Opened 21 months ago

Closed 20 months ago

#14550 closed defect (can't reproduce)

Could not find atom for bond

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.0-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.ras.6XHB.cxs"

Log from Wed Feb 7 11:21:55 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.inhibit.7MFE.cxs"

Log from Mon Jan 29 16:31:15 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.inactive.cxs"

Log from Fri Jan 26 10:57:50 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.inactive.cxs"

Log from Fri Jan 26 10:02:26 2024You can double click a model's Name or ID in
the model panel to edit those fields  
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  

> open /Users/gz2294/Downloads/0-backward.nosol.pdb

Summary of feedback from opening /Users/gz2294/Downloads/0-backward.nosol.pdb  
---  
warning | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
0-backward.nosol.pdb title:  
Backmapped structure from MARTINI to charmm36 [more info...]  
  
Chain information for 0-backward.nosol.pdb #1  
---  
Chain | Description  
? | No description available  
  

> select :576

13 atoms, 12 bonds, 1 residue, 1 model selected  

> color :576 red

> color :600,507 blue

> open /Users/gz2294/Downloads/POVME/volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Volume = 14524.0 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
14519 messages similar to the above omitted  
note | Combining 18837 symmetry atoms into XXX /X:1 X  
  
Chain information for volume_trajectory.pdb #2  
---  
Chain | Description  
X | No description available  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/adjacency_volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/adjacency_volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Feature Volume = 2854 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2849 messages similar to the above omitted  
note | Combining 47706 symmetry atoms into XXX /X:1 X  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/output_hbondDonor_volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/output_hbondDonor_volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Feature Volume = 91 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
86 messages similar to the above omitted  
note | Combining 29018 symmetry atoms into XXX /X:1 X  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/POVMEcontiguous_pocket_seed_points.pdb.gz

> delete #2

> open /Users/gz2294/Downloads/POVME/POVMEpoint_field.pdb.gz

Chain information for POVMEpoint_field.pdb.gz #2  
---  
Chain | Description  
X | No description available  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/POVMEcontiguous_pocket_seed_points.pdb.gz

Chain information for POVMEcontiguous_pocket_seed_points.pdb.gz #2  
---  
Chain | Description  
X | No description available  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/adjacency_volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/adjacency_volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Feature Volume = 6202 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
6197 messages similar to the above omitted  
note | Combining 19463 symmetry atoms into XXX /X:1 X  
  
Chain information for adjacency_volume_trajectory.pdb #2  
---  
Chain | Description  
X | No description available  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Volume = 2383.0 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2378 messages similar to the above omitted  
note | Combining 14726 symmetry atoms into XXX /X:1 X  
  

> delete #2

> open /Users/gz2294/Downloads/POVME/volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Volume = 159.0 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
154 messages similar to the above omitted  
note | Combining 1955 symmetry atoms into XXX /X:1 X  
  

> delete #2

> delete #1

> open /Users/gz2294/Downloads/0-backward.nosol.pdb

Summary of feedback from opening /Users/gz2294/Downloads/0-backward.nosol.pdb  
---  
warning | Ignored bad PDB record found on line 2  
REMARK THIS IS A SIMULATION BOX  
  
0-backward.nosol.pdb title:  
Backmapped structure from MARTINI to charmm36 [more info...]  
  
Chain information for 0-backward.nosol.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open /Users/gz2294/Downloads/POVME/adjacency_volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/POVME/adjacency_volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Feature Volume = 973 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
968 messages similar to the above omitted  
note | Combining 3489 symmetry atoms into XXX /X:1 X  
  

> color :576 red

> coulombic :600,507 green

Expected a keyword  

> color :600,507 green

> delete all

> open 4mne

4mne title:  
Crystal structure of the BRAF:MEK1 complex [more info...]  
  
Chain information for 4mne #1  
---  
Chain | Description | UniProt  
A D E H | Dual specificity mitogen-activated protein kinase kinase 1 |
MP2K1_HUMAN 62-393  
B C F G | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 432-726  
  
Non-standard residues in 4mne #1  
---  
573 —
7-fluoro-3-[(2-fluoro-4-iodophenyl)amino]-N-{[(2S)-2-hydroxypropyl]oxy}furo[3,2-c]pyridine-2-carboxamide  
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)  
CL — chloride ion  
MG — magnesium ion  
  
4mne mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide atoms

> show cartoons

> delete /C/D/E/F/G/H

> color /A:600,507 green

> color /B:600,507 green

> color /B:576 red

> delete /A

> save /Users/gz2294/Desktop/braf.active..pdb relModel #1

> save /Users/gz2294/Downloads/braf.active.pdb relModel #1

> save "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.cxs"

> delete all

> open 4ehe

Summary of feedback from opening 4ehe fetched from pdb  
---  
notes | Fetching compressed mmCIF 4ehe from
http://files.rcsb.org/download/4ehe.cif  
Fetching CCD RI8 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/8/RI8/RI8.cif  
  
4ehe title:  
B-Raf Kinase Domain in Complex with an Aminothienopyrimidine-based Inhibitor
[more info...]  
  
