'cartoon' command: 'Atoms' object has no attribute 'evaluate'

[chimerax-bug-report@…]

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"

[Eric Pettersen]

duplicate of #3024