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Opened 12 hours ago
#20587 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.4-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
I left this window open, and then suddenly it showed this error
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/pujanajmera/Downloads/tmp_viz/R1_NiFd_farpose.xyz
> /Users/pujanajmera/Downloads/tmp_viz/R1_NiFd_closepose.xyz
opened R1_NiFd_farpose.xyz as an XYZ coordinate file
opened R1_NiFd_closepose.xyz as an XYZ coordinate file
> open 2Z8Q
Summary of feedback from opening 2Z8Q fetched from pdb
---
notes | Fetching compressed mmCIF 2z8q from http://files.rcsb.org/download/2z8q.cif
Fetching CCD NCO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/NCO/NCO.cif
2z8q title:
ferredoxin from Pyrococcus furiosus, D14C variant [more info...]
Chain information for 2z8q #3
---
Chain | Description | UniProt
A B | Ferredoxin | FER_PYRFU 1-66
Non-standard residues in 2z8q #3
---
NCO — cobalt hexammine(III)
SF4 — iron/sulfur cluster
2z8q mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
61 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #3
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> ui mousemode right "structure eraser"
> ui mousemode right translate
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> open /Users/pujanajmera/Downloads/tmp_viz/orca_R2.xyz
> /Users/pujanajmera/Downloads/tmp_viz/orca_R5.xyz
> /Users/pujanajmera/Downloads/tmp_viz/orca_R4.xyz
> /Users/pujanajmera/Downloads/tmp_viz/orca_R3.xyz
opened orca_R2.xyz as an XYZ coordinate file
opened orca_R5.xyz as an XYZ coordinate file
opened orca_R4.xyz as an XYZ coordinate file
opened orca_R3.xyz as an XYZ coordinate file
> hide #3 models
> hide #4 models
> hide #5 models
> hide #6 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> align #3@C7,N1,C1 toAtoms #2@C2,N1,C1
RMSD between 3 atom pairs is 0.008 angstroms
> hide #!2 models
> select #3/a:1@C7
1 atom, 1 residue, 1 model selected
> ui tool show "Rotate Atoms"
> select #3/a:1@C7
1 atom, 1 residue, 1 model selected
> select add #3/a:1@N1
2 atoms, 1 residue, 1 model selected
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> select clear
> hide #!2 models
> select #3/a:1@C1
1 atom, 1 residue, 1 model selected
> select add #3/a:1@N1
2 atoms, 1 residue, 1 model selected
> select add #3/a:1@C7
3 atoms, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #3/a:1@N1
1 atom, 1 residue, 1 model selected
> select add #3/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #3/a:1@C2
3 atoms, 1 residue, 1 model selected
> select #3/a:1@C1
1 atom, 1 residue, 1 model selected
> select add #3/a:1@N1
2 atoms, 1 residue, 1 model selected
> select clear
> select #3/a:1@N1
1 atom, 1 residue, 1 model selected
> select add #3/a:1@C1
2 atoms, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> show #!2 models
> select clear
> show #!1 models
> hide #!2 models
> select add #3
19 atoms, 19 bonds, 1 residue, 1 model selected
> select add #1
136 atoms, 125 bonds, 17 pseudobonds, 2 residues, 3 models selected
> combine sel name R2_NiFd_farpose
Remapping chain ID 'a' in orca_R2 #3 to 'b'
> hide #!1 models
> hide #!3 models
> select #7/b:1@H7
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> select #7/a:1@H9
1 atom, 1 residue, 1 model selected
> select up
117 atoms, 106 bonds, 1 residue, 1 model selected
> select clear
> select #7/b:1@H8
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> hide sel target a
> select #7/a:1@C2
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 11 atoms, 11 bonds
> delete atoms sel
> delete bonds sel
> select #7/a:1@H1
1 atom, 1 residue, 1 model selected
> select add #7/a:1@C1
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #7/a:1@N1
1 atom, 1 residue, 1 model selected
> select add #7/a:1@C2
2 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #7
121 atoms, 111 bonds, 16 pseudobonds, 2 residues, 2 models selected
> show (#!7 & sel) target ab
> select clear
> hide #!7 models
> hide #7.1 models
> show #!2 models
> show #3 models
> select add #3
19 atoms, 19 bonds, 1 residue, 1 model selected
> select add #2
136 atoms, 125 bonds, 19 pseudobonds, 2 residues, 3 models selected
> combine sel name R2_NiFd_closepose
Remapping chain ID 'a' in orca_R2 #3 to 'b'
> hide #!2 models
> hide #!3 models
> select subtract #2
19 atoms, 19 bonds, 1 residue, 1 model selected
> select add #3
19 atoms, 19 bonds, 1 residue, 2 models selected
> select add #3
19 atoms, 19 bonds, 1 residue, 2 models selected
> select add #8
155 atoms, 144 bonds, 19 pseudobonds, 3 residues, 3 models selected
> select subtract #8
19 atoms, 19 bonds, 1 residue, 1 model selected
> select add #3
