![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17186 closed defect (limitation)
Save dialog slow on Windows
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Greg Couch, Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
'Save File'
whatever step in the file system I take from there on, whatever session file is loaded, it takes forever. It seems that Chimera struggles to read and navigate the file system. This does not occur upon the 'Open File' action.
I take this opportunity to thank you all very much for the marvels that you've been doing for the past 15 years or so!
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\Users\amaillard\Documents\Pseudo\MyPDB\240912 AF3 C-trunc\AF - ExlA
> C-trunc.cxs" format session
Log from Mon Mar 24 16:56:36 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\amaillard\\\Documents\\\Pseudo\\\MyPDB\\\240912 AF3
> C-trunc\\\AF - ExlA C-trunc.cxs"
Log from Wed Mar 12 18:25:35 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:\\\Users\\\amaillard\\\Documents\\\Pseudo\\\MyPDB\\\240912 AF3
> C-trunc\\\AF - ExlA C-trunc.cxs"
Log from Thu Feb 13 12:56:46 2025UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "D:\Pseudo\MyPDB\240912 AF3 C-trunc\AF - ExlA C-trunc.cxs" format
> session
Log from Wed Feb 12 18:32:30 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:\Pseudo\MyPDB\211216 Robetta ExlA 35-1651\ExlA
> 35-1651_robetta_models_comb 620-621_min 607-625.pdb" format pdb
Summary of feedback from opening D:\Pseudo\MyPDB\211216 Robetta ExlA
35-1651\ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK ID 163533 MODEL 1 ExlA C-half
Ignored bad PDB record found on line 142
METHOD ROSETTA provides both ab initio and
Ignored bad PDB record found on line 143
METHOD comparative models of protein domains.
Ignored bad PDB record found on line 144
METHOD Comparative models are built from structures
Ignored bad PDB record found on line 145
METHOD detected and aligned by HHSEARCH, SPARKS, and
6 messages similar to the above omitted
Chain information for ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb
#1
---
Chain | Description
A | No description available
> open "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0811_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0811_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0811_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0811_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0811_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0833_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0833_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0833_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0833_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0833_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0931_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0931_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0931_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0931_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0931_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1023_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1023_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1023_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1023_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1023_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1119_unrelaxed_rank_001_alphafold2_ptm_model_3.pdb"
> "D:/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1119_unrelaxed_rank_002_alphafold2_ptm_model_5.pdb"
> "D:/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1119_unrelaxed_rank_003_alphafold2_ptm_model_2.pdb"
> "D:/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1119_unrelaxed_rank_004_alphafold2_ptm_model_4.pdb"
> "D:/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1119_unrelaxed_rank_005_alphafold2_ptm_model_1.pdb"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1218_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1218_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1218_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1218_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1218_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1317_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1317_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1317_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1317_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1317_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1548_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1548_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1548_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1548_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1548_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1600_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1600_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1600_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1600_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1600_model_4.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1618_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1618_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1618_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1618_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c1618_model_4.cif"
Chain information for fold_c0811_model_0.cif #2
---
Chain | Description
A | .
Chain information for fold_c0811_model_1.cif #3
---
Chain | Description
A | .
Chain information for fold_c0811_model_2.cif #4
---
Chain | Description
A | .
Chain information for fold_c0811_model_3.cif #5
---
Chain | Description
A | .
Chain information for fold_c0811_model_4.cif #6
---
Chain | Description
A | .
Chain information for fold_c0833_model_0.cif #7
---
Chain | Description
A | .
Chain information for fold_c0833_model_1.cif #8
---
Chain | Description
A | .
Chain information for fold_c0833_model_2.cif #9
---
Chain | Description
A | .
Chain information for fold_c0833_model_3.cif #10
---
Chain | Description
A | .
Chain information for fold_c0833_model_4.cif #11
---
Chain | Description
A | .
Chain information for fold_c0931_model_0.cif #12
---
Chain | Description
A | .
Chain information for fold_c0931_model_1.cif #13
---
Chain | Description
A | .
Chain information for fold_c0931_model_2.cif #14
---
Chain | Description
A | .
Chain information for fold_c0931_model_3.cif #15
---
Chain | Description
A | .
Chain information for fold_c0931_model_4.cif #16
---
Chain | Description
A | .
Chain information for fold_c1023_model_0.cif #17
---
Chain | Description
A | .
Chain information for fold_c1023_model_1.cif #18
---
Chain | Description
A | .
Chain information for fold_c1023_model_2.cif #19
---
Chain | Description
A | .
Chain information for fold_c1023_model_3.cif #20
---
Chain | Description
A | .
Chain information for fold_c1023_model_4.cif #21
---
Chain | Description
A | .