Chain information for 4ehe #1  
---  
Chain | Description | UniProt  
A B | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 432-726  
  
Non-standard residues in 4ehe #1  
---  
RI8 —
4-amino-N-{2,6-difluoro-3-[(propylsulfonyl)amino]phenyl}thieno[3,2-d]pyrimidine-7-carboxamide  
  

> delete /B

> color :600,507 green

> color :576 red

> delete all

> open 4ehe format mmcif fromDatabase pdb

4ehe title:  
B-Raf Kinase Domain in Complex with an Aminothienopyrimidine-based Inhibitor
[more info...]  
  
Chain information for 4ehe #1  
---  
Chain | Description | UniProt  
A B | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 432-726  
  
Non-standard residues in 4ehe #1  
---  
RI8 —
4-amino-N-{2,6-difluoro-3-[(propylsulfonyl)amino]phenyl}thieno[3,2-d]pyrimidine-7-carboxamide  
  

> color :600,507 green

> color :576 red

> delete /A

> save "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.inactive.cxs"

——— End of log from Fri Jan 26 10:02:26 2024 ———

opened ChimeraX session  

> open /Users/gz2294/Downloads/BRAF.pdb/POVME.inactive/volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/BRAF.pdb/POVME.inactive/volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Volume = 2994.0 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
2989 messages similar to the above omitted  
note | Combining 14093 symmetry atoms into XXX /X:1 X  
  

> delete #2

> open /Users/gz2294/Downloads/BRAF.pdb/POVME.inactive/volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/BRAF.pdb/POVME.inactive/volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Volume = 397.0 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
392 messages similar to the above omitted  
note | Combining 1711 symmetry atoms into XXX /X:1 X  
  

> delete #2

> open /Users/gz2294/Downloads/BRAF.pdb/POVME.inactive/volume_trajectory.pdb

Summary of feedback from opening
/Users/gz2294/Downloads/BRAF.pdb/POVME.inactive/volume_trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Frame 1  
  
Ignored bad PDB record found on line 2  
REMARK Volume = 1185.0 Cubic Angstroms  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
1180 messages similar to the above omitted  
note | Combining 6009 symmetry atoms into XXX /X:1 X  
  

> save "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.inactive.cxs"

——— End of log from Fri Jan 26 10:57:50 2024 ———

opened ChimeraX session  

> delete all

> open 6xhb

Summary of feedback from opening 6xhb fetched from pdb  
---  
notes | Fetching compressed mmCIF 6xhb from
http://files.rcsb.org/download/6xhb.cif  
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif  
  
6xhb title:  
Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding
domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II)
[more info...]  
  
Chain information for 6xhb #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-188  
  
Non-standard residues in 6xhb #1  
---  
CAF — S-dimethylarsinoyl-cysteine (cystein-S-yl cacodylate)  
CL — chloride ion  
GNP — phosphoaminophosphonic acid-guanylate ester  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPA — isopropyl alcohol (2-propanol)  
MG — magnesium ion  
ZN — zinc ion  
  

> select /B:229

Nothing selected  

> select /B:229-235

Nothing selected  

> select /B:123-127

39 atoms, 38 bonds, 5 residues, 1 model selected  

> select /B:135-142

63 atoms, 65 bonds, 8 residues, 1 model selected  

> select /B:162-173

100 atoms, 103 bonds, 12 residues, 1 model selected  

> delete all

> open 7mfe

Summary of feedback from opening 7mfe fetched from pdb  
---  
warning | Atom NZ has no neighbors to form bonds with according to residue
template for LYS /B:103  
note | Fetching compressed mmCIF 7mfe from
http://files.rcsb.org/download/7mfe.cif  
  
7mfe title:  
Autoinhibited BRAF:(14-3-3)2 complex with the BRAF RBD resolved [more info...]  
  
