id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4309 ISOLDE: backrub failure chimerax-bug-report@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-66-generic-x86_64-with-debian-buster-sid ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/andrew/Documents/CombineFocusedMaps_220/composite_map.ccp4 format > ccp4 Opened composite_map.ccp4, grid size 512,512,512, pixel 0.83, shown at level 4.62, step 2, values float32 > open /home/andrew/ccpem_project/Refmac5_64/refined_2.pdb Summary of feedback from opening /home/andrew/ccpem_project/Refmac5_64/refined_2.pdb --- warnings | Ignored bad PDB record found on line 1062 LINKR C1 NAG A4414 ND2 ASN A 218 NAG-ASN Ignored bad PDB record found on line 1063 LINKR C1 NAG A4415 ND2 ASN A 340 NAG-ASN Ignored bad PDB record found on line 1064 LINKR C1 NAG A4416 ND2 ASN A 387 NAG-ASN Ignored bad PDB record found on line 1065 LINKR C1 NAG A4419 ND2 ASN A 462 NAG-ASN Ignored bad PDB record found on line 1066 LINKR C1 NAG A4422 ND2 ASN A 657 NAG-ASN 229 messages similar to the above omitted refined_2.pdb title: \--- [more info...] Chain information for refined_2.pdb #2 --- Chain | Description A B | No description available Non-standard residues in refined_2.pdb #2 --- BMA — (BMA) MAN — (MAN) NAG — (NAG) > ui tool show ISOLDE > set selectionWidth 4 refined_2.pdb title: \--- [more info...] Chain information for refined_2.pdb --- Chain | Description 2.2/A 2.2/B | No description available Non-standard residues in refined_2.pdb #2.2 --- BMA — (BMA) MAN — (MAN) NAG — (NAG) Done loading forcefield > select /a:126 24 atoms, 23 bonds, 1 residue, 1 model selected > volume #2.1.1.1 level 1.433 > volume #2.1.1.1 level 3.311 > select /a:140 24 atoms, 23 bonds, 1 residue, 1 model selected > select /a:140 48 atoms, 46 bonds, 2 residues, 2 models selected > select /a:142 10 atoms, 9 bonds, 1 residue, 1 model selected > select /a:157 10 atoms, 9 bonds, 1 residue, 1 model selected Traceback (most recent call last): File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2130, in _backrub_rotamer self._apply_backrub(None, None) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2140, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 410, in apply_backrub b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' See log for complete Python traceback. Traceback (most recent call last): File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2130, in _backrub_rotamer self._apply_backrub(None, None) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2140, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 410, in apply_backrub b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' See log for complete Python traceback. > select /a:164 10 atoms, 9 bonds, 1 residue, 1 model selected Traceback (most recent call last): File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2130, in _backrub_rotamer self._apply_backrub(None, None) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2140, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 410, in apply_backrub b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' See log for complete Python traceback. > save /home/andrew/ccpem_project/Refmac5_64/refined_2.pdb relModel #2.2 > select /a:170 10 atoms, 9 bonds, 1 residue, 1 model selected Traceback (most recent call last): File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2130, in _backrub_rotamer self._apply_backrub(None, None) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2140, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 410, in apply_backrub b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. TypeError: Too many residues bonded to the target! Backrub will not work with post-translational modifications. File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/refine/backrub_rotamer.py"", line 71, in __init__ raise TypeError('Too many residues bonded to the target! Backrub will not work' See log for complete Python traceback. > select /a:181 14 atoms, 13 bonds, 1 residue, 1 model selected > select /a:185 17 atoms, 16 bonds, 1 residue, 1 model selected > select /a:190 10 atoms, 9 bonds, 1 residue, 1 model selected > select /a:198 24 atoms, 23 bonds, 1 residue, 1 model selected > select /a:198 24 atoms, 23 bonds, 1 residue, 1 model selected reverting to start > select /a:200 21 atoms, 21 bonds, 1 residue, 1 model selected > select /b:4449 27 atoms, 27 bonds, 1 residue, 1 model selected > select /b:1733 14 atoms, 13 bonds, 1 residue, 1 model selected > select /b:1733@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /b:1733@hd22, /b:4449@c1 Expected an objects specifier or a keyword > select /b:1733@hd22 Nothing selected > select /b:1733@hd22 Nothing selected > select /b:1733@nd2 1 atom, 1 residue, 1 model selected > select /b:4449@c1 1 atom, 1 residue, 1 model selected > bond /b:1733@nd2 sel Unknown command: bond /b:1733@nd2 sel > bond /b:1733@nd2 /b:4449@c1 Unknown command: bond /b:1733@nd2 /b:4449@c1 > ui tool show ""Build Structure"" > build modify /B:4449@C1 C 4 geometry tetrahedral > undo > undo > undo > undo > undo > undo > undo Undo failed, probably because structures have been modified. > select /a:1733@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4449@c1 1 atom, 1 residue, 1 model selected > ui tool show ""Build Structure"" > build modify /A:4449@C1 C 4 geometry tetrahedral colorByElement false > select /a:4329@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4525@c1 1 atom, 1 residue, 1 model selected > build modify /A:4525@C1 C 4 geometry tetrahedral colorByElement false > select /a:2178@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4463@nd1 Nothing selected > select /a:4463@c1 1 atom, 1 residue, 1 model selected > build modify /A:4463@C1 C 4 geometry tetrahedral colorByElement false > select /a:2488@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4478@c1 1 atom, 1 residue, 1 model selected > build modify /A:4478@C1 C 4 geometry tetrahedral colorByElement false > select /a:3448@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4512@c1 1 atom, 1 residue, 1 model selected > build modify /A:4512@C1 C 4 geometry tetrahedral colorByElement false > select /a:4070@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4520@C1 1 atom, 1 residue, 1 model selected > build modify /A:4520@C1 C 4 geometry tetrahedral colorByElement false > select /a:387@HD22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4416@C1 1 atom, 1 residue, 1 model selected > build modify /A:4416@C1 C 4 geometry tetrahedral colorByElement false > select /a:2134@HD22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4458@C1 1 atom, 1 residue, 1 model selected > build modify /A:4458@C1 C 4 geometry tetrahedral colorByElement false > select /a:3127@HD22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4493@c1 1 atom, 1 residue, 1 model selected > build modify /A:4493@C1 C 4 geometry tetrahedral colorByElement false > select /a:462@hd22 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 125 atoms, 125 bonds, 9 residues, 1 model selected > select down 14 atoms, 13 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > delete sel You must select exactly one atom to modify. > select /a:4419@c1 1 atom, 1 residue, 1 model selected > build modify /A:4419@C1 C 4 geometry tetrahedral colorByElement false > save /home/andrew/ccpem_project/Refmac5_64/refined_2.pdb relModel #2.2 > select /a:2548@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4483@c1 1 atom, 1 residue, 1 model selected > build modify /A:4483@C1 C 4 geometry tetrahedral colorByElement false > select /a:1551@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4439@c1 1 atom, 1 residue, 1 model selected > build modify /A:4439@C1 C 4 geometry tetrahedral colorByElement false > select /a:3357@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4511@c1 1 atom, 1 residue, 1 model selected > build modify /A:4511@C1 C 4 geometry tetrahedral colorByElement false > select /a:3213@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4498@c1 1 atom, 1 residue, 1 model selected > build modify /A:4498@C1 C 4 geometry tetrahedral colorByElement false > select /a:3317@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4508@c1 1 atom, 1 residue, 1 model selected > build modify /A:4508@C1 C 4 geometry tetrahedral colorByElement false > select /a:2810@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4490@c1 1 atom, 1 residue, 1 model selected > build modify /A:4490@C1 C 4 geometry tetrahedral colorByElement false > select /a:2225@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4468@c1 1 atom, 1 residue, 1 model selected > build modify /A:4468@C1 C 4 geometry tetrahedral colorByElement false > select /a:865@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4425@c1 1 atom, 1 residue, 1 model selected > build modify /A:4425@C1 C 4 geometry tetrahedral colorByElement false > select /a:2396@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4473@c1 1 atom, 1 residue, 1 model selected > build modify /A:4473@C1 C 4 geometry tetrahedral colorByElement false > select /a:657@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4422@c1 1 atom, 1 residue, 1 model selected > build modify /A:4422@C1 C 4 geometry tetrahedral colorByElement false > select /a:16776@hd21 Nothing selected > select /a:1676@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4444@c1 1 atom, 1 residue, 1 model selected > build modify /A:4444@C1 C 4 geometry tetrahedral colorByElement false > select /a:2782@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4488@c1 1 atom, 1 residue, 1 model selected > build modify /A:4488@C1 C 4 geometry tetrahedral colorByElement false > select /a:218@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4414@c1 1 atom, 1 residue, 1 model selected > build modify /A:4414@C1 C 4 geometry tetrahedral colorByElement false > select /a:1384@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4429@c1 1 atom, 1 residue, 1 model selected > build modify /A:4429@C1 C 4 geometry tetrahedral colorByElement false > select /a:1187@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4428@c1 1 atom, 1 residue, 1 model selected > build modify /A:4428@C1 C 4 geometry tetrahedral colorByElement false > select /a:3840@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4519@c1 1 atom, 1 residue, 1 model selected > build modify /A:4519@C1 C 4 geometry tetrahedral colorByElement false > select /a:1436@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4530@c1 Nothing selected > select /a:4430@c1 1 atom, 1 residue, 1 model selected > build modify /A:4430@C1 C 4 geometry tetrahedral colorByElement false > select /a:1811@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4452@c1 1 atom, 1 residue, 1 model selected > build modify /A:4452@C1 C 4 geometry tetrahedral colorByElement false > select /a:3682@hd22 1 atom, 1 residue, 1 model selected > delete sel > select /a:4517@c1 1 atom, 1 residue, 1 model selected > build modify /A:4517@C1 C 4 geometry tetrahedral colorByElement false > select /a:340@hd21 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 1553 atoms, 1583 bonds, 110 residues, 1 model selected > select down 14 atoms, 13 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > delete