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Opened 11 hours ago
Closed 9 hours ago
#19316 closed defect (duplicate)
ffmpeg: Permission denied
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Build System | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-26.0.1-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/oswanson/Desktop/RdRp/RdRp.cxs
Opened cryosparc_P605_J52_005_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.45, shown at level 0.0717, step 1, values float32
Opened Lee_dimer.mrc as #9, grid size 256,256,256, pixel 1.45, shown at level
0.105, step 1, values float32
Opened map series J72_component_000_frame_000.mrc as #10, 20 images, grid size
256,256,256, pixel 1.45, shown at step 1, values float32
Opened map series J72_component_001_frame_000.mrc as #11, 20 images, grid size
256,256,256, pixel 1.45, shown at step 1, values float32
Opened map series J72_component_002_frame_000.mrc as #8, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0504, step 1, values float32
Opened map series J72_component_003_frame_000.mrc as #17, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.06, step 1, values float32
Opened map series J72_component_004_frame_000.mrc as #18, 20 images, grid size
256,256,256, pixel 1.45, shown at step 1, values float32
Opened map series J72_component_005_frame_000.mrc as #12, 20 images, grid size
256,256,256, pixel 1.45, shown at step 1, values float32
Opened cryosparc_P605_J56_008_volume_map_sharp.mrc as #19, grid size
256,256,256, pixel 1.45, shown at level 0.0482, step 1, values float32
Opened cryosparc_P605_J71_009_volume_map_sharp.mrc as #20, grid size
256,256,256, pixel 1.45, shown at level 0.0699, step 1, values float32
Log from Fri Nov 7 10:41:56 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/oswanson/Desktop/RdRp/RdRp.cxs format session
Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size
80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32
Opened cryosparc_P605_J52_005_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.45, shown at level 0.329, step 1, values float32
Opened cryosparc_P605_J45_class_00_final_volume.mrc as #2, grid size
256,256,256, pixel 1.45, shown at level 0.0414, step 1, values float32
Opened cryosparc_P605_J23_class_00_final_volume.mrc as #3, grid size
128,128,128, pixel 2.9, shown at level 0.115, step 1, values float32
Opened Lee_init map 6 as #8, grid size 131,81,96, pixel 2, shown at level
0.105, step 1, values float32
Opened Lee_dimer.mrc as #9, grid size 256,256,256, pixel 1.45, shown at level
0.105, step 1, values float32
Log from Thu Nov 6 10:37:56 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/oswanson/Desktop/Primocalins/Structures/initial_models_plusRdRp.cxs
Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size
80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32
Log from Wed Nov 5 13:19:26 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs
Log from Fri Oct 31 13:49:15 2025UCSF 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/oswanson/Desktop/Primocalins/231023_poly310-DH270UCA3_refine_001.pdb
Chain information for 231023_poly310-DH270UCA3_refine_001.pdb #1
---
Chain | Description
E | No description available
H | No description available
L | No description available
Computing secondary structure
> open /Users/oswanson/Desktop/Primocalins/Y513apo_refine_31.pdb
Summary of feedback from opening
/Users/oswanson/Desktop/Primocalins/Y513apo_refine_31.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2022-07-08 Time 12:55:39 CDT -0500 (1657302939.20 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/Users/danielwrapp/Desktop/PEDVnumber/Y513apo/Refine_4/Y513apo_refine_4.mtz
40 messages similar to the above omitted
Chain information for Y513apo_refine_31.pdb #2
---
Chain | Description
A B | No description available
Computing secondary structure
> hide #!1 models
> set bgColor white
> hide #2 models
> show #!1 models
> select #1/E:108
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
604 atoms, 618 bonds, 74 residues, 1 model selected
> select up
616 atoms, 629 bonds, 76 residues, 1 model selected
> select up
1313 atoms, 1346 bonds, 164 residues, 1 model selected
> select up
4851 atoms, 4757 bonds, 812 residues, 1 model selected
> select down
1313 atoms, 1346 bonds, 164 residues, 1 model selected
> color sel byhetero
> color sel bychain
> ui tool show H-Bonds
> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
1 231023_poly310-DH270UCA3_refine_001.pdb
25 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O no hydrogen 2.874 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 71 N 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 86 O no hydrogen 2.780 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O no hydrogen 2.993 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1 no hydrogen 3.440 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 N 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O no hydrogen 2.550 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E ASN 164 N 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 242 O no hydrogen 2.990 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 2.679 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.050 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.339 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 44 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O no hydrogen 3.746 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 49 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 O no hydrogen 2.651 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 49 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 OD2 no hydrogen 2.434 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.428 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD2 no hydrogen 2.642 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 75 O no hydrogen 3.183 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O no hydrogen 3.912 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 86 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 51 O no hydrogen 2.817 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 242 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E GLU 163 OE1 no hydrogen 2.752 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 409 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E VAL 34 O no hydrogen 2.557 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 409 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 169 O no hydrogen 3.211 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O no hydrogen 4.003 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.243 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 38 O no hydrogen 2.357 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E VAL 41 O no hydrogen 2.400 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E HIS 165 O no hydrogen 3.686 N/A
25 hydrogen bonds found
> select ::name="HOH"::name="SO4"
234 atoms, 24 bonds, 210 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1/E:109
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
61 atoms, 60 bonds, 8 residues, 1 model selected
> select up
604 atoms, 618 bonds, 74 residues, 1 model selected
> select up
616 atoms, 629 bonds, 76 residues, 1 model selected
> select up
1313 atoms, 1346 bonds, 164 residues, 1 model selected
> select up
4647 atoms, 4757 bonds, 608 residues, 1 model selected
> select down
1313 atoms, 1346 bonds, 164 residues, 1 model selected
> hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8
> intraMol false intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.8 angstroms and 20 degrees
Models used:
1 231023_poly310-DH270UCA3_refine_001.pdb
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O no hydrogen 2.874 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O no hydrogen 2.993 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1 no hydrogen 3.440 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 2.679 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.050 N/A
231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.339 N/A
6 hydrogen bonds found
> select up
93 atoms, 88 bonds, 10 residues, 1 model selected
> color sel byhetero
> select clear
> select #1/E:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> open /Users/oswanson/Downloads/9NPI-sf.cif
Summary of feedback from opening /Users/oswanson/Downloads/9NPI-sf.cif
---
warning | No mmCIF models found.
> open /Users/oswanson/Downloads/9NPI-sf.cif
Summary of feedback from opening /Users/oswanson/Downloads/9NPI-sf.cif
---
warning | No mmCIF models found.
> open /Users/oswanson/coot_sessions/3FW4.mtz
> /Users/oswanson/coot_sessions/3FW4.pdb
Install the Clipper bundle to open "MTZ" format files.
Opener for format 'MTZ' is not installed; see log for more info
> open /Users/oswanson/coot_sessions/3FW4.pdb
3FW4.pdb title:
Crystal structure of siderocalin (ngal, lipocalin 2) complexed with ferric
catechol [more info...]
Chain information for 3FW4.pdb #3
---
Chain | Description | UniProt
A B C | neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-178
Non-standard residues in 3FW4.pdb #3
---
CAQ — catechol (1,2-dihydroxybenzene)
CL — chloride ion
FE — Fe (III) ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
NA — sodium ion
31 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/oswanson/coot_sessions/3FW4-sf.cif
Summary of feedback from opening /Users/oswanson/coot_sessions/3FW4-sf.cif
---
warning | No mmCIF models found.