Chain information for 7mfe #1  
---  
Chain | Description | UniProt  
A | Serine/threonine-protein kinase B-raf | BRAF_HUMAN 1-766  
B C | 14-3-3 protein zeta/delta | 1433Z_HUMAN 1-245  
  
Non-standard residues in 7mfe #1  
---  
ZN — zinc ion  
  

> select /A:234-280

329 atoms, 339 bonds, 38 residues, 1 model selected  

> select /A/C:234-280

3293 atoms, 3364 bonds, 8 pseudobonds, 411 residues, 3 models selected  

> select /A:234-280

329 atoms, 339 bonds, 38 residues, 1 model selected  

> color /A:234-280 red

> save "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.inhibit.cxs"

——— End of log from Mon Jan 29 16:31:15 2024 ———

opened ChimeraX session  

> delete all

> open 6XHB

6xhb title:  
Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding
domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II)
[more info...]  
  
Chain information for 6xhb #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-188  
  
Non-standard residues in 6xhb #1  
---  
CAF — S-dimethylarsinoyl-cysteine (cystein-S-yl cacodylate)  
CL — chloride ion  
GNP — phosphoaminophosphonic acid-guanylate ester  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPA — isopropyl alcohol (2-propanol)  
MG — magnesium ion  
ZN — zinc ion  
  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.ras.pdb"

Chain information for braf.ras.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xhb, chain A (#1) with braf.ras.pdb, chain B (#2), sequence
alignment score = 827  
RMSD between 162 pruned atom pairs is 0.474 angstroms; (across all 166 pairs:
0.730)  
  

> show #2/A:234-280 atoms

> hide #1

> show #1:ZN

> delete #1/A

> delete #1/B

> undo

Undo failed, probably because structures have been modified.  

> open 6hhb

Summary of feedback from opening 6hhb fetched from pdb  
---  
notes | Fetching compressed mmCIF 6hhb from
http://files.rcsb.org/download/6hhb.cif  
Fetching CCD FE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif  
  
6hhb title:  
Structure of iron bound IbpS from Dickeya dadantii [more info...]  
  
Chain information for 6hhb #1  
---  
Chain | Description | UniProt  
A B C D | ABC-type Fe3+ transport system, periplasmic component | E0SCP7_DICD3
1-373  
  
Non-standard residues in 6hhb #1  
---  
ACT — acetate ion  
FE — Fe (III) ion  
  
6hhb mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete #2

> open 6xhb

6xhb title:  
Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding
domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II)
[more info...]  
  
Chain information for 6xhb #2  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-188  
  
Non-standard residues in 6xhb #2  
---  
CAF — S-dimethylarsinoyl-cysteine (cystein-S-yl cacodylate)  
CL — chloride ion  
GNP — phosphoaminophosphonic acid-guanylate ester  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPA — isopropyl alcohol (2-propanol)  
MG — magnesium ion  
ZN — zinc ion  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6hhb, chain B (#1) with 6xhb, chain A (#2), sequence alignment
score = 51.6  
RMSD between 8 pruned atom pairs is 1.241 angstroms; (across all 138 pairs:
18.895)  
  

> delete #2

> delete all

> open 6XI7

Summary of feedback from opening 6XI7 fetched from pdb  
---  
note | Fetching compressed mmCIF 6xi7 from
http://files.rcsb.org/download/6xi7.cif  
  
6xi7 title:  
Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding
domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form I)
[more info...]  
  
Chain information for 6xi7 #1  
---  
Chain | Description | UniProt  
A | Isoform 2B of GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-188  
  
Non-standard residues in 6xi7 #1  
---  
CL — chloride ion  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
SO4 — sulfate ion  
ZN — zinc ion  
  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.ras.pdb"

Chain information for braf.ras.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xi7, chain A (#1) with braf.ras.pdb, chain B (#2), sequence
alignment score = 829  
RMSD between 159 pruned atom pairs is 0.531 angstroms; (across all 169 pairs:
1.353)  
  

> mmaker #2/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xi7, chain B (#1) with braf.ras.pdb, chain A (#2), sequence
alignment score = 478.8  
RMSD between 114 pruned atom pairs is 0.960 angstroms; (across all 126 pairs:
1.525)  
  

> delete all

> open 6XHB

6xhb title:  
Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding
domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II)
[more info...]  
  
Chain information for 6xhb #1  
---  
Chain | Description | UniProt  
A | GTPase KRas | RASK_HUMAN 1-169  
B | RAF proto-oncogene serine/threonine-protein kinase | RAF1_HUMAN 52-188  
  
Non-standard residues in 6xhb #1  
---  
CAF — S-dimethylarsinoyl-cysteine (cystein-S-yl cacodylate)  
CL — chloride ion  
GNP — phosphoaminophosphonic acid-guanylate ester  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
IPA — isopropyl alcohol (2-propanol)  
MG — magnesium ion  
ZN — zinc ion  
  

> open "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.ras.pdb"