sel > select /a:4415@c1 1 atom, 1 residue, 1 model selected > build modify /A:4415@C1 C 4 geometry tetrahedral colorByElement false > select /a:1497@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4435@c1 1 atom, 1 residue, 1 model selected > build modify /A:4435@C1 C 4 geometry tetrahedral colorByElement false > select /a:3259@hd21 1 atom, 1 residue, 1 model selected > delete sel > select /a:4503@c1 1 atom, 1 residue, 1 model selected > build modify /A:4503@C1 C 4 geometry tetrahedral colorByElement false > select /a:1923 15 atoms, 14 bonds, 1 residue, 1 model selected > select /a:1963 17 atoms, 17 bonds, 1 residue, 1 model selected > select /a:1733@nd2 1 atom, 1 residue, 1 model selected > select /a:4449@c1 1 atom, 1 residue, 1 model selected > save /home/andrew/ccpem_project/Refmac5_64/refined_2.pdb relModel #2.2 > build modify /A:4449@C1 C 4 geometry tetrahedral colorByElement false > select /a:2600 14 atoms, 13 bonds, 1 residue, 1 model selected > select /a:1001 21 atoms, 21 bonds, 1 residue, 1 model selected > select /a:4467@c1 1 atom, 1 residue, 1 model selected > build modify /A:4467@C1 C 4 geometry tetrahedral colorByElement false > select /a:4502@c1 1 atom, 1 residue, 1 model selected > build modify /A:4502@C1 C 4 geometry tetrahedral colorByElement false > select /a:4472@c1 1 atom, 1 residue, 1 model selected > build modify /A:4472@C1 C 4 geometry tetrahedral colorByElement false > select /a:4701@c1 1 atom, 1 residue, 1 model selected > build modify /A:4701@C1 C 4 geometry tetrahedral colorByElement false > select /a:1225@hg1 1 atom, 1 residue, 1 model selected > delete sel > select /a:4701@c1 1 atom, 1 residue, 1 model selected > build modify /A:4701@C1 C 4 geometry tetrahedral colorByElement false > select /a:1225@og1 1 atom, 1 residue, 1 model selected > build modify /A:1225@OG1 O 4 geometry tetrahedral colorByElement false Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2229, in _update_selected_residue_info_live score = rot.score File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""changes"": IndexError: _Map_base::at File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. > select /a:1225@hg12 1 atom, 1 residue, 1 model selected Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1064, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1670, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2229, in _update_selected_residue_info_live score = rot.score File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > delete sel Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. > select /a:1225@hg11 1 atom, 1 residue, 1 model selected Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1064, in _selection_changed self._enable_rebuild_residue_frame(r) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 1670, in _enable_rebuild_residue_frame self._update_selected_residue_info_live(None, None) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/isolde.py"", line 2229, in _update_selected_residue_info_live score = rot.score File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) IndexError: _Map_base::at Error processing trigger ""selection changed"": IndexError: _Map_base::at File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/atomic/molc.py"", line 93, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. > delete sel Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/validation/rota_annotation.py"", line 191, in update_graphics non_favored_only = self._hide_favored) File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) IndexError: _Map_base::at Error processing trigger ""changes done"": IndexError: _Map_base::at File ""/home/andrew/.local/share/ChimeraX/1.1/site- packages/chimerax/isolde/molobject.py"", line 1655, in validate_scale_and_color_rotamers non_favored_only, visible_only, pointer(rot_out), pointer(scale_out), pointer(color_out)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.32.03 OpenGL renderer: GeForce GTX 1660/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: OptiPlex 7071 OS: Ubuntu 18.04 bionic Architecture: 64bit ELF CPU: 16 Intel(R) Core(TM) i9-9900 CPU @ 3.10GHz Cache Size: 16384 KB Memory: total used free shared buff/cache available Mem: 31G 17G 7.9G 657M 6.2G 13G Swap: 63G 0B 63G Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2184] (rev a1) Subsystem: Dell Device [1028:3794] Kernel driver in use: nvidia PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 chardet: 3.0.4 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.0 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.0 ChimeraX-Clipper: 0.15.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-ISOLDE: 1.1.0 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.0 ChimeraX-Log: 1.1.1 ChimeraX-LookingGlass: 1.1 ChimeraX-Map: 1.0.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.1 ChimeraX-MDcrds: 2.0 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.0 ChimeraX-mmCIF: 2.2 ChimeraX-MMTF: 2.0 ChimeraX-Modeller: 1.0 ChimeraX-ModelPanel: 1.0 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.0 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0 ChimeraX-OpenCommand: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.0 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0 ChimeraX-ToolshedUtils: 1.0 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.2.3 ChimeraX-uniprot: 2.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5 numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 ptyprocess: 0.6.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 }}} " defect assigned normal Third Party all ChimeraX