> open /Users/oswanson/Desktop/Primocalins/Structures/Cluster2c_lib1.pdb
> /Users/oswanson/Desktop/Primocalins/Structures/design_start.pdb
> /Users/oswanson/Desktop/Primocalins/Structures/RMSD4_NNK1.pdb
> /Users/oswanson/Desktop/Primocalins/Structures/RMSD6_NNK1.pdb
Chain information for Cluster2c_lib1.pdb #4
---
Chain | Description
A | No description available
G | No description available
H | No description available
Chain information for design_start.pdb #5
---
Chain | Description
A | No description available
G | No description available
H | No description available
Chain information for RMSD4_NNK1.pdb #6
---
Chain | Description
A | No description available
G | No description available
H | No description available
Chain information for RMSD6_NNK1.pdb #7
---
Chain | Description
A | No description available
G | No description available
H | No description available
Computing secondary structure
[Repeated 3 time(s)]
> select #1/E:68
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
53 atoms, 53 bonds, 7 residues, 1 model selected
> select up
709 atoms, 728 bonds, 90 residues, 1 model selected
> select up
727 atoms, 746 bonds, 92 residues, 1 model selected
> select up
1313 atoms, 1346 bonds, 164 residues, 1 model selected
> select up
4647 atoms, 4757 bonds, 608 residues, 1 model selected
> select down
1313 atoms, 1346 bonds, 164 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2,4-7#!3 to #1 & sel
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 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Y513apo_refine_31.pdb, chain B (#2), sequence alignment score = 692
RMSD between 154 pruned atom pairs is 0.689 angstroms; (across all 164 pairs:
1.591)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Cluster2c_lib1.pdb, chain A (#4), sequence alignment score = 692
RMSD between 151 pruned atom pairs is 0.676 angstroms; (across all 164 pairs:
1.416)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
design_start.pdb, chain A (#5), sequence alignment score = 709.7
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
1.402)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD4_NNK1.pdb, chain A (#6), sequence alignment score = 692.2
RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
1.442)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD6_NNK1.pdb, chain A (#7), sequence alignment score = 683.1
RMSD between 152 pruned atom pairs is 0.697 angstroms; (across all 164 pairs:
1.421)
Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
3FW4.pdb, chain A (#3), sequence alignment score = 709.7
RMSD between 150 pruned atom pairs is 0.624 angstroms; (across all 164 pairs:
1.389)
> matchmaker #4 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 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Cluster2c_lib1.pdb, chain A (#4), sequence alignment score = 692
RMSD between 151 pruned atom pairs is 0.676 angstroms; (across all 164 pairs:
1.416)
> matchmaker #5 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 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
design_start.pdb, chain A (#5), sequence alignment score = 709.7
RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs:
1.402)
> matchmaker #6 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 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD4_NNK1.pdb, chain A (#6), sequence alignment score = 692.2
RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs:
1.442)
> matchmaker #7 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 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
RMSD6_NNK1.pdb, chain A (#7), sequence alignment score = 683.1
RMSD between 152 pruned atom pairs is 0.697 angstroms; (across all 164 pairs:
1.421)
> show #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #4 models
> hide #!1 models
> hide #5 models
> hide #6 models
> hide #7 models
> show #!1 models
> show #!3 models
> hide #!3 models
> select #2/A:126
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
76 atoms, 78 bonds, 9 residues, 1 model selected
> select up
1459 atoms, 1497 bonds, 181 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #2 & sel 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 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with
Y513apo_refine_31.pdb, chain A (#2), sequence alignment score = 689
RMSD between 154 pruned atom pairs is 0.695 angstroms; (across all 164 pairs:
1.580)
> hide #!1 models
> show #5 models
> show #6 models
> hide #5 models
> select add #6
7768 atoms, 7887 bonds, 591 residues, 2 models selected
> color sel bychain
> color sel byhetero
> hide #6 models
> show #7 models
> color sel & #2 bychain
> select add #7
14068 atoms, 14269 bonds, 1001 residues, 3 models selected
> select subtract #6
7759 atoms, 7879 bonds, 591 residues, 2 models selected
> color sel bychain
> color sel byhetero
> show #6 models
> hide #6 models
> show #6 models
> select add #6
14068 atoms, 14269 bonds, 1001 residues, 3 models selected
> color sel bychain
> select subtract #6
7759 atoms, 7879 bonds, 591 residues, 2 models selected
> select add #2
9248 atoms, 9400 bonds, 778 residues, 2 models selected
> select subtract #2
6300 atoms, 6382 bonds, 410 residues, 1 model selected
> hide #6 models
> hide #2 models
> show #2 models
> hide #7 models
> select #2/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
79 atoms, 81 bonds, 9 residues, 1 model selected
> select up
1459 atoms, 1497 bonds, 181 residues, 1 model selected
> ui tool show "Color Actions"
> color sel blue
> color sel royal blue
> show #6 models
> hide #6 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #4 models
> select clear
> hide #2 models
> select #4/A:71
20 atoms, 20 bonds, 1 residue, 1 model selected
> select up
150 atoms, 151 bonds, 9 residues, 1 model selected
> select up
2813 atoms, 2852 bonds, 174 residues, 1 model selected
> color sel dark sea green
> color sel olive drab
> color sel medium sea green
> color sel forest green
> select clear
> show #5 models
> hide #4 models
> select #5/A:70
19 atoms, 18 bonds, 1 residue, 1 model selected
> select up
155 atoms, 156 bonds, 9 residues, 1 model selected
> select up
2845 atoms, 2882 bonds, 174 residues, 1 model selected
> color sel sienna
> color sel indian red
> color sel saddle brown
> color sel maroon
> select clear
> hide #5 models
> show #6 models
> show #7 models
> hide #6 models
> select #7/G:81
17 atoms, 16 bonds, 1 residue, 1 model selected
> select add #7/H:21
28 atoms, 26 bonds, 2 residues, 1 model selected
> select up
183 atoms, 182 bonds, 12 residues, 1 model selected
> select up
3494 atoms, 3537 bonds, 236 residues, 1 model selected
> color sel silver
> select #7/A:104
22 atoms, 21 bonds, 1 residue, 1 model selected
> select up
147 atoms, 147 bonds, 8 residues, 1 model selected
> select up
2806 atoms, 2845 bonds, 174 residues, 1 model selected
> color sel midnight blue
> select clear
> show #!1 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #!1 models
> show #6 models
> hide #6 models
> show #!1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #4 models
> show #5 models
> show #!3 models
> hide #!3 models
> show #2 models
> hide #2 models
> hide #4 models
> hide #!1 models
> show #2 models
> show #6 models
> hide #5 models
> hide #2 models
> show #5 models
> show #7 models
> hide #6 models
> show #6 models
> show #4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> tile
4 models tiled
> hide #5 models
> show #5 models
> select clear
> select #5/G:124
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add #5/H:67
25 atoms, 23 bonds, 2 residues, 1 model selected
> select up
161 atoms, 160 bonds, 11 residues, 1 model selected
> select up
3494 atoms, 3537 bonds, 236 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #4,6-7#!1 to #5 & sel
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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #4 models
> hide #6 models
> hide #7 models
> show #7 models
> matchmaker #4,6-7#!1 to #5 & sel
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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #7 models
> show #6 models
> matchmaker #4,6-7#!1 to #5 & sel
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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #6 models
> show #4 models
> matchmaker #4,6-7#!1 to #5 & sel
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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #4 models
> show #!1 models
> matchmaker #4,6-7#!1 to #5 & sel
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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> matchmaker #4,6-7#!1 to #5 & sel
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 design_start.pdb, chain G (#5) with Cluster2c_lib1.pdb, chain G
(#4), sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.098 angstroms; (across all 126 pairs:
0.098)
Matchmaker design_start.pdb, chain G (#5) with RMSD4_NNK1.pdb, chain G (#6),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.168 angstroms; (across all 126 pairs:
0.168)
Matchmaker design_start.pdb, chain G (#5) with RMSD6_NNK1.pdb, chain G (#7),
sequence alignment score = 665.8
RMSD between 126 pruned atom pairs is 0.200 angstroms; (across all 126 pairs:
0.200)
Matchmaker design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 638.8
RMSD between 125 pruned atom pairs is 0.800 angstroms; (across all 126 pairs:
0.817)
> hide #5 models
> select #1/L:106
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1/H:112C
12 atoms, 10 bonds, 2 residues, 1 model selected
> select add #1/H:110
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #1/H:59
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #1/H:35
35 atoms, 30 bonds, 5 residues, 1 model selected
> select up
307 atoms, 318 bonds, 39 residues, 1 model selected
> select up
3334 atoms, 3411 bonds, 444 residues, 1 model selected
> select down
307 atoms, 318 bonds, 39 residues, 1 model selected
> select add #1/H:38
319 atoms, 330 bonds, 40 residues, 1 model selected
> select up
331 atoms, 344 bonds, 41 residues, 1 model selected
> select add #1/H:40
341 atoms, 354 bonds, 42 residues, 1 model selected
> select add #1/H:67
353 atoms, 366 bonds, 43 residues, 1 model selected
> select up
417 atoms, 434 bonds, 50 residues, 1 model selected
> show #5 models
> matchmaker #!1 & sel to #5 & sel
No 'to' model specified
> matchmaker #!1 & sel to #5 & sel
No 'to' model specified
> matchmaker #!1 & sel to #5 & sel
No 'to' model specified
> matchmaker #!1 & sel to #5
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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 227.4
RMSD between 42 pruned atom pairs is 0.783 angstroms; (across all 42 pairs:
0.783)
> select add #5/G:109
428 atoms, 444 bonds, 51 residues, 2 models selected
> select up
744 atoms, 770 bonds, 72 residues, 2 models selected
> select add #5/G:72
768 atoms, 793 bonds, 73 residues, 2 models selected
> select up
841 atoms, 866 bonds, 78 residues, 2 models selected
> select up
5259 atoms, 5364 bonds, 570 residues, 2 models selected
> select down
841 atoms, 866 bonds, 78 residues, 2 models selected
> select add #5/G:80
862 atoms, 887 bonds, 79 residues, 2 models selected
> select up
937 atoms, 962 bonds, 84 residues, 2 models selected
> select add #5/G:75
948 atoms, 972 bonds, 85 residues, 2 models selected
> select up
992 atoms, 1018 bonds, 88 residues, 2 models selected
> matchmaker #!1 & sel to #5
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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 227.4
RMSD between 42 pruned atom pairs is 0.783 angstroms; (across all 42 pairs:
0.783)
> select add #5/G:56
999 atoms, 1024 bonds, 89 residues, 2 models selected
> select subtract #5/G:56
992 atoms, 1018 bonds, 88 residues, 2 models selected
> select clear
> select #1/H:111C
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #5/G:102
31 atoms, 30 bonds, 2 residues, 2 models selected
> select up
508 atoms, 526 bonds, 44 residues, 2 models selected
> matchmaker #!1 & sel to #5 & sel
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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 121.6
RMSD between 22 pruned atom pairs is 0.765 angstroms; (across all 22 pairs:
0.765)
> matchmaker #!1 & sel to #5 & sel
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 design_start.pdb, chain G (#5) with
231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1), sequence alignment
score = 121.6
RMSD between 22 pruned atom pairs is 0.765 angstroms; (across all 22 pairs:
0.765)
Desktop color scheme is dark
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,)
)
Window position QRect(2345,363 600x300) outside any known screen, using
primary screen
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.
