id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3659 Failure to correct ligand when no CCD template available assaf_alon@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1062.1.1.el7.x86_64-x86_64-with-centos-7.7.1908-Core ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Trying to use ISOLDE on a receptor bound to a ligand. I loaded the paraqmater file for the ligand but it still fails 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 > ui tool show ISOLDE > set selectionWidth 4 Done loading forcefield > open /nfs/userdocs/ak/aalon/ISOLDE/Z1241145220/maestro_clean_no_ZNC.pdb Chain information for maestro_clean_no_ZNC.pdb #1 --- Chain | Description A | No description available B | No description available Chain information for maestro_clean_no_ZNC.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available (CLIPPER) NOTE: No symmetry information found in model. Using symmetry from MTZ file. Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > isolde sim start #1 Updating bulk solvent parameters... Fetching CCD LYS_LL_DHZ3 from http://ligand- expo.rcsb.org/reports/L/LYS_LL_DHZ3/LYS_LL_DHZ3.cif Fetching CCD LYS_LSN3 from http://ligand- expo.rcsb.org/reports/L/LYS_LSN3/LYS_LSN3.cif Fetching CCD LYS_LEO2 from http://ligand- expo.rcsb.org/reports/L/LYS_LEO2/LYS_LEO2.cif Fetching CCD LYZ from http://ligand-expo.rcsb.org/reports/L/LYZ/LYZ.cif Fetching CCD MLZ from http://ligand-expo.rcsb.org/reports/M/MLZ/MLZ.cif Fetching CCD LYS_LFZW from http://ligand- expo.rcsb.org/reports/L/LYS_LFZW/LYS_LFZW.cif Updating bulk solvent parameters... > select clear > select up 23 atoms, 22 bonds, 1 model selected > delete sel > delete sel > isolde sim start #1 > open > /nfs/userdocs/ak/aalon/Phenix/Z1241145220/Refine_26/Z1241145220_refine_26.pdb Chain information for Z1241145220_refine_26.pdb #2 --- Chain | Description A | No description available B | No description available > close #1 Deleting atomic symmetry model... Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) MDFF potential Deleting (LIVE) 2mFo-DFc_smooth_5 Deleting Crystallographic maps (Z1241145220_refine_26.mtz) Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1013, in _sim_end_cb self._pr_sim_end_cb() File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 1070, in _pr_sim_end_cb restraints = self.position_restraint_mgr.get_restraints(self.sim_construct.all_atoms) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 2216, in get_restraints return self._get_restraints(atoms) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 2169, in _get_restraints num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret)) AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer' Error processing trigger ""sim terminated"": AttributeError: 'PositionRestraintMgr' object has no attribute '_c_pointer' File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/molobject.py"", line 2169, in _get_restraints num = f(self._c_pointer, atoms._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/validation/ramaplot.py"", line 197, in _sim_end_cb self._mode_change_cb() File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/validation/ramaplot.py"", line 233, in _mode_change_cb self.selection_mode = mode File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/validation/ramaplot.py"", line 288, in selection_mode self.set_target_residues(self.current_model.residues) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 43, in _getattr_ return base.__getattr__(self, attr_name, look_in_class=base) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 39, in _getattr_ return look_in_class._attr_registration.get_attr(attr_name) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 65, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None AttributeError: Execution of 'Structure' object's 'residues' property raised AttributeError Error processing trigger ""simulation terminated"": AttributeError: Execution of 'Structure' object's 'residues' property raised AttributeError File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/atomic/attr_registration.py"", line 65, in get_attr raise AttributeError(""Execution of '%s' object's '%s' property raised AttributeError"" % (self.class_.__name__, attr_name)) from None See log for complete Python traceback. > ui tool show ISOLDE > set selectionWidth 4 Chain information for Z1241145220_refine_26.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available Done loading forcefield Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... > addh Summary of feedback from adding hydrogens to Z1241145220_refine_26.pdb #1.2 --- warnings | Not adding hydrogens to /A LYS 125 CB because it is missing heavy- atom bond partners Not adding hydrogens to /A HIS 128 CB because it is missing heavy-atom bond partners Not adding hydrogens to /A LYS 168 CB because it is missing heavy-atom bond partners Not adding hydrogens to /B LYS 168 CB because it is missing heavy-atom bond partners notes | No usable SEQRES records for Z1241145220_refine_26.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for Z1241145220_refine_26.pdb (#1.2) chain B; guessing termini instead Chain-initial residues that are actual N termini: /A GLY 5, /B GLY 2 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A LYS 168, /B LYS 168 435 hydrogen bonds /A LYS 168 is not terminus, removing H atom from 'C' /B LYS 168 is not terminus, removing H atom from 'C' 3205 hydrogens added Loading residue template for CLR from internal database Loading residue template for OLC from internal database Traceback (most recent call last): File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/validation/unparameterised.py"", line 134, in _show_selected_unparameterised_residue ccd_template, description = get_ccd_template_and_name(self.session, tname) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/isolde/validation/unparameterised.py"", line 126, in get_ccd_template_and_name tmpl = mmcif.find_template_residue(session, ccd_name) File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 378, in find_template_residue return _mmcif.find_template_residue(name) ValueError: No template for residue type ZNC ValueError: No template for residue type ZNC File ""/programs/x86_64-linux/chimerax/1.0/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 378, in find_template_residue return _mmcif.find_template_residue(name) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 440.44 OpenGL renderer: Quadro K4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: X9SRA/X9SRA-3 OS: CentOS Linux 7 Core Architecture: 64bit ELF CPU: 12 Intel(R) Core(TM) i7-4960X CPU @ 3.60GHz Cache Size: 15360 KB Memory: total used free shared buff/cache available Mem: 15G 2.8G 9.7G 76M 3.0G 12G Swap: 4.0G 0B 4.0G Graphics: 03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK106GL [Quadro K4000] [10de:11fa] (rev a1) Subsystem: NVIDIA Corporation Device [10de:097c] Kernel driver in use: nvidia 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