Opened 2 years ago

Last modified 2 years ago

#9225 assigned defect

ISOLDE: Residue has multiple bonds to neighbor

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

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Custom presets folder 'ui tool show "Model Panel"' does not exist  
note | available bundle cache has not been initialized yet  
  

> set bgColor white

> ~display atoms

> display cart

> ui tool show "Model Panel"

UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: Internal Server Error  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/03 SARS
> CoV 2 S2/01 Amaro Lab
> Mutations/Phenix/RealSpaceRefine_24/230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
> coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb"

Chain information for
230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb
#1  
---  
Chain | Description  
A B C | No description available  
  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2020-2022/02
> SARS-CoV-2-S2/amaro lab
> mutations/cryosparc_P439_J46_005_volume_map_half_A_deepEMhancer-
> sharpened.mrc"

Opened cryosparc_P439_J46_005_volume_map_half_A_deepEMhancer-sharpened.mrc as
#2, grid size 240,240,240, pixel 0.94, shown at level 0.0134, step 1, values
float32  

> hide #!2 models

> select /C:1074@HD21

1 atom, 1 residue, 1 model selected  

> select add /C:1143@C7

2 atoms, 2 residues, 1 model selected  

> isolde start

> set selectionWidth 4

> 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  

> undo

[Repeated 1 time(s)]

> select H

10152 atoms, 1323 residues, 1 model selected  

> hide sel target a

> undo

[Repeated 1 time(s)]

> delete bonds sel

> clipper associate #2 toModel #1

Opened cryosparc_P439_J46_005_volume_map_half_A_deepEMhancer-sharpened.mrc as
#1.1.1.1, grid size 240,240,240, pixel 0.94, shown at level 0.353, step 1,
values float32  
Chain information for
230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C | No description available  
  

> addh

Summary of feedback from adding hydrogens to
230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb
#1.2  
---  
warning | Skipped 3 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for
230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb
(#1.2) chain A; guessing termini instead  
No usable SEQRES records for
230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb
(#1.2) chain B; guessing termini instead  
No usable SEQRES records for
230529_AmaroS2_phenix_isolde_real_space_refined_007_isolde-
coot-0_isolde1_real_space_refined_009_isolde1_real_space_refined_018-isolde5_real_space_refined_024.pdb
(#1.2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A CYS 704, /B CYS 704, /C
CYS 704  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A PRO 1140, /B PRO 1140, /C
PRO 1140  
Chain-final residues that are not actual C termini:  
Skipping possible acceptor with bad geometry: /C NAG 1143 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1143 O7  
  
Skipping possible acceptor with bad geometry: /C NAG 1143 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1143 O7  
  
Skipping possible acceptor with bad geometry: /C NAG 1143 O7  
Wrong number of grandchild atoms for phi/psi acceptor /C NAG 1143 O7  
  
1001 hydrogen bonds  
0 hydrogens added  
  

> isolde start

> view #1/C:811

> volume #1.1.1.1 level 0.183

> volume #1.1.1.1 level 0.1546

> volume #1.1.1.1 level 0.04617

> ui tool show "Ramachandran Plot"

> view #1/C:811

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 307, in process  
func(*args, **kwargs)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/validation/ramaplot/ramaplot.py", line 292, in
on_resize  
c.draw()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 405, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 74, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 51, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 3071, in draw  
artists = self._get_draw_artists(renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 209, in _get_draw_artists  
ax.apply_aspect(locator(ax, renderer) if locator else None)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1935, in apply_aspect  
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 545, in shrunk_to_aspect  
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")  
ValueError: 'box_aspect' and 'fig_aspect' must be positive  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_qt.py", line 454, in _draw_idle  
self.draw()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/backends/backend_agg.py", line 405, in draw  
self.figure.draw(self.renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 74, in draw_wrapper  
result = draw(artist, renderer, *args, **kwargs)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/artist.py", line 51, in draw_wrapper  
return draw(artist, renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 3071, in draw  
artists = self._get_draw_artists(renderer)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/figure.py", line 209, in _get_draw_artists  
ax.apply_aspect(locator(ax, renderer) if locator else None)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/axes/_base.py", line 1935, in apply_aspect  
pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/matplotlib/transforms.py", line 545, in shrunk_to_aspect  
raise ValueError("'box_aspect' and 'fig_aspect' must be positive")  
ValueError: 'box_aspect' and 'fig_aspect' must be positive  

> hide (#1.2 & sel) target a

Created disulphide bond between A1126 and A1082.  