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.
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.
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.
Desktop color scheme is light
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/gui.py", line 873, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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/gui.py", line 172, in _update_color_scheme
self.session.logger.status(msg)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
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.
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.
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.
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.
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.
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.
Desktop color scheme is light
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/gui.py", line 873, in customEvent
func(*args, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
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.
> show #2 models
> hide #!1 models
> hide #5 models
> select add #1
4974 atoms, 5093 bonds, 7 pseudobonds, 630 residues, 4 models selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select add #5
10986 atoms, 11176 bonds, 7 pseudobonds, 1018 residues, 4 models selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select subtract #1
6339 atoms, 6419 bonds, 410 residues, 1 model selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> select subtract #5
Nothing selected
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/model_panel/tool.py", line 475, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1085, in status
sbar.status(msg, color, secondary)
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.
> view orient
> hide #2 models
> show #!1 models
> view orient
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.
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.
> show #4 models
> hide #4 models
> show #5 models
> hide #!1 models
> show #6 models
> show #7 models
> show #4 models
> show #!1 models
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.
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.
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.
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.
[deleted to fit within ticket limits]
> select subtract #16
Nothing selected
> select add #4
17915 atoms, 18256 bonds, 2248 residues, 1 model selected
> hide sel atoms
> color sel bychain
> view matrix models
> #4,-0.52817,-0.35076,0.77331,205.03,0.035652,0.90073,0.43291,162.1,-0.84839,0.25622,-0.46323,102.84
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.52817,-0.35076,0.77331,182.44,0.035652,0.90073,0.43291,167.6,-0.84839,0.25622,-0.46323,99.949
> fitmap #4 inMap #1
Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) to map
cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) using 17915 atoms
average map value = 0.1316, steps = 156
shifted from previous position = 2.49
rotated from previous position = 8.27 degrees
atoms outside contour = 15420, contour level = 0.32879
Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#4) relative to
cryosparc_P605_J52_005_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.45639053 -0.46884908 0.75623292 188.93732548
0.01413364 0.84598320 0.53302219 169.32110539
-0.88966731 0.25395462 -0.37947218 98.27103944
Axis -0.16058166 0.94708742 0.27791895
Axis point 125.56081403 0.00000000 -41.43776642
Rotation angle (degrees) 119.66577777
Shift along axis 157.33340476
> select add #16
53745 atoms, 54768 bonds, 6744 residues, 5 models selected
> combine sel name Lee_init
Remapping chain ID 'B' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'G'
Remapping chain ID 'D' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'H'
Remapping chain ID 'F' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'I'
> select subtract #16
17915 atoms, 18256 bonds, 2248 residues, 4 models selected
> select subtract #4
3 models selected
> hide #!4 models
> hide #16 models
> select add #6
53745 atoms, 54768 bonds, 6744 residues, 1 model selected
> color sel bychain
> color sel byhetero
> save /Users/oswanson/Desktop/RdRp.cxs
> select clear
[Repeated 1 time(s)]
> select #6/I:631
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #6
53745 atoms, 54768 bonds, 6744 residues, 1 model selected
> show sel atoms
> select clear
> ui mousemode right select
Drag select of 9878 atoms
> select up
10379 atoms, 10548 bonds, 1294 residues, 1 model selected
> select up
11979 atoms, 12194 bonds, 1498 residues, 1 model selected
> select up
17915 atoms, 18256 bonds, 2248 residues, 1 model selected
> select up
53745 atoms, 54768 bonds, 6744 residues, 1 model selected
> select down
17915 atoms, 18256 bonds, 2248 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> save /Users/oswanson/Desktop/RdRp.cxs
> select clear
> select #6/I:630@OG
1 atom, 1 residue, 1 model selected
> select add #6/F:588@CE
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #6/I:630@OG #6/F:588@CE
Distance between Lee_init #6/I SER 630 OG and /F LYS 588 CE: 224.395Å
> molmap #6 6
Opened Lee_init map 6 as #8, grid size 131,81,96, pixel 2, shown at level
0.105, step 1, values float32
> sample #8 onGrid#1
Unknown command: sample #8 onGrid#1
> volume resample #8 onGrid#1
Expected a keyword
> volume resample #8 onGrid #1
Opened Lee_init map 6 resampled as #9, grid size 256,256,256, pixel 1.45,
shown at step 1, values float32
> hide #!1 models
> hide #6 models
> hide #!7 models
> select add #6
35830 atoms, 36512 bonds, 1 pseudobond, 4496 residues, 2 models selected
> select subtract #6
Nothing selected
> save /Users/oswanson/Desktop/RdRp.cxs
No map chosen to save
> save /Users/oswanson/Desktop/Lee_dimer.mrc models #9
Desktop color scheme is light
No map chosen to save
> save /Users/oswanson/Desktop/RdRp/RdRp.cxs
——— End of log from Thu Nov 6 10:37:56 2025 ———
> view name session-start
opened ChimeraX session
> pwd
Current working directory is: /Users/oswanson/Desktop
> cd ../Downloads
Current working directory is: /Users/oswanson/Downloads
> ls
Unknown command: ls
> cd ./cryosparc_P605_J72_component_000
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_000
> open *.mrc vseries true
Opened map series J72_component_000_frame_000.mrc as #10, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0298, step 1, values float32
> hide #!9 models
> vseries play #10 loop ture
Invalid "loop" argument: Expected true or false (or 1 or 0)
> vseries play #10 loop true
> volume #10.1 level 0.0298 color #b2b2b2
> volume #10.1 level 0.04788
> surface dust #10.17 size 14.5
> surface dust #10.16 size 14.5
> select add #10
22 models selected
> surface dust #10.3 size 14.5
> volume #10.1 level 0.03626 color #b2b2b2
[Repeated 1 time(s)]
> volume #10.1 level 0.04659
> vseries stop #10
> cd ../
Current working directory is: /Users/oswanson/Downloads
> cd ./cryosparc_P605_J72_component_001
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_001
> open *.mrc vseries true
Opened map series J72_component_001_frame_000.mrc as #11, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0523, step 1, values float32
> hide #!10 models
> select add #11
43 models selected
> select add #10
45 models selected
> select subtract #11
23 models selected
> volume #11.1 level 0.08108
> surface dust #11.1 size 14.5
> vseries play #11 loop true
> vseries stop #11
> show #!10 models
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,-33.342,0,1,0,133.63,0,0,1,-6.6484
> vseries play #10,11 loop true
> volume #11.9 level 0.08115 color #ffffb2
> volume #11 level 0.0811
> volume #10 level 0.0811
> vseries stop #10,11
> hide #!11 models
> hide #!10 models
> show #!1 models
> show #6 models
> select add #6
35830 atoms, 36512 bonds, 1 pseudobond, 4496 residues, 23 models selected
> hide sel atoms
> show sel cartoons
> volume #1 level 0.1035
> volume #1 level 0.3127
> open pdb:7aap
Summary of feedback from opening 7aap fetched from pdb
---
notes | Fetching compressed mmCIF 7aap from http://files.rcsb.org/download/7aap.cif
Fetching CCD GE6 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/GE6/GE6.cif
Fetching CCD MG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Fetching CCD POP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/POP/POP.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
7aap title:
Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with
template:primer dsRNA and favipiravir-RTP [more info...]