19 atoms, 19 bonds, 1 residue, 2 models selected
> hide #3.1 models
> select add #3
19 atoms, 19 bonds, 1 residue, 2 models selected
> select add #3
19 atoms, 19 bonds, 1 residue, 2 models selected
> select add #3
19 atoms, 19 bonds, 1 residue, 2 models selected
> select add #8
155 atoms, 144 bonds, 19 pseudobonds, 3 residues, 3 models selected
> select subtract #8
19 atoms, 19 bonds, 1 residue, 1 model selected
> select ~
Expected an objects specifier or a keyword
> select clear
[Repeated 2 time(s)]
> select #8/b:1@H7
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 19 bonds, 1 residue, 1 model selected
> hide sel target a
Drag select of 9 atoms, 8 bonds
> delete atoms sel
> delete bonds sel
> select #8/a:1@H1
1 atom, 1 residue, 1 model selected
> select add #8/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #8/a:1@H2
3 atoms, 1 residue, 1 model selected
> select add #8/a:1@N1
4 atoms, 1 bond, 1 residue, 1 model selected
> select add #8/a:1@C2
5 atoms, 1 bond, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #8 target ab
> select clear
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> show #7.1 models
> hide #7.1 models
> hide #!8 models
> hide #8.1 models
> hide #!7 models
> show #3 models
> show #!2 models
> show #!1 models
> hide #!1 models
> close #3
> rename #6 id #3
> rename #7 id #6
> rename #8 id #7
> show #3 models
> align #3@C8,N1,C7 toAtoms #2@C2,N1,C1
RMSD between 3 atom pairs is 0.005 angstroms
> show #!1 models
> hide #!1 models
> hide #!2 models
> select #3/a:1@N1
1 atom, 1 residue, 1 model selected
> select clear
> select #3/a:1@C8
1 atom, 1 residue, 1 model selected
> select add #3/a:1@N1
2 atoms, 1 residue, 1 model selected
> select clear
> select add #3
16 atoms, 16 bonds, 1 residue, 1 model selected
> show #!2 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> select clear
> select add #2
117 atoms, 106 bonds, 19 pseudobonds, 1 residue, 2 models selected
> select add #3
133 atoms, 122 bonds, 19 pseudobonds, 2 residues, 3 models selected
> combine sel name R3_NiFd_closepose
Remapping chain ID 'a' in orca_R3 #3 to 'b'
> select subtract #2
16 atoms, 16 bonds, 1 residue, 1 model selected
> select add #1
133 atoms, 122 bonds, 17 pseudobonds, 2 residues, 3 models selected
> combine sel name R3_NiFd_farpose
Remapping chain ID 'a' in orca_R3 #3 to 'b'
> select clear
> hide #!2 models
> hide #3 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> select #8/b:1@H6
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel target a
Drag select of 9 atoms, 9 bonds
> delete atoms sel
> delete bonds sel
> select #8/a:1@H1
1 atom, 1 residue, 1 model selected
> select add #8/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #8/a:1@H2
3 atoms, 1 residue, 1 model selected
> select add #8/a:1@N1
4 atoms, 1 residue, 1 model selected
> select add #8/a:1@C2
5 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #8 target ab
> select clear
> show #!9 models
> hide #!8 models
> select #9/b:1@H5
1 atom, 1 residue, 1 model selected
> select up
16 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> select #9/a:1@H9
1 atom, 1 residue, 1 model selected
> select up
117 atoms, 106 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select clear
Drag select of 10 atoms, 9 bonds
> delete atoms sel
> delete bonds sel
> select #9/a:1@H2
1 atom, 1 residue, 1 model selected
> select add #9/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #9/a:1@H1
3 atoms, 1 residue, 1 model selected
> select add #9/a:1@N1
4 atoms, 1 residue, 1 model selected
> select add #9/a:1@C2
5 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #9 target ab
> select clear
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> hide #!8 models
> close #3
> show #!2 models
> show #4 models
> align #4@C9,N1,C8 toAtoms #2@C2,N1,C1
RMSD between 3 atom pairs is 0.012 angstroms
> hide #!2 models
> select clear
> select #4/a:1@N1
1 atom, 1 residue, 1 model selected
> select add #4/a:1@C9
2 atoms, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 1 residue, 1 model selected
> show #!2 models
> select clear
> select add #4
22 atoms, 22 bonds, 1 residue, 1 model selected
> select add #2
139 atoms, 128 bonds, 19 pseudobonds, 2 residues, 3 models selected
> show #!1 models
> hide #!1 models
> combine sel name R5_NiFd_closepose
Remapping chain ID 'a' in orca_R5 #4 to 'b'
> select subtract #2
22 atoms, 22 bonds, 1 residue, 1 model selected
> select add #1
139 atoms, 128 bonds, 17 pseudobonds, 2 residues, 3 models selected
> combine sel name R5_NiFd_farpose
Remapping chain ID 'a' in orca_R5 #4 to 'b'
> rename #3 id #11
> close #4
> select subtract #1
Nothing selected
> hide #!2 models
