id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3054 'cartoon' command: 'Atoms' object has no attribute 'evaluate' chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 0.93 (2020-03-20) 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 (2020-03-20) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/rafLa/Desktop/hE2 > structure/cryosparc_P4_J156__localfilter_GOOD.mrc"" Opened cryosparc_P4_J156__localfilter_GOOD.mrc, grid size 450,450,450, pixel 0.84, shown at level 0.395, step 2, values float32 > open ""C:/Users/rafLa/Desktop/hE2 structure/hE2_60mer from trimer > best_trimer.pdb"" Chain information for hE2_60mer from trimer best_trimer.pdb #2 --- Chain | Description D H W | No description available > toolshed show ISOLDE > set selectionWidth 4 Chain information for hE2_60mer from trimer best_trimer.pdb --- Chain | Description 2.2/D 2.2/H 2.2/W | No description available Traceback (most recent call last): File ""D:\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\symmetry.py"", line 1222, in _set_default_cartoon_cb set_to_default_cartoon(self.session, model = self.structure) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\clipper\util.py"", line 55, in set_to_default_cartoon cartoon.cartoon(session, atoms = atoms, suppress_backbone_display=False) File ""D:\ChimeraX\bin\lib\site-packages\chimerax\std_commands\cartoon.py"", line 71, in cartoon results = atoms.evaluate(session) AttributeError: 'Atoms' object has no attribute 'evaluate' Error processing trigger ""frame drawn"": AttributeError: 'Atoms' object has no attribute 'evaluate' File ""D:\ChimeraX\bin\lib\site-packages\chimerax\std_commands\cartoon.py"", line 71, in cartoon results = atoms.evaluate(session) See log for complete Python traceback. Done loading forcefield > select #2.2 5307 atoms, 5397 bonds, 5 models selected > select #2.2 5307 atoms, 5397 bonds, 5 models selected > select #2.2 5307 atoms, 5397 bonds, 5 models selected > select #2.2 5307 atoms, 5397 bonds, 5 models selected > select clear > select #2.2 5307 atoms, 5397 bonds, 5 models selected Traceback (most recent call last): File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 591, in __init__ isolde.forcefield_mgr) File ""C:\Users\rafLa\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\rafLa\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 ""D:\ChimeraX\bin\lib\site-packages\simtk\openmm\app\forcefield.py"", line 1114, 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 CYM does not match the residue 72 (CYS) During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""C:\Users\rafLa\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\rafLa\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\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 593, in __init__ self._sim_end_cb(None, None) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1012, in _sim_end_cb self._dihe_r_sim_end_cb() File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\openmm\openmm_interface.py"", line 1163, in _dihe_r_sim_end_cb pdrs = self.proper_dihedral_restraint_mgr.get_all_restraints_for_residues(sc.mobile_residues) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 3613, in get_all_restraints_for_residues return self._get_all_restraints_for_residues(residues, False) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 3601, in _get_all_restraints_for_residues dihedrals = pdm.get_all_dihedrals(residues) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 601, in get_all_dihedrals self.create_all_dihedrals(residues) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 521, in create_all_dihedrals self._find_peptide_backbone_dihedrals(dihedral_dict, aa_residues, f) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 529, in _find_peptide_backbone_dihedrals len(aa_residues), True) TypeError: All atoms must be in the same structure! TypeError: All atoms must be in the same structure! File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 529, in _find_peptide_backbone_dihedrals len(aa_residues), True) See log for complete Python traceback. Traceback (most recent call last): File ""D:\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\validation\rama_annotation.py"", line 222, in _update_graphics_if_needed self.update_graphics() File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\validation\rama_annotation.py"", line 234, in update_graphics coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas, self.hide_favored) File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) TypeError: All atoms must be in the same structure! Error processing trigger ""changes"": TypeError: All atoms must be in the same structure! File ""C:\Users\rafLa\AppData\Local\UCSF\ChimeraX\0.93\site- packages\chimerax\isolde\molobject.py"", line 1067, in _ca_positions_colors_and_selecteds pointer(coords), pointer(colors), pointer(selecteds)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 442.50 OpenGL renderer: GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Acer Model: Aspire GX-785 OS: Microsoft Windows 10 Home (Build 18363) Memory: 17,117,134,848 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-7700 CPU @ 3.60GHz"" }}} " defect closed normal Depiction duplicate all ChimeraX