Chain information for 7aap #12
---
Chain | Description | UniProt
A | Non-structural protein 12 | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
P | RNA (5'-R(P*UP*UP*AP*AP*GP*UP*UP*AP*U)-3') |
T | RNA (5'-R(P*UP*UP*CP*AP*UP*AP*AP*CP*UP*UP*AP*A)-3') |
Non-standard residues in 7aap #12
---
GE6 —
[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxidanylidene-
pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]
phosphono hydrogen phosphate
MG — magnesium ion
POP — pyrophosphate 2-
ZN — zinc ion
> hide #!1 models
> select add #12
45276 atoms, 46204 bonds, 36 pseudobonds, 5644 residues, 27 models selected
> select add #10
45276 atoms, 46204 bonds, 36 pseudobonds, 5644 residues, 28 models selected
> select add #7
45276 atoms, 46204 bonds, 36 pseudobonds, 5644 residues, 29 models selected
> select subtract #7
45276 atoms, 46204 bonds, 35 pseudobonds, 5644 residues, 27 models selected
> select subtract #10
45276 atoms, 46204 bonds, 35 pseudobonds, 5644 residues, 5 models selected
> select subtract #6
9446 atoms, 9692 bonds, 35 pseudobonds, 1148 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select ::name="GE6"::name="MG"::name="POP"::name="ZN"
46 atoms, 41 bonds, 5 pseudobonds, 7 residues, 2 models selected
> show sel atoms
> style sel stick
Changed 46 atom styles
> select add #9
46 atoms, 41 bonds, 5 pseudobonds, 7 residues, 4 models selected
> select subtract #9
46 atoms, 41 bonds, 5 pseudobonds, 7 residues, 2 models selected
> select add #6
35876 atoms, 36553 bonds, 6 pseudobonds, 4503 residues, 4 models selected
> select ::name="GE6"::name="MG"::name="POP"::name="ZN"
46 atoms, 41 bonds, 5 pseudobonds, 7 residues, 2 models selected
> show sel atoms
> select add #6
35876 atoms, 36553 bonds, 6 pseudobonds, 4503 residues, 4 models selected
> select add #12
45276 atoms, 46204 bonds, 36 pseudobonds, 5644 residues, 6 models selected
> select subtract #12
35830 atoms, 36512 bonds, 1 pseudobond, 4496 residues, 2 models selected
> select ::name="GE6"::name="MG"::name="POP"::name="ZN"
46 atoms, 41 bonds, 5 pseudobonds, 7 residues, 2 models selected
> hide #!12 models
> show #!12 models
> ui tool show Matchmaker
> matchmaker #!12 to #6
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 Lee_init, chain D (#6) with 7aap, chain A (#12), sequence alignment
score = 151.7
RMSD between 43 pruned atom pairs is 1.290 angstroms; (across all 479 pairs:
25.781)
> hide #!12 models
> show #!5 models
> hide #6 models
> select add #5
10454 atoms, 10709 bonds, 29 pseudobonds, 1277 residues, 5 models selected
> select ::name="GE6"::name="MG"::name="POP"::name="ZN"
46 atoms, 41 bonds, 5 pseudobonds, 7 residues, 2 models selected
> select ::name="A"::name="C"::name="G"::name="U"
992 atoms, 1104 bonds, 37 pseudobonds, 47 residues, 4 models selected
> show sel & #!5 atoms
> nucleotides sel & #!5 atoms
> style nucleic & sel & #!5 stick
Changed 553 atom styles
> show #6 models
> matchmaker #!5 to #6
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 Lee_init, chain D (#6) with 6qwl, chain K (#5), sequence alignment
score = 3220.4
RMSD between 304 pruned atom pairs is 1.202 angstroms; (across all 539 pairs:
3.076)
> show #!1 models
> matchmaker #!12 to #5
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 6qwl, chain K (#5) with 7aap, chain A (#12), sequence alignment
score = 100.3
RMSD between 22 pruned atom pairs is 1.328 angstroms; (across all 405 pairs:
28.884)
> show #!12 models
> hide #6 models
> hide #!12 models
> show #!12 models
> hide #!12 models
> show #!12 models
> hide #!1 models
> select add #12
9999 atoms, 10308 bonds, 53 pseudobonds, 1174 residues, 6 models selected
> color sel bychain
> select add #5
19854 atoms, 20360 bonds, 59 pseudobonds, 2418 residues, 7 models selected
> select subtract #5
9446 atoms, 9692 bonds, 35 pseudobonds, 1148 residues, 4 models selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select clear
> hide #!12 models
> show #!12 models
> select #12/A:738
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
136 atoms, 140 bonds, 15 residues, 1 model selected
> select up
7174 atoms, 7352 bonds, 892 residues, 1 model selected
> matchmaker #!12 & sel to #5
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 6qwl, chain K (#5) with 7aap, chain A (#12), sequence alignment
score = 100.4
RMSD between 21 pruned atom pairs is 1.187 angstroms; (across all 391 pairs:
29.006)
> select #12/P:19
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #12/T:14
44 atoms, 48 bonds, 2 residues, 1 model selected
> select up
439 atoms, 488 bonds, 21 residues, 1 model selected
> matchmaker #!12 & sel to #5
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 6qwl, chain E (#5) with 7aap, chain T (#12), sequence alignment
score = 25.6
Fewer than 3 residues aligned; cannot match 6qwl, chain E with 7aap, chain T
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.92467,-0.3542,-0.13972,356.14,0.38067,-0.85191,-0.35963,288.42,0.008349,-0.38573,0.92258,83.957
> view matrix models
> #12,-0.99829,0.045825,-0.0363,311.4,-0.057317,-0.88942,0.45348,256.01,-0.011505,0.45479,0.89052,1.0555
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.99829,0.045825,-0.0363,307.67,-0.057317,-0.88942,0.45348,221.87,-0.011505,0.45479,0.89052,3.6595
> view matrix models
> #12,-0.99829,0.045825,-0.0363,276.94,-0.057317,-0.88942,0.45348,207.95,-0.011505,0.45479,0.89052,8.5811
> ui mousemode right "rotate selected models"
> view matrix models
> #12,0.86054,-0.14803,0.4874,36.321,-0.1334,0.85796,0.49609,28.053,-0.49161,-0.49193,0.71856,179.47
> view matrix models
> #12,0.89902,0.082393,0.43009,13.79,-0.25964,0.89118,0.372,51.535,-0.35263,-0.44611,0.82258,148.35
> view matrix models
> #12,0.97031,-0.021021,0.24093,36.527,-0.066703,0.93432,0.35015,27.867,-0.23247,-0.35583,0.90518,116.88
> ui mousemode right "translate selected models"
> view matrix models
> #12,0.97031,-0.021021,0.24093,64.066,-0.066703,0.93432,0.35015,47.61,-0.23247,-0.35583,0.90518,118.42
> hide #!5 models
> show #!5 models
> hide #!12 models
> select #5/E:307
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
107 atoms, 108 bonds, 13 residues, 1 model selected
> select up
4084 atoms, 4170 bonds, 511 residues, 1 model selected
> matchmaker #!12 to #5 & sel
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 6qwl, chain E (#5) with 7aap, chain A (#12), sequence alignment
score = 83.3
RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 434 pairs:
40.903)
> show #!12 models
> matchmaker #!12 to #5 & sel
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 6qwl, chain E (#5) with 7aap, chain A (#12), sequence alignment
score = 83.3
RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 434 pairs:
40.903)
> matchmaker #!12 to #5 & sel
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 6qwl, chain E (#5) with 7aap, chain A (#12), sequence alignment
score = 83.3
RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 434 pairs:
40.903)
> matchmaker #!12 to #5
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 6qwl, chain K (#5) with 7aap, chain A (#12), sequence alignment
score = 100.3
RMSD between 22 pruned atom pairs is 1.328 angstroms; (across all 405 pairs:
28.884)
> matchmaker #!12 to #5
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 6qwl, chain K (#5) with 7aap, chain A (#12), sequence alignment
score = 100.3
RMSD between 22 pruned atom pairs is 1.328 angstroms; (across all 405 pairs:
28.884)
> hide #!12 models
> show #6 models
> hide #6 models
> open pdb:7as0
Summary of feedback from opening 7as0 fetched from pdb
---
notes | Fetching compressed mmCIF 7as0 from http://files.rcsb.org/download/7as0.cif
Fetching CCD 21G from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/21G/21G.cif
Fetching CCD BR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BR/BR.cif
7as0 title:
Influenza A PB2 in complex with VX-787 [more info...]
