id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3566 OpenMM: No template found for residue mks131@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.93 (2020-04-03) Description (Describe the actions that caused this problem to occur here) Log: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\safesave.py"", line 96, in __exit__ os.replace(self._tmp_filename, self.name) PermissionError: [WinError 32] The process cannot access the file because it is being used by another process: 'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp' -> 'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 621, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\\__init__.py"", line 1613, in start_tool return cls._get_func(api, ""start_tool"")(session, ti.name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\model_panel\\__init__.py"", line 21, in start_tool return model_panel(session, tool_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\model_panel\tool.py"", line 345, in model_panel _mp = ModelPanel(session, tool_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\model_panel\tool.py"", line 29, in __init__ now = self.settings.last_use = time() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\settings.py"", line 190, in __setattr__ ConfigFile.__setattr__(self, name, value) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\configfile.py"", line 365, in __setattr__ ConfigFile.save(self) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\configfile.py"", line 315, in save self._config.write(f) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\safesave.py"", line 98, in __exit__ os.remove(self._tmp_filename) FileNotFoundError: [WinError 2] The system cannot find the file specified: 'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\tools.py"", line 426, in start_tools bi.start_tool(session, tool_name) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 627, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Model Panel in bundle ChimeraX-ModelPanel: [WinError 2] The system cannot find the file specified: 'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp' Tool ""Model Panel"" failed to start: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Model Panel in bundle ChimeraX-ModelPanel: [WinError 2] The system cannot find the file specified: 'C:\\\Users\\\Manoj\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\ModelPanel-1.tmp' File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\toolshed\info.py"", line 627, in start_tool ""start_tool() failed for tool %s in bundle %s:\n%s"" % (tool_name, self.name, str(e))) See log for complete Python traceback. 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 > C:\Users\Manoj\Downloads\relion_postprocess_job126_masked_refined_pixelsize.ccp4 > format ccp4 Opened relion_postprocess_job126_masked_refined_pixelsize.ccp4, grid size 376,376,376, pixel 0.649, shown at level 0.00472, step 2, values float32 > volume #1 level 0.009646 > toolshed show ISOLDE > set selectionWidth 4 Done loading forcefield > clipper spotlight radius 13.00 > clipper spotlight radius 40.00 Traceback (most recent call last): File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 1297, in add_xtal_data map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 174, in get_map_mgr sh = get_symmetry_handler(structure, create=create, auto_add_to_session=auto_add_to_session) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 159, in get_symmetry_handler sh = _get_symmetry_handler(structure, create) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 166, in _get_symmetry_handler p = structure.parent AttributeError: 'NoneType' object has no attribute 'parent' AttributeError: 'NoneType' object has no attribute 'parent' File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 166, in _get_symmetry_handler p = structure.parent See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 1271, in _choose_reflections_file self.add_xtal_data(filename) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 1297, in add_xtal_data map_mgr = get_map_mgr(m, create=True, auto_add_to_session=True) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 174, in get_map_mgr sh = get_symmetry_handler(structure, create=create, auto_add_to_session=auto_add_to_session) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 159, in get_symmetry_handler sh = _get_symmetry_handler(structure, create) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 166, in _get_symmetry_handler p = structure.parent AttributeError: 'NoneType' object has no attribute 'parent' AttributeError: 'NoneType' object has no attribute 'parent' File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 166, in _get_symmetry_handler p = structure.parent See log for complete Python traceback. > open2 C:/Users/Manoj/Documents/phenix_lin28/lin28b_DNA.pdb Chain information for lin28b_DNA.pdb #2 --- Chain | Description I | No description available J | No description available Chain information for lin28b_DNA.pdb --- Chain | Description 2.2/I | No description available 2.2/J | No description available Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 652, in _rebuild_molecule hide_residues = make_ladder(nd, residues, mol._ladder_params) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 1237, in make_ladder va, na, ta = get_cylinder(params.rung_radius, ep0, ep1) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 733, in get_cylinder h = distance(p0, p1) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 71, in distance