Chain information for braf.ras.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> mmaker #2/A to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6xhb, chain B (#1) with braf.ras.pdb, chain A (#2), sequence
alignment score = 467.5  
RMSD between 122 pruned atom pairs is 0.872 angstroms; (across all 131 pairs:
1.161)  
  

> delete #1/A

> save "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.ras.6XHB.cxs"

——— End of log from Wed Feb 7 11:21:55 2024 ———

opened ChimeraX session  

> select #1/B:184,168,165,139,176,173,155,152,204,203#2

5623 atoms, 5732 bonds, 8 pseudobonds, 701 residues, 3 models selected  

> delete ~sel

> select subtract #2

58 atoms, 50 bonds, 8 pseudobonds, 10 residues, 2 models selected  

> select add #1

58 atoms, 50 bonds, 15 pseudobonds, 10 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select #2/A:235,280,264,261,269,272,251,248

56 atoms, 50 bonds, 8 residues, 1 model selected  

> delete sel

> select all

5567 atoms, 5666 bonds, 23 pseudobonds, 693 residues, 5 models selected  

> combine sel

Remapping chain ID 'B' in braf.ras.pdb #2 to 'C'  

> select subtract #1

5509 atoms, 5616 bonds, 8 pseudobonds, 683 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!2 models

> hide #!1 models

> delete #1

> delete #2

> save "/Users/gz2294/CGC Dropbox/Guojie Zhong/Mode of Actions
> Manuscript/braf.ras.ZINC.2.pdb" relModel #3

> addh bonds

Expected a keyword  

> ui tool show "Build Structure"

> bond sel

Must specify two or more atoms  

> select /A:271/B:176

17 atoms, 15 bonds, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> ~bond sel

> bond sel

Created 16 bonds  

> bond sel

Created 0 bonds  

> select /A:271/A:176/A:273

30 atoms, 27 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> bond sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 772, in add_but_clicked  
run(self.session, "bond sel" + kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.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
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/cmd.py", line 20, in cmd_bond  
created = create_bonds(*args, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/bond.py", line 54, in create_bonds  
created_bonds.append(add_bond(a1, a2))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 173, in add_bond  
b = a1.structure.new_bond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: map::at: key not found  
  
IndexError: map::at: key not found  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select /A:176/A:273

19 atoms, 16 bonds, 3 residues, 1 model selected  

> bond sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 772, in add_but_clicked  
run(self.session, "bond sel" + kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.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
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/cmd.py", line 20, in cmd_bond  
created = create_bonds(*args, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/bond.py", line 54, in create_bonds  
created_bonds.append(add_bond(a1, a2))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 173, in add_bond  
b = a1.structure.new_bond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: map::at: key not found  
  
IndexError: map::at: key not found  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> bond sel reasonable false

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 772, in add_but_clicked  
run(self.session, "bond sel" + kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.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
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/cmd.py", line 20, in cmd_bond  
created = create_bonds(*args, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/bond.py", line 59, in create_bonds  
created_bonds.append(add_bond(a1, a2))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 173, in add_bond  
b = a1.structure.new_bond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: map::at: key not found  
  
IndexError: map::at: key not found  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> bond length /A:176@CA/A:176@C 1.643

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.714

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.786

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.786

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.786

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.786

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.786

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.786

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond length /A:176@CA/A:176@C 1.857

Missing or invalid "bond" argument: must specify exactly one bond (specified
2)  

> bond sel

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/tool.py", line 772, in add_but_clicked  
run(self.session, "bond sel" + kw)  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.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
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/cmd.py", line 20, in cmd_bond  
created = create_bonds(*args, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/build_structure/bond.py", line 54, in create_bonds  
created_bonds.append(add_bond(a1, a2))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/struct_edit.py", line 173, in add_bond  
b = a1.structure.new_bond(a1, a2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
IndexError: map::at: key not found  
  
IndexError: map::at: key not found  
  
File
"/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 1819, in new_bond  
return f(self._c_pointer, atom1._c_pointer, atom2._c_pointer)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: 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: Mac
      Model Identifier: Mac14,12
      Model Number: Z170000FYLL/A
      Chip: Unknown
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 121 days, 2 hours, 18 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2720QM:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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-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
    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-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
    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: 1.5.13
    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: 1.0.3
    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: 1.1.2
    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: 1.12.3
    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: 2.2.2
    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by pett, 21 months ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Could not find atom for bond

Also seems like there's multiple bonds between the same atoms.

comment:2 by pett, 20 months ago

Resolution: → can't reproduce
Status: accepted → closed

Error is *somewhere* in the C++ layer, and likely in the sequence/chain code (since almost all the calls to at() are there), but would need the braf.ras.6XHB.cxs session to have any hope of tracking this down.

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