Chain information for 7as0 #13
---
Chain | Description | UniProt
A | Polymerase basic protein 2 | C3W5X5_9INFA 320-483
Non-standard residues in 7as0 #13
---
21G —
(2S,3S)-3-[[5-fluoranyl-2-(5-fluoranyl-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic
acid
(3-[[5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl]amino]bicyclo[2.2.2]octane-2-carboxylic
acid; VX787;
(2S,3S)-3-((5-fluoro-2-(5-fluoro-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-4-yl)amino)bicyclo[2.2.2]octane-2-carboxylic
acid)
BR — bromide ion
47 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> matchmaker #13 to #6
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 Lee_init, chain F (#6) with 7as0, chain A (#13), sequence alignment
score = 424.3
RMSD between 131 pruned atom pairs is 0.934 angstroms; (across all 161 pairs:
2.641)
> hide #!5 models
> show #6 models
> show #!1 models
> ui tool show "Volume Viewer"
> volume #1 level 0.06807
> open pdb:6fs8
Summary of feedback from opening 6fs8 fetched from pdb
---
notes | Fetching compressed mmCIF 6fs8 from http://files.rcsb.org/download/6fs8.cif
Fetching CCD E4Z from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/E4Z/E4Z.cif
Fetching CCD MN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MN/MN.cif
6fs8 title:
Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid
(BXA) [more info...]
Chain information for 6fs8 #14
---
Chain | Description | UniProt
A B | Polymerase acidic protein | Q5V8Z9_9INFB 1-197
Non-standard residues in 6fs8 #14
---
E4Z — Baloxavir acid
MN — manganese (II) ion
6fs8 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
77 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> matchmaker #!14 to #6
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 Lee_init, chain B (#6) with 6fs8, chain B (#14), sequence alignment
score = 944.6
RMSD between 175 pruned atom pairs is 0.671 angstroms; (across all 183 pairs:
0.906)
> hide #13 models
> select clear
> select add #14
3190 atoms, 3075 bonds, 26 pseudobonds, 543 residues, 4 models selected
> color sel bychain
> select clear
> select add #14
3190 atoms, 3075 bonds, 26 pseudobonds, 543 residues, 4 models selected
> color sel byhetero
> color #14 #00fa92ff
> color sel byhetero
> select #14/A:94
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #14/A:93
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
138 atoms, 141 bonds, 17 residues, 1 model selected
> select up
984 atoms, 1003 bonds, 120 residues, 1 model selected
> select up
992 atoms, 1010 bonds, 121 residues, 1 model selected
> select up
1435 atoms, 1462 bonds, 176 residues, 1 model selected
> select up
1573 atoms, 1501 bonds, 281 residues, 1 model selected
> select up
3190 atoms, 3075 bonds, 543 residues, 1 model selected
> select down
1573 atoms, 1501 bonds, 281 residues, 1 model selected
> color #14 #941100ff
> undo
> hide #6 models
> select clear
> select #14/A:166
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
172 atoms, 171 bonds, 22 residues, 1 model selected
> select up
984 atoms, 1003 bonds, 120 residues, 1 model selected
> select up
992 atoms, 1010 bonds, 121 residues, 1 model selected
> select up
1435 atoms, 1462 bonds, 176 residues, 1 model selected
> select up
1573 atoms, 1501 bonds, 281 residues, 1 model selected
> select up
3190 atoms, 3075 bonds, 543 residues, 1 model selected
> select down
1573 atoms, 1501 bonds, 281 residues, 1 model selected
> color #14 #945200ff
> undo
> select clear
> color #14/A magenta
> show #6 models
> show #!1 models
> select #14/A
1573 atoms, 1501 bonds, 13 pseudobonds, 281 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> volume #1 level 0.07129
> select up
3190 atoms, 3075 bonds, 26 pseudobonds, 543 residues, 3 models selected
> select up
3190 atoms, 3075 bonds, 26 pseudobonds, 543 residues, 3 models selected
> open pdb:7r1f
Summary of feedback from opening 7r1f fetched from pdb
---
notes | Fetching compressed mmCIF 7r1f from http://files.rcsb.org/download/7r1f.cif
Fetching CCD GTA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/GTA/GTA.cif
Fetching CCD K1F from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/K1F/K1F.cif
7r1f title:
Early transcription elongation state of influenza B polymerase backtracked due
to double incoproation of nucleotide analogue T1106 [more info...]
Chain information for 7r1f #15
---
Chain | Description | UniProt
A | Polymerase acidic protein | Q5V8Z9_9INFB 1-726
B | RNA-directed RNA polymerase catalytic subunit | Q5V8Y6_9INFB 1-752
C | Polymerase basic protein 2 | Q5V8X3_9INFB 1-770
M | mRNA |
R | 3' vRNA |
V | 5' vRNA |
Non-standard residues in 7r1f #15
---
GTA — P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate (7-methyl-gpppa)
K1F — [(2R,3S,4R,5R)-5-(3-aminocarbonyl-2-oxidanylidene-
pyrazin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (Beta-
D-riboruranosyl-3-oxo-2-pyrazinecarboxamide; T1106 nucleoside analogue)
MG — magnesium ion
47 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!1 models
> hide #!14 models
> select clear
> select add #15
18325 atoms, 18758 bonds, 42 pseudobonds, 2231 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> view matrix models #15,1,0,0,103.08,0,1,0,15.844,0,0,1,-42.641
> matchmaker #!15 to #6
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 Lee_init, chain D (#6) with 7r1f, chain B (#15), sequence alignment
score = 3737.6
RMSD between 631 pruned atom pairs is 0.757 angstroms; (across all 727 pairs:
3.662)
> show #!1 models
> hide #!1 models
> hide #6 models
> show #!1 models
> hide #!1 models
> select
> ::name="21G"::name="BR"::name="E4Z"::name="GE6"::name="GTA"::name="HOH"::name="K1F"::name="MG"::name="MN"::name="POP"::name="ZN"
633 atoms, 255 bonds, 17 pseudobonds, 408 residues, 6 models selected
> show sel & #!15 atoms
> select :K1F
44 atoms, 47 bonds, 2 residues, 1 model selected
> show sel atoms
> select :K1F
44 atoms, 47 bonds, 2 residues, 1 model selected
> view orient
> select :K1F
44 atoms, 47 bonds, 2 residues, 1 model selected
> select ::name="A"::name="C"::name="G"::name="U"
1886 atoms, 2102 bonds, 67 pseudobonds, 89 residues, 6 models selected
> show sel & #!15 atoms
> nucleotides sel & #!15 atoms
> style nucleic & sel & #!15 stick
Changed 894 atom styles
> select ::name="K1F"
44 atoms, 47 bonds, 2 residues, 1 model selected
> color sel purple
> nucleotides sel atoms
> style nucleic & sel stick
Changed 44 atom styles
> show #!9 models
> hide #!9 models
> show #6 models
> show #!1 models
> hide #!15 models
> show #!15 models
> hide #6 models
> hide #!1 models
> hide #!15 models
> show #!4 models
> mlp #!4
Map values for surface "copy of fold_lee_rdrp_trimer_dimer_model_0.cif_B SES
surface": minimum -30.32, mean -4.634, maximum 22.79
Map values for surface "copy of fold_lee_rdrp_trimer_dimer_model_0.cif_D SES
surface": minimum -29.04, mean -4.17, maximum 24.02
Map values for surface "copy of fold_lee_rdrp_trimer_dimer_model_0.cif_F SES
surface": minimum -29.79, mean -4.296, maximum 23.03
To also show corresponding color key, enter the above mlp command and add key
true
> select add #15
18325 atoms, 18758 bonds, 42 pseudobonds, 2231 residues, 4 models selected
> select subtract #15
Nothing selected
> show #!9 models
> hide #!9 models
> show #!8 models
> show #!9 models
> hide #!9 models
> close #8
> show #16 models
> select add #16
35830 atoms, 36512 bonds, 4496 residues, 1 model selected
> mlp sel
Map values for surface "fold_lee_rdrp_trimer_dimer_model_0.cif_A SES surface":
minimum -30.1, mean -4.687, maximum 23.81
Map values for surface "fold_lee_rdrp_trimer_dimer_model_0.cif_B SES surface":
minimum -30.8, mean -4.631, maximum 22.97
Map values for surface "fold_lee_rdrp_trimer_dimer_model_0.cif_C SES surface":
minimum -29.34, mean -4.166, maximum 24.15
