Opened 6 months ago

Last modified 6 months ago

#17346 assigned defect

"isolde add aa" on non-amino acid

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-15.4-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/ts3435/Library/CloudStorage/Dropbox/GrantProposals/Fairjourney_FJB_IgG_oligos/Hexamerising-
> peptide/Patent/1dn2_clean.pdb

Chain information for 1dn2_clean.pdb #1  
---  
Chain | Description  
A B | No description available  
E F | No description available  
  
Drag select of 11 residues  
Drag select of 2 residues  

> select up

110 atoms, 111 bonds, 7 residues, 1 model selected  

> select up

199 atoms, 204 bonds, 13 residues, 1 model selected  

> select up

6981 atoms, 7087 bonds, 440 residues, 1 model selected  

> select down

199 atoms, 204 bonds, 13 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select clear

> show atoms

> hide atoms

> color bychain

Drag select of 5 residues  

> select up

173 atoms, 177 bonds, 11 residues, 1 model selected  

> select up

199 atoms, 204 bonds, 13 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> color sel byhetero

> hide H

> select clear

Drag select of 2 atoms, 1 bonds  
Alignment identifier is 1/F  

> select clear

[Repeated 2 time(s)]

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for 1dn2_clean.pdb  
---  
Chain | Description  
1.2/A 1.2/B | No description available  
1.2/F | No description available  
  

> select clear

> isolde add aa glu sel

[Repeated 1 time(s)]

> select up

227 atoms, 232 bonds, 15 residues, 1 model selected  

> select up

6810 atoms, 6911 bonds, 429 residues, 2 models selected  

> select up

6810 atoms, 6911 bonds, 429 residues, 3 models selected  

> select down

6810 atoms, 6911 bonds, 429 residues, 2 models selected  

> select down

227 atoms, 232 bonds, 15 residues, 2 models selected  

> isolde sim start /F

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/ts3435/Desktop/EDTA.pdb

> select up

30 atoms, 28 bonds, 2 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde add aa pro sel

> isolde add aa gly sel

> isolde add aa phe sel

> isolde add aa his sel

> ui tool show Rotamers

Populating font family aliases took 58 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.  

> swapaa interactive sel TYR rotLib Dunbrack

/F TRP 4: phi -134.3, psi 140.8 trans  
Changed 180 bond radii  

> swapaa #!1.2/F:4 TYR criteria 1 rotLib Dunbrack

Using Dunbrack library  
1dn2_clean.pdb #!1.2/F TRP 4: phi -134.3, psi 140.8 trans  
Applying TYR rotamer (chi angles: -62.6 88.5) to 1dn2_clean.pdb #!1.2/F TYR 4  

> ui tool show Rotamers

> swapaa interactive sel ARG rotLib Dunbrack

/F LEU 6: phi 48.0, psi 33.4 trans  
Changed 600 bond radii  

> swapaa #!1.2/F:6 ARG criteria 10 rotLib Dunbrack

Using Dunbrack library  
1dn2_clean.pdb #!1.2/F LEU 6: phi 48.0, psi 33.4 trans  
Applying ARG rotamer (chi angles: -59.1 -64.1 -169.1 -94.8) to 1dn2_clean.pdb
#!1.2/F ARG 6  

> addh

Summary of feedback from adding hydrogens to 1dn2_clean.pdb #1.2  
---  
notes | Termini for 1dn2_clean.pdb (#1.2) chain A determined from SEQRES
records  
Termini for 1dn2_clean.pdb (#1.2) chain B determined from SEQRES records  
No usable SEQRES records for 1dn2_clean.pdb (#1.2) chain F; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLY 237, /B GLY 237, /F
GLY -1  
Chain-initial residues that are not actual N termini: /F GLY -1  
Chain-final residues that are actual C termini: /A LEU 443, /B LEU 443, /F HIS
15  
Chain-final residues that are not actual C termini: /F HIS 15  
Missing OXT added to C-terminal residue /F HIS 15  
326 hydrogen bonds  
18 hydrogens added  
  

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

58 atoms, 59 bonds, 4 residues, 2 models selected  

> select up

259 atoms, 266 bonds, 17 residues, 2 models selected  

> select up

6842 atoms, 6945 bonds, 431 residues, 2 models selected  

> select down

259 atoms, 266 bonds, 17 residues, 2 models selected  

> isolde sim start /F

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /F:-1-0,14-15

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Users/ts3435/Desktop/2019_1.pdb

> select up

259 atoms, 266 bonds, 17 residues, 2 models selected  

> select down

60 atoms, 22 bonds, 4 residues, 2 models selected  

> select up

60 atoms, 61 bonds, 4 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> select clear

> isolde add aa cys sel

[Repeated 1 time(s)]Created disulphide bond between F14 and F0.  

