clipper/maps/mask_handler.py"", line 177, in _unique_structure raise TypeError('All atoms for zone mask must be from a single model!') See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 48, in _show_main_frame self._update_unparameterised_residues_list() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA A535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. > close session Deleting atomic symmetry model... > open ""/home/kartikmanne/Documents/CH235 > structures/588AMS_CH235.12-M5-293/RealSpaceRefine_34/588AMS- > CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb"" Chain information for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1 --- Chain | Description A E I | No description available B F J | No description available C G K | No description available D H L | No description available > addh Summary of feedback from adding hydrogens to 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1 --- notes | No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain A; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain B; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain C; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain D; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /A NAG 534, /B VAL 518, /C GLN 1, /D GLU 1, /E BMA 535, /F VAL 518, /G GLN 1, /H GLU 1, /I BMA 535, /J VAL 518, /K GLN 1, /L GLU 1 Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157, /A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY 312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I ASN 409, /J GLY 572, /K GLY 134 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU 62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K SER 128, /L GLY 212 2226 hydrogen bonds /A VAL 503 is not terminus, removing H atom from 'C' /A GLU 62 is not terminus, removing H atom from 'C' /A ASN 147 is not terminus, removing H atom from 'C' /A ILE 309 is not terminus, removing H atom from 'C' /A ASN 398 is not terminus, removing H atom from 'C' 25 messages similar to the above omitted 133 hydrogens added > open ""/home/kartikmanne/Documents/CH235 > structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"" Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size 320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32 > volume #2 step 1 > clipper associate #2 toModel #1 Chain information for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb --- Chain | Description 1.2/A 1.2/E 1.2/I | No description available 1.2/B 1.2/F 1.2/J | No description available 1.2/C 1.2/G 1.2/K | No description available 1.2/D 1.2/H 1.2/L | No description available > isolde start > set selectionWidth 4 Done loading forcefield Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 48, in _show_main_frame self._update_unparameterised_residues_list() File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 79, in _update_unparameterised_residues_list template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3091, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number RuntimeError: Residue BMA E535 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue BMA E535 is linked to a glycan, but no parameters are available for this type of linkage. File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 271, in find_glycan_anchor_name residue.name, residue.chain_id, residue.number See log for complete Python traceback. > close session Deleting atomic symmetry model... > open ""/home/kartikmanne/Documents/CH235 > structures/588AMS_CH235.12-M5-293/RealSpaceRefine_34/588AMS- > CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb"" Chain information for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1 --- Chain | Description A E I | No description available B F J | No description available C G K | No description available D H L | No description available > addh Summary of feedback from adding hydrogens to 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1 --- notes | No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain A; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain B; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain C; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain D; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /A NAG 534, /B VAL 518, /C GLN 1, /D GLU 1, /E NAG 534, /F VAL 518, /G GLN 1, /H GLU 1, /I NAG 534, /J VAL 518, /K GLN 1, /L GLU 1 Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157, /A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY 312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I ASN 409, /J GLY 572, /K GLY 134 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU 62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K SER 128, /L GLY 212 2218 hydrogen bonds /A VAL 503 is not terminus, removing H atom from 'C' /A GLU 62 is not terminus, removing H atom from 'C' /A ASN 147 is not terminus, removing H atom from 'C' /A ILE 309 is not terminus, removing H atom from 'C' /A ASN 398 is not terminus, removing H atom from 'C' 25 messages similar to the above omitted 69 hydrogens added > open ""/home/kartikmanne/Documents/CH235 > structures/588AMS_CH235.12-M5-293/cryosparc_P41_J32_009_volume_map_sharp_local.mrc"" Opened cryosparc_P41_J32_009_volume_map_sharp_local.mrc, grid size 320,320,320, pixel 1.07, shown at level 0.659, step 2, values float32 > volume #2 step 1 > clipper associate #2 toModel #1 Chain information for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb --- Chain | Description 1.2/A 1.2/E 1.2/I | No description available 1.2/B 1.2/F 1.2/J | No description available 1.2/C 1.2/G 1.2/K | No description available 1.2/D 1.2/H 1.2/L | No description available > isolde start > set selectionWidth 4 Done loading forcefield Fetching CCD ASN_LL from http://ligand- expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif Fetching CCD ASN_LSN3 from http://ligand- expo.rcsb.org/reports/A/ASN_LSN3/ASN_LSN3.cif Fetching CCD ASN_LEO2 from http://ligand- expo.rcsb.org/reports/A/ASN_LEO2/ASN_LEO2.cif Deleted the following atoms from residue ASN I392: HD22 Deleted the following atoms from residue ASN I386: HD22 Deleted the following atoms from residue ASN I339: HD22 Deleted the following atoms from residue ASN I262: HD22 Deleted the following atoms from residue ASN I197: HD22 Deleted the following atoms from residue ASN E392: HD22 Deleted the following atoms from residue ASN E386: HD22 Deleted the following atoms from residue ASN E339: HD22 Deleted the following atoms from residue ASN E262: HD22 Deleted the following atoms from residue ASN E197: HD22 Deleted the following atoms from residue ASN A392: HD22 Deleted the following atoms from residue ASN A386: HD22 Deleted the following atoms from residue ASN A339: HD22 Deleted the following atoms from residue ASN A262: HD22 Deleted the following atoms from residue ASN A197: HD22 Fetching CCD A2G from http://ligand-expo.rcsb.org/reports/A/A2G/A2G.cif Fetching CCD NGA from http://ligand-expo.rcsb.org/reports/N/NGA/NGA.cif Fetching CCD BM3 from http://ligand-expo.rcsb.org/reports/B/BM3/BM3.cif Fetching CCD BM7 from http://ligand-expo.rcsb.org/reports/B/BM7/BM7.cif Fetching CCD NDG from http://ligand-expo.rcsb.org/reports/N/NDG/NDG.cif Deleted the following atoms from residue NAG I532: H11, H12 Deleted the following atoms from residue NAG I528: H11 Deleted the following atoms from residue NAG I522: H11 Deleted the following atoms from residue NAG E532: H12, H11 Deleted the following atoms from residue NAG E528: H11 Deleted the following atoms from residue NAG E522: H11 Deleted the following atoms from residue NAG A532: H11, H12 Deleted the following atoms from residue NAG A528: H11 Deleted the following atoms from residue NAG A522: H11 Fetching CCD CYS_LL from http://ligand- expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif Fetching CCD CYS_LL_DHG from http://ligand- expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif Fetching CCD CYS_LSN3 from http://ligand- expo.rcsb.org/reports/C/CYS_LSN3/CYS_LSN3.cif Fetching CCD CYS_LSN3_DHG from http://ligand- expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif Fetching CCD CYS_LEO2 from http://ligand- expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif Fetching CCD CYS_LEO2_DHG from http://ligand- expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif Fetching CCD CYS_LFZW from http://ligand- expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif Fetching CCD SC2 from http://ligand-expo.rcsb.org/reports/S/SC2/SC2.cif Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. > select #1 47448 atoms, 47985 bonds, 48 pseudobonds, 13 models selected Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. > delete H > addh Summary of feedback from adding hydrogens to 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb #1.2 --- notes | No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for 588AMS- CH235p12-M5-293_apply_ncs_31-coot0-rsr34_real_space_refined-coot-0.pdb (#1.2) chain