Map values for surface "fold_lee_rdrp_trimer_dimer_model_0.cif_D SES surface":
minimum -28.78, mean -4.17, maximum 24.05
Map values for surface "fold_lee_rdrp_trimer_dimer_model_0.cif_E SES surface":
minimum -29.31, mean -4.31, maximum 23.48
Map values for surface "fold_lee_rdrp_trimer_dimer_model_0.cif_F SES surface":
minimum -30.07, mean -4.297, maximum 23.11
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!16 models
> show #!16 models
> select add #4
53745 atoms, 54768 bonds, 6744 residues, 8 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
[Repeated 1 time(s)]Coulombic values for
fold_lee_rdrp_trimer_dimer_model_0.cif_A SES surface #16.1: minimum, -22.93,
mean -1.70, maximum 15.96
Coulombic values for fold_lee_rdrp_trimer_dimer_model_0.cif_B SES surface
#16.2: minimum, -23.14, mean -1.68, maximum 15.36
Coulombic values for fold_lee_rdrp_trimer_dimer_model_0.cif_C SES surface
#16.3: minimum, -14.88, mean 0.58, maximum 16.57
Coulombic values for fold_lee_rdrp_trimer_dimer_model_0.cif_D SES surface
#16.4: minimum, -14.53, mean 0.55, maximum 16.73
Coulombic values for fold_lee_rdrp_trimer_dimer_model_0.cif_E SES surface
#16.5: minimum, -13.14, mean 1.37, maximum 14.94
Coulombic values for fold_lee_rdrp_trimer_dimer_model_0.cif_F SES surface
#16.6: minimum, -16.16, mean 1.35, maximum 17.93
Coulombic values for copy of fold_lee_rdrp_trimer_dimer_model_0.cif_B SES
surface #4.2: minimum, -23.14, mean -1.68, maximum 15.36
Coulombic values for copy of fold_lee_rdrp_trimer_dimer_model_0.cif_D SES
surface #4.4: minimum, -14.53, mean 0.55, maximum 16.73
Coulombic values for copy of fold_lee_rdrp_trimer_dimer_model_0.cif_F SES
surface #4.6: minimum, -16.16, mean 1.35, maximum 17.93
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!16 models
> show #!16 models
> hide sel surfaces
> select clear
> show #!1 models
> show #!12 models
> hide #!12 models
> show #13 models
> show #!17 models
> hide #!16 models
> hide #13 models
> hide #!1 models
> hide #!4 models
> select add #17
2 models selected
> close #17
> show #!16 models
> hide #!16 models
> save /Users/oswanson/Desktop/RdRp/RdRp.cxs
> show #!10 models
> pwd
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_001
> cd ../
Current working directory is: /Users/oswanson/Downloads
> cd ./cryosparc_P605_J72_component_002
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_002
> open *.mrc vseries true
Opened map series J72_component_002_frame_000.mrc as #8, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0504, step 1, values float32
> show #!11 models
> hide #!11 models
> color #8 #ff9300ff models
> vseries play #8 loop true
> show #6 models
> vseries stop #8
> cd ../cryosparc_P605_J72_component_003
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_003
> open *.mrc vseries true
Opened map series J72_component_003_frame_000.mrc as #17, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0519, step 1, values float32
> hide #!8 models
> vseries play #17 loop true
> vseries stop #17
> hide #!17 models
> cd ../cryosparc_P605_J72_component_004
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_004
> open *.mrc vseries true
Opened map series J72_component_004_frame_000.mrc as #18, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0563, step 1, values float32
> vseries play #18 loop true
> hide #!10 models
> show #!5 models
> hide #!5 models
> show #13 models
> hide #13 models
> show #!14 models
> hide #!14 models
> show #!12 models
> hide #!12 models
> vseries stop #18
> show #!12 models
> hide #!18 models
> close #12
> cd ../cryosparc_P605_J72_component_005
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_005
> open *.mrc vseries true
Opened map series J72_component_005_frame_000.mrc as #12, 20 images, grid size
256,256,256, pixel 1.45, shown at level 0.0557, step 1, values float32
> vseries play #12 loop true
> vseries stop #12
> transparency #12.20.1 50
> hide #!12 models
> show #!1 models
> open /Users/oswanson/Downloads/cryosparc_P605_J56_008_volume_map_sharp.mrc
Opened cryosparc_P605_J56_008_volume_map_sharp.mrc as #19, grid size
256,256,256, pixel 1.45, shown at level 0.0482, step 1, values float32
> open /Users/oswanson/Downloads/cryosparc_P605_J71_009_volume_map_sharp.mrc
Opened cryosparc_P605_J71_009_volume_map_sharp.mrc as #20, grid size
256,256,256, pixel 1.45, shown at level 0.0495, step 1, values float32
> surface dust #1 size 14.5
> surface dust #19 size 14.5
> surface dust #20 size 14.5
> hide #6 models
> hide #!1 models
> hide #!19 models
> transparency #20.1 50
> show #6 models
> show #!19 models
> transparency #19.1#20.1 0
> transparency #19.1#20.1 50
> hide #!20 models
> show #!20 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!19 models
> volume #1 level 0.0495
> surface dust #1 size 14.5
> surface dust #20 size 14.5
> volume #1 level 0.0717
> hide #!1 models
> show #!2 models
> show #!3 models
> close #2
> close #3
> show #!19 models
> hide #!19 models
> volume #20 level 0.08774
> volume #20 level 0.0342
> volume #20 level 0.1872
> hide #6 models
> volume #20 level 0.1489
> show #!15 models
> ui tool show "Fit in Map"
> fitmap #15 inMap #20
Fit molecule 7r1f (#15) to map cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) using 18325 atoms
average map value = 0.1335, steps = 108
shifted from previous position = 2.69
rotated from previous position = 1.01 degrees
atoms outside contour = 12849, contour level = 0.14894
Position of 7r1f (#15) relative to cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) coordinates:
Matrix rotation and translation
0.25994972 0.08916868 0.96149628 -60.70287645
-0.62472884 0.77478743 0.09704802 136.42819333
-0.73630158 -0.62590206 0.25711202 334.68269600
Axis -0.36538624 0.85808411 -0.36081098
Axis point 229.09128025 0.00000000 232.43571372
Rotation angle (degrees) 81.60917674
Shift along axis 18.48966768
> hide #!15 models
> show #!14 models
> volume #20 level 0.05296
> show #!15 models
> show #6 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> hide #6 models
> show #!14 models
> hide #!14 models
> show #!14 models
> show #!9 models
> hide #!9 models
> show #6 models
> hide #6 models
> show #6 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #13 models
> select add #13
1483 atoms, 1298 bonds, 369 residues, 1 model selected
> view matrix models
> #13,-0.60913,-0.72867,0.31305,183.03,-0.64137,0.68479,0.34598,166.62,-0.46648,0.0099651,-0.88448,89.999
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.42035,-0.90735,-0.0034562,183.35,-0.84233,0.38881,0.37323,166.73,-0.33731,0.1598,-0.92773,89.965
> view matrix models
> #13,-0.31451,-0.94216,-0.11584,183.45,-0.91174,0.26585,0.31313,166.84,-0.26422,0.20409,-0.94262,89.949
> fitmap #13 inMap #20
Fit molecule 7as0 (#13) to map cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) using 1483 atoms
average map value = 0.02795, steps = 120
shifted from previous position = 2.42
rotated from previous position = 13.4 degrees
atoms outside contour = 1264, contour level = 0.052961
Position of 7as0 (#13) relative to cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) coordinates:
Matrix rotation and translation
-0.40298263 -0.91489750 -0.02382364 182.76631971
-0.90825948 0.39658622 0.13335695 169.08895285
-0.11255981 0.07537858 -0.99078169 90.47055386
Axis -0.54590608 0.83551189 0.06250147
Axis point 148.01442722 0.00000000 35.59540884
Rotation angle (degrees) 176.95599763
Shift along axis 47.15712747
> volume #20 level 0.06425
> volume #20 level 0.03602
> volume #20 level 0.04732
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.40298,-0.9149,-0.023824,172.62,-0.90826,0.39659,0.13336,171.6,-0.11256,0.075379,-0.99078,91.044
> volume #20 level 0.05861