return sqrt(distance_squared(p, q)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 63, in distance_squared if len(p) == 3: TypeError: object of type 'NoneType' has no len() Error processing trigger ""changes"": TypeError: object of type 'NoneType' has no len() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 63, in distance_squared if len(p) == 3: See log for complete Python traceback. Traceback (most recent call last): File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 525, in rebuild _rebuild_molecule('internal', mol) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 652, in _rebuild_molecule hide_residues = make_ladder(nd, residues, mol._ladder_params) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 1237, in make_ladder va, na, ta = get_cylinder(params.rung_radius, ep0, ep1) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\atomic\nucleotides\\_data.py"", line 733, in get_cylinder h = distance(p0, p1) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 71, in distance return sqrt(distance_squared(p, q)) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 63, in distance_squared if len(p) == 3: TypeError: object of type 'NoneType' has no len() Error processing trigger ""new frame"": TypeError: object of type 'NoneType' has no len() File ""C:\Program Files\ChimeraX\bin\lib\site- packages\chimerax\geometry\vector.py"", line 63, in distance_squared if len(p) == 3: See log for complete Python traceback. No template found for residue I-64 (DT) Adding hydrogens Summary of feedback from adding hydrogens to lin28b_DNA.pdb #2.2 --- notes | No usable SEQRES records for lin28b_DNA.pdb (#2.2) chain I; guessing termini instead No usable SEQRES records for lin28b_DNA.pdb (#2.2) chain J; guessing termini instead Chain-initial residues that are actual N termini: /I DT -64, /J DG -72 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /I DC 72, /J DA 64 Chain-final residues that are not actual C termini: 384 hydrogen bonds 3098 hydrogens added No template found for residue I-64 (DT) Excluding residue Traceback (most recent call last): File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1327, in __init__ sim_params, residue_templates) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1424, in _create_openmm_system sys = forcefield.createSystem(top, **system_params) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 1147, in createSystem raise ValueError('No template found for residue %d (%s). %s' % (res.index+1, res.name, _findMatchErrors(self, res))) ValueError: No template found for residue 1 (DT). The set of atoms is similar to DT, but it is missing 12 hydrogen atoms. During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1327, in __init__ sim_params, residue_templates) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1424, in _create_openmm_system sys = forcefield.createSystem(top, **system_params) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\simtk\openmm\app\forcefield.py"", line 1147, in createSystem raise ValueError('No template found for residue %d (%s). %s' % (res.index+1, res.name, _findMatchErrors(self, res))) ValueError: No template found for residue 1 (DT). The set of atoms matches DT3, but the bonds are different. Perhaps the chain is missing a terminal group? During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2679, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\Manoj\AppData\Local\UCSF\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 ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 597, in __init__ self._parse_auto_template_error(e) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 647, in _parse_auto_template_error self.isolde._handle_bad_template(residue) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2791, in _handle_bad_template self.start_sim() File ""C:\Users\Manoj\AppData\Local\UCSF\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 ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 597, in __init__ self._parse_auto_template_error(e) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 647, in _parse_auto_template_error self.isolde._handle_bad_template(residue) File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2799, in _handle_bad_template self.start_sim() File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\isolde.py"", line 2709, in start_sim sm.start_sim() File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 667, in start_sim sh.start_sim() File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1570, in start_sim self._prepare_sim() File ""C:\Users\Manoj\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1531, in _prepare_sim integrator, platform, properties) File ""C:\Program Files\ChimeraX\bin\lib\site- packages\simtk\openmm\app\simulation.py"", line 105, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 6265, in __init__ this = _openmm.new_Context(*args) Exception: Error creating array TabulatedFunction: clCreateBuffer (-61) Exception: Error creating array TabulatedFunction: clCreateBuffer (-61) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 6265, in __init__ this = _openmm.new_Context(*args) See log for complete Python traceback. OpenGL version: 3.3.0 - Build 20.19.15.4531 OpenGL renderer: Intel(R) HD Graphics 5500 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: Inspiron 7348 OS: Microsoft Windows 10 Home (Build 18362) Memory: 8,501,149,696 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i7-5500U CPU @ 2.40GHz"" }}} " defect closed normal Third Party fixed all ChimeraX