E; guessing termini instead 7 messages similar to the above omitted Chain-initial residues that are actual N termini: /A NAG 534, /B VAL 518, /C GLN 1, /D GLU 1, /E NAG 534, /F VAL 518, /G GLN 1, /H GLU 1, /I NAG 534, /J VAL 518, /K GLN 1, /L GLU 1 Chain-initial residues that are not actual N termini: /A THR 71, /A CYS 157, /A GLY 312, /A ASN 409, /B GLY 572, /C GLY 134, /E THR 71, /E CYS 157, /E GLY 312, /E ASN 409, /F GLY 572, /G GLY 134, /I THR 71, /I CYS 157, /I GLY 312, /I ASN 409, /J GLY 572, /K GLY 134 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A VAL 503, /A GLU 62, /A ASN 147, /A ILE 309, /A ASN 398, /B ASP 664, /B SER 546, /C CYS 216, /C SER 128, /D GLY 212, /E VAL 503, /E GLU 62, /E ASN 147, /E ILE 309, /E ASN 398, /F ASP 664, /F SER 546, /G CYS 216, /G SER 128, /H GLY 212, /I VAL 503, /I GLU 62, /I ASN 147, /I ILE 309, /I ASN 398, /J ASP 664, /J SER 546, /K CYS 216, /K SER 128, /L GLY 212 2660 hydrogen bonds Adding 'H' to /A THR 71 Adding 'H' to /A CYS 157 Adding 'H' to /A GLY 312 Adding 'H' to /A ASN 409 Adding 'H' to /B GLY 572 13 messages similar to the above omitted /A VAL 503 is not terminus, removing H atom from 'C' /A GLU 62 is not terminus, removing H atom from 'C' /A ASN 147 is not terminus, removing H atom from 'C' /A ILE 309 is not terminus, removing H atom from 'C' /A ASN 398 is not terminus, removing H atom from 'C' 25 messages similar to the above omitted 23532 hydrogens added Fetching CCD ASP_LL_DHD2 from http://ligand- expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif Fetching CCD ASP_LL from http://ligand- expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif Fetching CCD ASP_LSN3_DHD2 from http://ligand- expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif Fetching CCD ASP_LEO2_DHD2 from http://ligand- expo.rcsb.org/reports/A/ASP_LEO2_DHD2/ASP_LEO2_DHD2.cif Fetching CCD ASP_LFZW_DHD2 from http://ligand- expo.rcsb.org/reports/A/ASP_LFZW_DHD2/ASP_LFZW_DHD2.cif Fetching CCD HIS_LEO2_DHE2 from http://ligand- expo.rcsb.org/reports/H/HIS_LEO2_DHE2/HIS_LEO2_DHE2.cif Fetching CCD HIS_LEO2_DHD1 from http://ligand- expo.rcsb.org/reports/H/HIS_LEO2_DHD1/HIS_LEO2_DHD1.cif Fetching CCD HIS_LEO2 from http://ligand- expo.rcsb.org/reports/H/HIS_LEO2/HIS_LEO2.cif Fetching CCD HIS_LFZW_DHE2 from http://ligand- expo.rcsb.org/reports/H/HIS_LFZW_DHE2/HIS_LFZW_DHE2.cif Fetching CCD HIS_LFZW_DHD1 from http://ligand- expo.rcsb.org/reports/H/HIS_LFZW_DHD1/HIS_LFZW_DHD1.cif Fetching CCD HIS_LFZW from http://ligand- expo.rcsb.org/reports/H/HIS_LFZW/HIS_LFZW.cif Deleted the following atoms from residue NAG I534: HO4 Deleted the following atoms from residue NAG E534: HO4 Deleted the following atoms from residue NAG A534: HO4 Deleted the following atoms from residue NAG I532: HO4, H11, H12 Deleted the following atoms from residue NAG I528: H11, HO4, H12 Deleted the following atoms from residue NAG I522: H11, HO4, H12 Deleted the following atoms from residue NAG E532: H12, HO4, H11 Deleted the following atoms from residue NAG E528: H12, H11, HO4 Deleted the following atoms from residue NAG E522: HO4, H11, H12 Deleted the following atoms from residue NAG A532: HO4, H12, H11 Deleted the following atoms from residue NAG A528: H12, HO4, H11 Deleted the following atoms from residue NAG A522: H12, H11, HO4 > select #1 47439 atoms, 47976 bonds, 48 pseudobonds, 19 models selected > select #1 47451 atoms, 47988 bonds, 48 pseudobonds, 19 models selected Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. Traceback (most recent call last): File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data ValueError: not enough values to unpack (expected 3, got 2) ValueError: not enough values to unpack (expected 3, got 2) File ""/home/kartikmanne/.local/share/ChimeraX/1.0/site- packages/chimerax/isolde/validation/unparameterised.py"", line 113, in _show_selected_unparameterised_residue residue, by_name, by_comp = item.data See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 430.40 OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: TYAN Model: B7105F48TV8HR-2T-G OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 64 Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz Cache Size: 22528 KB Memory: total used free shared buff/cache available Mem: 187G 10G 169G 240M 7.0G 175G Swap: 9G 0B 9G Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] Kernel driver in use: ast PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Third Party fixed all ChimeraX