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.23577,-0.97063,-0.047841,172.63,-0.96857,0.23067,0.093119,171.71,-0.079348,0.068291,-0.9945,91.043
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.23577,-0.97063,-0.047841,183.05,-0.96857,0.23067,0.093119,166.47,-0.079348,0.068291,-0.9945,57.531
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.17154,-0.9745,0.14466,182.85,-0.86248,0.21951,0.456,166.1,-0.47613,-0.046542,-0.87814,57.54
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.17154,-0.9745,0.14466,178.24,-0.86248,0.21951,0.456,162.15,-0.47613,-0.046542,-0.87814,89.843
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #6 models
> volume #20 level 0.3352
> volume #20 level 0.05861
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.79735,-0.59581,0.096129,178.3,-0.56868,0.79507,0.21087,162.14,-0.20207,0.11347,-0.97278,89.825
> view matrix models
> #13,-0.72829,0.48568,-0.48343,178.49,0.051312,0.74213,0.66829,161.58,0.68334,0.4619,-0.56541,89.129
> view matrix models
> #13,-0.91843,-0.3378,0.20586,178.13,-0.37993,0.60822,-0.69694,163.04,0.11022,-0.7183,-0.68695,89.749
> view matrix models
> #13,-0.8948,-0.37372,-0.24427,178.57,-0.13198,0.74408,-0.65493,162.9,0.42651,-0.55379,-0.71512,89.656
> view matrix models
> #13,-0.31078,-0.16497,-0.93606,179.05,-0.22083,0.97041,-0.097708,162.31,0.92447,0.17634,-0.33801,88.949
> view matrix models
> #13,0.27209,-0.82212,0.50009,177.75,0.86476,-0.019048,-0.50182,162.79,0.42208,0.569,0.70575,87.918
> view matrix models
> #13,0.7563,-0.3354,0.56171,177.43,0.49061,-0.27723,-0.8261,163.27,0.4328,0.90036,-0.045125,88.537
> view matrix models
> #13,0.77646,-0.3352,0.53361,177.45,0.47297,-0.24957,-0.84499,163.28,0.41642,0.90849,-0.035237,88.528
> view matrix models
> #13,0.78926,-0.30762,0.53145,177.44,0.46783,-0.25937,-0.84491,163.28,0.39775,0.91548,-0.060795,88.554
> view matrix models
> #13,0.79492,-0.25234,0.55175,177.4,0.4744,-0.3084,-0.82452,163.28,0.37822,0.91718,-0.12544,88.621
> view matrix models
> #13,0.85811,-0.14497,0.49257,177.41,0.42934,-0.32359,-0.84318,163.31,0.28162,0.93503,-0.21543,88.723
> view matrix models
> #13,0.90143,-0.051247,0.42989,177.43,0.39781,-0.29372,-0.86918,163.33,0.17081,0.95452,-0.24438,88.768
> view matrix models
> #13,0.94034,-0.071973,0.33255,177.53,0.23233,-0.57823,-0.78209,163.37,0.24858,0.81269,-0.52701,89.071
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.94034,-0.071973,0.33255,178.25,0.23233,-0.57823,-0.78209,166.53,0.24858,0.81269,-0.52701,92.193
> fitmap #13 inMap #20
Fit molecule 7as0 (#13) to map cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) using 1483 atoms
average map value = 0.02949, steps = 88
shifted from previous position = 2.83
rotated from previous position = 19.6 degrees
atoms outside contour = 1322, contour level = 0.058607
Position of 7as0 (#13) relative to cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) coordinates:
Matrix rotation and translation
0.79167986 0.06155030 0.60782774 180.61294780
0.51563866 -0.60091077 -0.61075610 167.57733463
0.32765802 0.79694279 -0.50746666 91.44022340
Axis 0.93508341 0.18610661 0.30163446
Axis point 0.00000000 60.28868795 46.97794067
Rotation angle (degrees) 131.17406317
Shift along axis 227.65694251
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.27148,0.88287,-0.38319,181.54,-0.54452,-0.46919,-0.69524,167.84,-0.7936,0.019907,0.60812,90.847
> view matrix models
> #13,-0.30347,-0.9202,0.24727,181.51,-0.32631,0.34418,0.88038,166.01,-0.89523,0.18648,-0.40472,91.798
> view matrix models
> #13,0.12154,-0.63318,0.7644,180.83,-0.60407,0.56389,0.56314,166.3,-0.78761,-0.53019,-0.31395,91.917
> view matrix models
> #13,0.63007,-0.42826,0.64776,180.77,-0.5318,0.36988,0.76182,166.16,-0.56585,-0.82449,0.0053007,91.655
> view matrix models
> #13,-0.69506,-0.35336,0.62613,181.05,-0.19636,0.93108,0.30748,166.35,-0.69162,0.090766,-0.71654,92.087
> view matrix models
> #13,0.39023,-0.66623,0.6355,180.91,-0.35978,0.52501,0.77131,166.06,-0.84751,-0.52963,-0.034817,91.659
> view matrix models
> #13,0.30594,-0.67879,0.66757,180.9,-0.35577,0.56888,0.74149,166.08,-0.88308,-0.46435,-0.06745,91.677
> view matrix models
> #13,-0.34451,-0.48885,0.80146,180.84,-0.36167,0.85694,0.36723,166.35,-0.86632,-0.16335,-0.47203,91.969
> view matrix models
> #13,-0.050102,-0.50001,0.86457,180.72,-0.48118,0.77065,0.41781,166.35,-0.87519,-0.39508,-0.2792,91.859
> view matrix models
> #13,-0.1896,-0.526,0.82908,180.8,-0.41106,0.80936,0.41949,166.32,-0.89167,-0.26127,-0.36967,91.907
> view matrix models
> #13,-0.095274,-0.96267,0.25334,181.48,-0.992,0.113,0.056334,167.02,-0.082859,-0.24595,-0.96574,92.308
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.095274,-0.96267,0.25334,179.31,-0.992,0.113,0.056334,167.69,-0.082859,-0.24595,-0.96574,87.805
> fitmap #13 inMap #20
Fit molecule 7as0 (#13) to map cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) using 1483 atoms
average map value = 0.02608, steps = 64
shifted from previous position = 1.52
rotated from previous position = 4.14 degrees
atoms outside contour = 1351, contour level = 0.058607
Position of 7as0 (#13) relative to cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) coordinates:
Matrix rotation and translation
-0.07673651 -0.97910746 0.18830847 179.07981168
-0.99538432 0.08614656 0.04229454 167.41261432
-0.05763303 -0.18419376 -0.98119880 89.23211324
Axis -0.67661493 0.73472973 -0.04862574
Axis point 171.73610550 0.00000000 39.98219695
Rotation angle (degrees) 170.36513605
Shift along axis -2.50402716
> fitmap #13 inMap #20
Fit molecule 7as0 (#13) to map cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) using 1483 atoms
average map value = 0.02608, steps = 80
shifted from previous position = 0.00575
rotated from previous position = 0.0227 degrees
atoms outside contour = 1351, contour level = 0.058607
Position of 7as0 (#13) relative to cryosparc_P605_J71_009_volume_map_sharp.mrc
(#20) coordinates:
Matrix rotation and translation
-0.07646026 -0.97907617 0.18858335 179.08098865
-0.99540826 0.08587864 0.04227603 167.41797749
-0.05758674 -0.18448499 -0.98114681 89.23035948
Axis -0.67671164 0.73463315 -0.04873903
Axis point 171.76626017 0.00000000 39.98436156
Rotation angle (degrees) 170.35481552
Shift along axis -2.54439379
> show #6 models
> volume #20 level 0.04732
> combine #13
> ui mousemode right select
Drag select of 516 residues, 20 cryosparc_P605_J71_009_volume_map_sharp.mrc
> select subtract #20
4148 atoms, 516 residues, 1 model selected
> select up
4844 atoms, 4917 bonds, 604 residues, 1 model selected
> select up
17915 atoms, 18256 bonds, 2248 residues, 1 model selected
> matchmaker #2 to #6
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 Lee_init, chain F (#6) with copy of 7as0, chain A (#2), sequence
alignment score = 424.3
RMSD between 131 pruned atom pairs is 0.934 angstroms; (across all 161 pairs:
2.641)
> matchmaker #2 to #6
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 Lee_init, chain F (#6) with copy of 7as0, chain A (#2), sequence
alignment score = 424.3
RMSD between 131 pruned atom pairs is 0.934 angstroms; (across all 161 pairs:
2.641)
> select down
4844 atoms, 4917 bonds, 604 residues, 1 model selected
> matchmaker #2 to #6
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 Lee_init, chain F (#6) with copy of 7as0, chain A (#2), sequence
alignment score = 424.3
RMSD between 131 pruned atom pairs is 0.934 angstroms; (across all 161 pairs:
2.641)
> matchmaker #2 to #6 & sel
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 Lee_init, chain I (#6) with copy of 7as0, chain A (#2), sequence
alignment score = 195.4
RMSD between 52 pruned atom pairs is 0.764 angstroms; (across all 67 pairs:
3.814)
> select clear
> hide #6 models
> volume #20 level 0.132