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> select #10/b:1@H1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 1 residue, 1 model selected
> hide sel target a
Drag select of 9 atoms, 8 bonds
> select add #10/a:1@H5
10 atoms, 8 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #10/a:1@H1
1 atom, 1 residue, 1 model selected
> select add #10/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #10/a:1@H2
3 atoms, 1 residue, 1 model selected
> select add #10/a:1@N1
4 atoms, 1 bond, 1 residue, 1 model selected
> select add #10/a:1@C2
5 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #10 target ab
> show #!11 models
> hide #!10 models
> select add #11/b:1@H1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 1 residue, 1 model selected
> hide sel target a
Drag select of 11 atoms, 11 bonds
> delete atoms sel
> delete bonds sel
> select #11/a:1@H1
1 atom, 1 residue, 1 model selected
> select add #11/a:1@C2
2 atoms, 1 residue, 1 model selected
> select add #11/a:1@N1
3 atoms, 1 residue, 1 model selected
> select add #11/a:1@C1
4 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #11 target ab
> rename #5 id #3
> rename #6 id #4
> rename #7 id #5
> rename #8 id #6
> rename #9 id #7
> rename #11 id #8
> rename #10 id #9
> show #3 models
> hide #!8 models
> show #!2 models
> align #3@C2,N1,C1 toAtoms #2@C2,N1,C1
RMSD between 3 atom pairs is 0.022 angstroms
> hide #!2 models
> show #!4 models
> hide #!4 models
> select #3/a:1@N1
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #3/a:1@C2
1 atom, 1 residue, 1 model selected
> select add #3/a:1@N1
2 atoms, 1 residue, 1 model selected
> select clear
> select add #3
17 atoms, 17 bonds, 1 residue, 1 model selected
> show #!2 models
> select clear
> select add #3
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add #2
134 atoms, 123 bonds, 19 pseudobonds, 2 residues, 3 models selected
> combine sel name R4_NiFd_closepose
Remapping chain ID 'a' in orca_R4 #3 to 'b'
> select add #1
251 atoms, 229 bonds, 36 pseudobonds, 3 residues, 5 models selected
> select subtract #2
134 atoms, 123 bonds, 17 pseudobonds, 2 residues, 3 models selected
> show #!1 models
> hide #!2 models
> hide #!10 models
> combine sel name R4_NiFd_farpose
Remapping chain ID 'a' in orca_R4 #3 to 'b'
> hide #!3 models
> hide #!1 models
> select subtract #1
17 atoms, 17 bonds, 1 residue, 1 model selected
> select add #3
17 atoms, 17 bonds, 1 residue, 2 models selected
> select add #3
17 atoms, 17 bonds, 1 residue, 2 models selected
> select add #3
17 atoms, 17 bonds, 1 residue, 2 models selected
> show #!10 models
> hide #!11 models
> hide #!10 models
> show #!11 models
> select #11/b:1@O1
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel target a
Drag select of 9 atoms, 8 bonds
> delete atoms sel
> delete bonds sel
> select clear
> select #11/a:1@C2
1 atom, 1 residue, 1 model selected
> select add #11/a:1@N1
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #11/a:1@H1
3 atoms, 1 bond, 1 residue, 1 model selected
> select add #11/a:1@C1
4 atoms, 1 bond, 1 residue, 1 model selected
> select add #11/a:1@H2
5 atoms, 1 bond, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #11 target ab
> select clear
> show #!10 models
> hide #!11 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 17 bonds, 1 residue, 1 model selected
> hide sel target a
> select #10/a:1@N1
1 atom, 1 residue, 1 model selected
Drag select of 12 atoms, 12 bonds
> delete atoms sel
> delete bonds sel
> select #10/a:1@C2
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> show #10 target ab
> show #!11 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> close #3
> hide #!7 models
> hide #!6 models
> hide #!9 models
> hide #!10 models
> hide #10.1 models
> hide #!11 models
> save /Users/pujanajmera/Downloads/tmp_viz/R2_NiFd_farpose.xyz models #4
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R2_NiFd_closepose.xyz models #5
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R3_NiFd_farpose.xyz models #7
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R3_NiFd_closepose.xyz models #6
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R5_NiFd_closepose.xyz models #8
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R5_NiFd_farpose.xyz models #9
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R4_NiFd_closepose.xyz models #10
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/R4_NiFd_farpose.xyz models #11
> coordsets false
> show #!4 models
> hide #!4 models
> show #!1 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> select add #1
117 atoms, 106 bonds, 17 pseudobonds, 1 residue, 2 models selected
> combine sel name CN_NiFd_farpose
> rename #3 id #12
> select add #2
234 atoms, 212 bonds, 36 pseudobonds, 2 residues, 4 models selected
> select subtract #1
