ISOLDE: backrub failure

[chimerax-bug-report@…]

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
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[Tristan Croll]

A bit of a messy scenario happening in that log... I suspect he's filling in missing sidechains atom-by-atom? Anyway, the string of error messages at the end is a bug I know about, and need to fix. It happens when an amino acid residue has been initialised with ISOLDE's rotamer validation, but then gets renamed to something that isn't in the rotamer database (e.g. some modified amino acid like 2MR or FME... or UNK, which might be the case here with all that editing happening). Hasn't been high priority up until now since it's a rare occurrence. Also need to downgrade the error raised when a user tries to auto-fit post-translationally modified residue to a UserError (and/or just grey out the auto-fit rotamer button when fitting isn't supported).