> volume #20 level 0.0699
> show #6 models
> volume #20 level 0.1151
> matchmaker #13 to #6
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 Lee_init, chain F (#6) with 7as0, chain A (#13), sequence alignment
score = 424.3
RMSD between 131 pruned atom pairs is 0.934 angstroms; (across all 161 pairs:
2.641)
> hide #6 models
> show #!17 models
> hide #13 models
> hide #!20 models
> hide #2 models
> surface dust #17.1 size 14.5
> vseries play #17 loop true
> volume #17.1 level 0.0635
> volume #17 level 0.06
> surface dust #17.19 size 14.5
> surface dust #17.11 size 14.5
> surface dust #17.14 size 14.5
> surface dust #17.17 size 14.5
> surface dust #17.20 size 14.5
> surface dust #17.2 size 14.5
> surface dust #17 size 14.5
[Repeated 2 time(s)]
> vseries stop #17
> vseries play #18 loop true
> show #!18 models
> hide #!17 models
> surface dust #18 size 14.5
> volume #18 level 0.06
> vseries stop #18
> show #!17 models
> hide #!18 models
> vseries play #17 loop true
> vseries stop #17
> hide #!17 models
> show #!1 models
> hide #!1 models
> show #!20 models
> show #6 models
> show #2 models
> hide #2 models
> show #13 models
> hide #13 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> hide #!20 models
Drag select of 44 residues
> show sel atoms
> style sel stick
Changed 367 atom styles
> ui tool show "Show Sequence Viewer"
> sequence chain #16/A #16/B #4/B #6/B #6/G
Alignment identifier is 1
> sequence chain #16/C #16/D #4/D #6/D #6/H
Alignment identifier is 2
> select #16/A-B:350-351 #4/B:350-351 #6/B,G:350-351
90 atoms, 85 bonds, 10 residues, 3 models selected
> select #16/A-B:350-364 #4/B:350-364 #6/B,G:350-364
635 atoms, 645 bonds, 75 residues, 3 models selected
. [ID: 1] region 5 chains [350-364] RMSD: 37.738
> select #16/A-B:301-392 #4/B:301-392 #6/B,G:301-392
3795 atoms, 3860 bonds, 460 residues, 3 models selected
. [ID: 1] region 5 chains [350-364] + 1 other block RMSD: 42.772
> select #6/G:338
11 atoms, 10 bonds, 1 residue, 1 model selected
Drag select of 11 atoms, 14 residues, 10 bonds
> select up
120 atoms, 119 bonds, 15 residues, 1 model selected
> select up
124 atoms, 123 bonds, 15 residues, 1 model selected
> select up
349 atoms, 352 bonds, 42 residues, 1 model selected
> save /Users/oswanson/Desktop/RdRp/RdRp.cxs
> show #!20 models
> hide #6 models
> color #20 #919191ff models
> volume #20 level 0.08684
> lighting soft
> show #6 models
> hide #6 models
> turn y 1 360 #20
Expected a keyword
> turn y 1 360 #20
Expected a keyword
> turn y 1 360
> ui tool show "Side View"
> surface dust #20 size 14.5
> turn y 1 360
> volume #20 level 0.1772
> volume #20 level 0.1489
> turn y 1 360
> volume #20 level 0.1264
> volume #20 level 0.1151
> volume #20 level 0.1376
> movie record
> turn y 1 360
> movie encode test.mp4
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/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
> pwd
Current working directory is:
/Users/oswanson/Downloads/cryosparc_P605_J72_component_005
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/oswanson/Desktop/movie1.mp4
Currently encoding a movie
> save /Users/oswanson/Desktop/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/oswanson/Desktop/movie1.mp4
Currently encoding a movie
> show #6 models
> select add #20
349 atoms, 352 bonds, 42 residues, 3 models selected
> transparency sel 50
> select clear
> volume #20 level 0.0699
> hide #!20 models
> show #!17 models
> hide #6 models
> vseries play #17 loop true
> vseries stop #17
> movie record
> vseries play #17
> movie encode vseries.mp4
Currently encoding a movie
Desktop color scheme is dark
> ui tool show "Show Volume Menu"
>
Incomplete command: vseries
> vseries slider
Missing or invalid "series" argument: empty atom specifier
> vseries slider #17
> movie record
> movie encode /Users/oswanson/Desktop/movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Currently encoding a movie
> movie record
> movie encode /Users/oswanson/Desktop/movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Currently encoding a movie
Desktop color scheme is light
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,)
)
Window position QRect(2288,361 600x300) outside any known screen, using
primary screen
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.
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.
> surface dust #17.19 size 14.5
> surface dust #17.20 size 14.5
> surface dust #17.1 size 14.5
> surface dust #17.2 size 14.5
> surface dust #17.3 size 14.5
> surface dust #17.4 size 14.5
> surface dust #17.5 size 14.5
> surface dust #17.6 size 14.5
> surface dust #17.7 size 14.5
> surface dust #17.8 size 14.5
> surface dust #17.9 size 14.5
> surface dust #17.10 size 14.5
> surface dust #17.11 size 14.5
> surface dust #17.12 size 14.5
> surface dust #17.13 size 14.5
> surface dust #17.14 size 14.5
> surface dust #17.15 size 14.5
> surface dust #17.16 size 14.5
> surface dust #17.17 size 14.5
> surface dust #17.18 size 14.5
> movie record
> movie encode /Users/oswanson/Desktop/movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Currently encoding a movie
> movie record
> movie encode /Users/oswanson/Desktop/movie1.mp4 framerate 25.0
Error processing trigger "new frame":
Currently encoding a movie
> save /Users/oswanson/Desktop/RdRp/RdRp.cxs
——— End of log from Fri Nov 7 10:41:56 2025 ———
> view name session-start
opened ChimeraX session
> movie record
> movie encode /Users/oswanson/Desktop/movie1.mp4 framerate 25.0
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/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 164, in next_value_cb
self.stop()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 148, in stop
self.record_cb()
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/slider.py", line 211, in record_cb
run(ses, f'movie encode %s framerate %.1f'
File
"/Applications/ChimeraX-1.10.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-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 202, in movie_encode
encode_op(session, output[-1], format, quality, qscale, bitrate,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/moviecmd.py", line 260, in encode_op
movie.start_encoding(output, f['ffmpeg_name'], output_size, f['ffmpeg_codec'],
"yuv420p", f['size_restriction'],
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/movie.py", line 324, in start_encoding
self.encoder.run(Status_Reporter())
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/movie/encode.py", line 232, in run
p = Popen(self.arg_list, stdin=DEVNULL, stdout=PIPE, stderr=PIPE)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1026, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
Error processing trigger "new frame":
PermissionError: [Errno 13] Permission denied:
'/Applications/ChimeraX-1.10.app/Contents/bin/ffmpeg'
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py",
line 1950, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
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 Air
Model Identifier: Mac15,13
Model Number: Z1BP0006TLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 13822.1.2
OS Loader Version: 13822.1.2
Software:
System Software Overview:
System Version: macOS 26.0.1 (25A362)
Kernel Version: Darwin 25.0.0
Time since boot: 1 day, 3 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG Ultra HD:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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
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
Change History (2)
comment:1 by , 9 hours ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Build System |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ffmpeg: Permission denied |
comment:2 by , 9 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Hi,
--Eric