117 atoms, 106 bonds, 19 pseudobonds, 1 residue, 2 models selected
> hide #!1 models
> hide #!12 models
> show #!2 models
> combine sel name CN_NiFd_closepose
> close #3,12
> open /Users/pujanajmera/Downloads/tmp_viz/orca_CN.xyz
opened orca_CN.xyz as an XYZ coordinate file
> select clear
> align #3@C1,N1 toAtoms #2@C2,N1
RMSD between 2 atom pairs is 0.006 angstroms
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #3
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #2
119 atoms, 107 bonds, 19 pseudobonds, 2 residues, 3 models selected
> combine sel name CN_NiFd_closepose
Remapping chain ID 'a' in orca_CN #3 to 'b'
> select subtract #2
2 atoms, 1 bond, 1 residue, 1 model selected
> hide #!2 models
> show #!1 models
> select add #1
119 atoms, 107 bonds, 17 pseudobonds, 2 residues, 3 models selected
> combine sel name CN_NiFd_farpose
Remapping chain ID 'a' in orca_CN #3 to 'b'
> close #3
> select clear
> hide #!1 models
> hide #!13 models
> select clear
> select #12/b:1@C1
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel target a
> select clear
Drag select of 9 atoms, 9 bonds
> delete atoms sel
> delete bonds sel
> select #12/a:1@H2
1 atom, 1 residue, 1 model selected
> select add #12/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #12/a:1@N1
3 atoms, 1 residue, 1 model selected
> select add #12/a:1@C2
4 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #12 target ab
> select clear
> show #!13 models
> hide #!12 models
> select #13/b:1@C1
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel target a
> select clear
Drag select of 13 atoms, 12 bonds
> delete atoms sel
> delete bonds sel
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> close #13
> open /Users/pujanajmera/Downloads/tmp_viz/orca_CN.xyz
opened orca_CN.xyz as an XYZ coordinate file
> align #3@C1,N1 toAtoms #2@C2,N1
RMSD between 2 atom pairs is 0.006 angstroms
> select clear
> hide #3 models
> show #3 models
> show #!1 models
> select add #3
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #1
119 atoms, 107 bonds, 17 pseudobonds, 2 residues, 3 models selected
> combine sel name CN_NiFd_farpose
Remapping chain ID 'a' in orca_CN #3 to 'b'
> hide #!1 models
> hide #3 models
> select subtract #3
117 atoms, 106 bonds, 17 pseudobonds, 1 residue, 2 models selected
> select subtract #1
Nothing selected
> select #13/b:1@C1
1 atom, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel target a
Drag select of 8 atoms, 9 bonds
> delete atoms sel
> delete bonds sel
> select #13/a:1@H2
1 atom, 1 residue, 1 model selected
> select add #13/a:1@C1
2 atoms, 1 residue, 1 model selected
> select add #13/a:1@H1
3 atoms, 1 residue, 1 model selected
> select add #13/a:1@N1
4 atoms, 1 residue, 1 model selected
> select add #13/a:1@C2
5 atoms, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> show #13 target ab
> select clear
> save /Users/pujanajmera/Downloads/tmp_viz/CN_NiFd_closepose.xyz models #12
> coordsets false
> save /Users/pujanajmera/Downloads/tmp_viz/CN_NiFd_farpose.xyz models #13
> coordsets false
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 239, in _draw_scene
camera.draw_background(vnum, r)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py", line 195, in draw_background
render.draw_background()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Unsupported scale factor (0.000000) detected on Display0
[Repeated 7 time(s)]
> show #!12 models
> hide #!13 models
> show #!13 models
> hide #!12 models
> hide #!13 models
> select clear
> show #!13 models
> hide #!13 models
> graphics reset
Expected a keyword
> graphics
Background color: 0,0,0
> graphics restart
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 233, in _draw_scene
camera.draw_background(vnum, r)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py", line 195, in draw_background
render.draw_background()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
> graphics restart
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 233, in _draw_scene
camera.draw_background(vnum, r)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/camera.py", line 195, in draw_background
render.draw_background()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGP3LL/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 Performance and 2 Efficiency)
Memory: 16 GB
System Firmware Version: 18000.101.7
OS Loader Version: 18000.101.7
Software:
System Software Overview:
System Version: macOS 26.4 (25E246)
Kernel Version: Darwin 25.4.0
Time since boot: 12 days, 5 hours, 36 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
Send2Trash: 1.8.3
SEQCROW: 1.9.7
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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