> hide (#1.2 & sel) target a

> undo

> hide (#1.2 & sel) target a

Created disulphide bond between B1082 and B1126.  

> view #1/B:1126

> view #1/A:1126

> view #1/C:1126

> hide (#1.2 & sel) target a

Created disulphide bond between C1082 and C1126.  

> volume #1.1.1.1 level 0.01269

> volume #1.1.1.1 level 0.009644

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 62 residues in model #1.2 to IUPAC-IUB
standards.  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s1:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  
s2:
CVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYCTPPIKDFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNQNAEALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEWQIDRLIWGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

The same chain is being used to restrain distances for two different chains in
your working model, which is incompatible with the "Restrain Interfaces"
option. This option is ignored - distances across chain boundaries will not be
restrained.  

> isolde restrain distances "#1.2/A","#1.2/B","#1.2/C" templateAtoms
> "#1.2/A","#1.2/A","#1.2/A" perChain true adjustForConfidence false
> useCoordinateAlignment false kappa 4.40 fallOff 2.50 groupName "Reference
> Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/B templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/C templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

"Adjust for PAE" is checked in the distance restraint options, but the
reference model has no PAE matrix assigned. This option has been ignored.  

The same chain is being used to restrain distances for two different chains in
your working model, which is incompatible with the "Restrain Interfaces"
option. This option is ignored - distances across chain boundaries will not be
restrained.  

> isolde restrain distances "#1.2/A","#1.2/B","#1.2/C" templateAtoms
> "#1.2/A","#1.2/A","#1.2/A" perChain true adjustForConfidence false
> useCoordinateAlignment false kappa 4.40 fallOff 2.50 groupName "Reference
> Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/A templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/B templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain torsions #1.2/C templateResidues #1.2/A adjustForConfidence
> false sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde sim start /A-C

Sim termination reason: None  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 876, in start_sim  
sm = self._sim_manager = SimManager(self, self.selected_model, main_sel,  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 343, in __init__  
raise e  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 321, in __init__  
sh = self.sim_handler = SimHandler(session, sim_params, sc,  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in __init__  
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3010, in
find_residue_templates  
tname, prot_res = find_glycan_template_name_and_link(sugar)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link  
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(  
RuntimeError: Residue C1143 has multiple bonds to neighbor C1074  
  
RuntimeError: Residue C1143 has multiple bonds to neighbor C1074  
  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link  
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(  
  
See log for complete Python traceback.  
  

> isolde sim start /A-C

Sim termination reason: None  
ISOLDE: stopped sim  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/isolde.py", line 876, in start_sim  
sm = self._sim_manager = SimManager(self, self.selected_model, main_sel,  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 343, in __init__  
raise e  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 321, in __init__  
sh = self.sim_handler = SimHandler(session, sim_params, sc,  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in __init__  
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3010, in
find_residue_templates  
tname, prot_res = find_glycan_template_name_and_link(sugar)  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link  
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(  
RuntimeError: Residue C1143 has multiple bonds to neighbor C1074  
  
RuntimeError: Residue C1143 has multiple bonds to neighbor C1074  
  
File "/Users/zhouling95/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link  
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 1.7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 48 days, 2 hours, 12 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG ULTRAGEAR:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 202NTCZHP955
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.59


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    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: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (3)

comment:1 by Eric Pettersen, 2 years ago

Cc: Eric Pettersen added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: Residue has multiple bonds to neighbor

comment:2 by Eric Pettersen, 2 years ago

This looks to be a PDB file with bad CONECT records (based on the addh log output)

comment:3 by Tristan Croll, 2 years ago 

Yup. That being said, I should probably make ISOLDE do something more
user-friendly in that scenario.

On Wed, Jun 21, 2023 at 7:09 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
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