id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3050 OpenMM: User-supplied template does not match the residue didny1@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 0.91 (2019-10-05) 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: 0.91 (2019-10-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Successfully installed 'ChimeraX_ISOLDE-1.0b4-cp37-cp37m-win_amd64.whl' Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\didny\appdata\local\ucsf\chimerax\cache\0.91\installers\chimerax_isolde-1.0b4-cp37-cp37m-win_amd64.whl Requirement already satisfied, skipping upgrade: ChimeraX-Atomic>=1.0 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b4) (1.0) Requirement already satisfied, skipping upgrade: ChimeraX-Clipper==0.10.* in c:\users\didny\appdata\local\ucsf\chimerax\0.91\site-packages (from ChimeraX- ISOLDE==1.0b4) (0.10.0) Requirement already satisfied, skipping upgrade: ChimeraX-Core==0.91 in c:\program files\chimerax\bin\lib\site-packages (from ChimeraX-ISOLDE==1.0b4) (0.91) Installing collected packages: ChimeraX-ISOLDE Found existing installation: ChimeraX-ISOLDE 1.0b3.dev5 Uninstalling ChimeraX-ISOLDE-1.0b3.dev5: Successfully uninstalled ChimeraX-ISOLDE-1.0b3.dev5 Successfully installed ChimeraX-ISOLDE-1.0b4 Lock 2142724852488 acquired on C:\Users\didny\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock Lock 2142724852488 released on C:\Users\didny\AppData\Local\UCSF\ChimeraX\Cache\0.91\toolshed\bundle_info.cache.lock WARNING: You are using pip version 19.2.3, however version 20.0.2 is available. You should consider upgrading via the 'python -m pip install --upgrade pip' command. > open F:\cryoEM\UMOD\umod_fixedseq_cistem_172-isolde2.cif format mmCIF Summary of feedback from opening F:\cryoEM\UMOD\umod_fixedseq_cistem_172-isolde2.cif --- warnings | Unknown polymer entity '1' near line 135 Unknown polymer entity '2' near line 4075 Unable to infer polymer connectivity due to unspecified label_seq_id for residue ""NAG"" near line 6114 Unknown polymer entity '3' near line 6170 Atom H1 is not in the residue template for LEU #329 in chain A Atom H1 is not in the residue template for VAL #450 in chain B Atom H11 is not in the residue template for NAG #585 in chain B Atom H1 is not in the residue template for ALA #326 in chain C Atom HD2 is not in the residue template for ASN #396 in chain C Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Chain information for umod_fixedseq_cistem_172-isolde2.cif #1 --- Chain | Description A | ? B | ? C | ? > open F:/cryoEM/UMOD/denmod_map.ccp4 Opened denmod_map.ccp4, grid size 133,77,185, pixel 1.45, shown at level 0.235, step 1, values float32 > toolshed show ISOLDE > set selectionWidth 4 Chain information for umod_fixedseq_cistem_172-isolde2.cif --- Chain | Description 1.1/A | ? 1.1/B | ? 1.1/C | ? Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield > clipper spotlight radius 24.00 > clipper spotlight radius 24.00 > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 6 models selected No template found for residue B585 (NAG) Excluding residue Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1313, in __init__ sim_params, residue_templates) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1409, 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 1108, in createSystem raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name)) Exception: User-supplied template GLYCAM_4YB does not match the residue 392 (NAG) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2676, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2696, in start_sim self.params, self.sim_params, excluded_residues = self.ignored_residues) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 606, in __init__ if self._parse_explicit_template_error(e): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 644, in _parse_explicit_template_error self.isolde._handle_bad_template(residue) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2796, in _handle_bad_template self.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2706, in start_sim sm.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 653, in start_sim sh.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1555, in start_sim self._prepare_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1500, in _prepare_sim self.initialize_implicit_solvent(params) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 2741, in initialize_implicit_solvent gbforce.addParticles(params) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 9186, in __getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 74, in _swig_getattr return _swig_getattr_nondynamic(self, class_type, name, 0) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) AttributeError: type object 'object' has no attribute '__getattr__' AttributeError: type object 'object' has no attribute '__getattr__' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2676, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2706, in start_sim sm.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 653, in start_sim sh.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1555, in start_sim self._prepare_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1500, in _prepare_sim self.initialize_implicit_solvent(params) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 2741, in initialize_implicit_solvent gbforce.addParticles(params) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 9186, in __getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 74, in _swig_getattr return _swig_getattr_nondynamic(self, class_type, name, 0) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) AttributeError: type object 'object' has no attribute '__getattr__' AttributeError: type object 'object' has no attribute '__getattr__' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) See log for complete Python traceback. > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2676, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2706, in start_sim sm.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 653, in start_sim sh.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1555, in start_sim self._prepare_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1500, in _prepare_sim self.initialize_implicit_solvent(params) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 2741, in initialize_implicit_solvent gbforce.addParticles(params) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 9186, in __getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 74, in _swig_getattr return _swig_getattr_nondynamic(self, class_type, name, 0) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) AttributeError: type object 'object' has no attribute '__getattr__' AttributeError: type object 'object' has no attribute '__getattr__' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) See log for complete Python traceback. > select #1.1 7984 atoms, 8075 bonds, 338 pseudobonds, 12 models selected Traceback (most recent call last): File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2676, in _start_sim_or_toggle_pause self.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\isolde.py"", line 2706, in start_sim sm.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 653, in start_sim sh.start_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1555, in start_sim self._prepare_sim() File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1500, in _prepare_sim self.initialize_implicit_solvent(params) File ""C:\Users\didny\AppData\Local\UCSF\ChimeraX\0.91\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 2741, in initialize_implicit_solvent gbforce.addParticles(params) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 9186, in __getattr__ = lambda self, name: _swig_getattr(self, CustomGBForce, name) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 74, in _swig_getattr return _swig_getattr_nondynamic(self, class_type, name, 0) File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) AttributeError: type object 'object' has no attribute '__getattr__' AttributeError: type object 'object' has no attribute '__getattr__' File ""C:\Program Files\ChimeraX\bin\lib\site-packages\simtk\openmm\openmm.py"", line 69, in _swig_getattr_nondynamic return object.__getattr__(self, name) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 450.12 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Third Party fixed all ChimeraX