> select up

20 atoms, 19 bonds, 2 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde add aa HCY sel

Fetching CCD HCY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/HCY/HCY.cif  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 132, in add_aa_cmd  
add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res,
next_res=next_res,  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/build_utils.py", line 217, in
add_amino_acid_residue  
add_bond(r.find_atom('C'), next_res.find_atom('N'))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde add aa hcy sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 132, in add_aa_cmd  
add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res,
next_res=next_res,  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/build_utils.py", line 217, in
add_amino_acid_residue  
add_bond(r.find_atom('C'), next_res.find_atom('N'))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde add aa hcy sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 132, in add_aa_cmd  
add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res,
next_res=next_res,  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/build_utils.py", line 217, in
add_amino_acid_residue  
add_bond(r.find_atom('C'), next_res.find_atom('N'))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde add aa hcy sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/cmd.py", line 132, in add_aa_cmd  
add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res,
next_res=next_res,  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/atomic/building/build_utils.py", line 210, in
add_amino_acid_residue  
add_bond(r.find_atom('N'), prev_res.find_atom('C'))  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 161, in add_bond  
if a1.num_bonds > 0:  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde add aa cys sel

> select clear

> show atoms

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde sim start /F:14

Loading residue template for HCY from internal database  

Chain F, residue 0 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

[Repeated 1 time(s)]

Chain F, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

Sim termination reason: None  
ISOLDE: stopped sim  

Chain F, residue 0 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

[Repeated 1 time(s)]

Chain F, residue 14 specifies more than one residue! The simulation can still
run, but this will probably cause problems later if not rectified by
renumbering.  

> select up

14 atoms, 10 bonds, 4 residues, 1 model selected  

> select up

220 atoms, 232 bonds, 4 residues, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde sim start /F:14

Sim termination reason: None  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 160, in
_table_item_clicked_cb  
residue.atoms.displays = True  
^^^^^^^^^^^^^  
File "atomic_cpp/cymol.pyx", line 1038, in
chimerax.atomic.cymol.CyResidue.atoms.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 1038, in
chimerax.atomic.cymol.CyResidue.atoms.__get__  
  
See log for complete Python traceback.  
  
Fetching CCD AAC from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif  
Fetching CCD CSO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CSO/CSO.cif  
Fetching CCD CSS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CSS/CSS.cif  

MD template CYS for residue CYS F14 contains extra atoms that are not in a
coordinate template, and are not directly connected to existing atoms. Since
MD templates do not explicitly provide geometry,these atoms will not be built.  

> isolde sim start /F:14

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> show sel atoms

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> isolde add aa cys sel

> ui tool show Rotamers

> swapaa interactive sel CYH rotLib Dunbrack

/F CYS 14: phi -143.5, psi none trans  
No rotamers for CYH in Dunbrack rotamer library  

> swapaa interactive sel CYD rotLib Dunbrack

/F CYS 14: phi -143.5, psi none trans  
No rotamers for CYD in Dunbrack rotamer library  

> delete atoms (#!1.2 & sel)

> delete bonds (#!1.2 & sel)

> ui tool show "Build Structure"

> build modify /F:14@SG C 4 geometry tetrahedral name C1 resName UNK

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> addh

Summary of feedback from adding hydrogens to 1dn2_clean.pdb #1.2  
---  
warnings | Not adding hydrogens to /F UNK 14 HA because it is missing heavy-
atom bond partners  
Not adding hydrogens to /F UNK 14 HB2 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F UNK 14 HB3 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F UNK 14 C1 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F UNK 14 H11 because it is missing heavy-atom bond
partners  
2 messages similar to the above omitted  
notes | Termini for 1dn2_clean.pdb (#1.2) chain A determined from SEQRES
records  
Termini for 1dn2_clean.pdb (#1.2) chain B determined from SEQRES records  
No usable SEQRES records for 1dn2_clean.pdb (#1.2) chain F; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLY 237, /B GLY 237, /F
ASP 1  
Chain-initial residues that are not actual N termini: /F ASP 1  
Chain-final residues that are actual C termini: /A LEU 443, /B LEU 443, /F UNK
14  
Chain-final residues that are not actual C termini: /F UNK 14  
Missing OXT added to C-terminal residue /F UNK 14  
328 hydrogen bonds  
0 hydrogens added  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 210, in
_update_graphics_if_needed  
self.track_whole_model = True  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 108, in
track_whole_model  
self.update_graphics()  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
[deleted to fit within ticket limits]

IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/validation/rama_annotation.py", line 239, in
update_graphics  
coords, colors, selecteds = mgr._ca_positions_colors_and_selecteds(ramas,
self.hide_favored)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: No dihedral with that name is registered for this residue type!  
  
Error processing trigger "changes done":  
IndexError: No dihedral with that name is registered for this residue type!  
  
File "/Users/ts3435/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/molobject.py", line 1207, in
_ca_positions_colors_and_selecteds  
count = f(self._c_pointer, ramas._c_pointers, n, hide_favored,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,9
      Model Number: Z1CM000EEB/A
      Chip: Apple M3 Max
      Total Number of Cores: 16 (12 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4 (24E248)
      Kernel Version: Darwin 24.4.0
      Time since boot: 5 days, 2 hours, 15 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 40
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2421:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported
        DELL P2422H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 0.5
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (1)

comment:1 by pett, 6 months ago

Component: Unassigned → Third Party
Description: modified (diff)
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "isolde add aa" on non-amino acid
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