Chain information for fold_c1119_unrelaxed_rank_001_alphafold2_ptm_model_3.pdb
#22
---
Chain | Description
A | No description available
Chain information for fold_c1119_unrelaxed_rank_002_alphafold2_ptm_model_5.pdb
#23
---
Chain | Description
A | No description available
Chain information for fold_c1119_unrelaxed_rank_003_alphafold2_ptm_model_2.pdb
#24
---
Chain | Description
A | No description available
Chain information for fold_c1119_unrelaxed_rank_004_alphafold2_ptm_model_4.pdb
#25
---
Chain | Description
A | No description available
Chain information for fold_c1119_unrelaxed_rank_005_alphafold2_ptm_model_1.pdb
#26
---
Chain | Description
A | No description available
Chain information for fold_c1218_model_0.cif #27
---
Chain | Description
A | .
Chain information for fold_c1218_model_1.cif #28
---
Chain | Description
A | .
Chain information for fold_c1218_model_2.cif #29
---
Chain | Description
A | .
Chain information for fold_c1218_model_3.cif #30
---
Chain | Description
A | .
Chain information for fold_c1218_model_4.cif #31
---
Chain | Description
A | .
Chain information for fold_c1317_model_0.cif #32
---
Chain | Description
A | .
Chain information for fold_c1317_model_1.cif #33
---
Chain | Description
A | .
Chain information for fold_c1317_model_2.cif #34
---
Chain | Description
A | .
Chain information for fold_c1317_model_3.cif #35
---
Chain | Description
A | .
Chain information for fold_c1317_model_4.cif #36
---
Chain | Description
A | .
Chain information for fold_c1548_model_0.cif #37
---
Chain | Description
A | .
Chain information for fold_c1548_model_1.cif #38
---
Chain | Description
A | .
Chain information for fold_c1548_model_2.cif #39
---
Chain | Description
A | .
Chain information for fold_c1548_model_3.cif #40
---
Chain | Description
A | .
Chain information for fold_c1548_model_4.cif #41
---
Chain | Description
A | .
Chain information for fold_c1600_model_0.cif #42
---
Chain | Description
A | .
Chain information for fold_c1600_model_1.cif #43
---
Chain | Description
A | .
Chain information for fold_c1600_model_2.cif #44
---
Chain | Description
A | .
Chain information for fold_c1600_model_3.cif #45
---
Chain | Description
A | .
Chain information for fold_c1600_model_4.cif #46
---
Chain | Description
A | .
Chain information for fold_c1618_model_0.cif #47
---
Chain | Description
A | .
Chain information for fold_c1618_model_1.cif #48
---
Chain | Description
A | .
Chain information for fold_c1618_model_2.cif #49
---
Chain | Description
A | .
Chain information for fold_c1618_model_3.cif #50
---
Chain | Description
A | .
Chain information for fold_c1618_model_4.cif #51
---
Chain | Description
A | .
Computing secondary structure
[Repeated 49 time(s)]Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
> ui tool show "Renumber Residues"
> renumber #2/A #3/A #4/A #5/A #6/A seqStart 34
3890 residues renumbered
> renumber #7/A #8/A #9/A #10/A #11/A seqStart 34
4000 residues renumbered
> renumber #12/A #13/A #14/A #15/A #16/A seqStart 34
4490 residues renumbered
> renumber #17/A #18/A #19/A #20/A #21/A seqStart 34
4950 residues renumbered
> renumber #22/A #23/A #24/A #25/A #26/A seqStart 35
5425 residues renumbered
> renumber #27/A #28/A #29/A #30/A #31/A seqStart 34
5925 residues renumbered
> renumber #32/A #33/A #34/A #35/A #36/A seqStart 35
6415 residues renumbered
> renumber #37/A #38/A #39/A #40/A #41/A seqStart 35
7570 residues renumbered
> renumber #42/A #43/A #44/A #45/A #46/A seqStart 34
7835 residues renumbered
> renumber #47/A #48/A #49/A #50/A #51/A seqStart 34
7925 residues renumbered
> renumber #47/A #48/A #49/A #50/A #51/A seqStart 34
0 residues renumbered
No presets found in custom preset folder D:/Pseudo/MyPDB\220113 Robetta
ExlA_Pe 35-1416
No presets found in custom preset folder D:/Pseudo/MyPDB\220415 Robetta ExlA
RV4
No presets found in custom preset folder D:/Pseudo/MyPDB\220617 Alpha CnrYX
No presets found in custom preset folder D:/Pseudo/MyPDB\Obsolete models
No presets found in custom preset folder D:/Pseudo/MyPDB\231127 Robetta
ExlA_Ppsy 33-1145
No presets found in custom preset folder D:/Pseudo/MyPDB\240104 Robetta ExlB
ShlB
No presets found in custom preset folder D:/Pseudo/MyPDB\240108 Alpha Exl TPS-
POTRA
No presets found in custom preset folder D:/Pseudo/MyPDB\240107 HMW1B
No presets found in custom preset folder D:/Pseudo/MyPDB\240912 AF3 HPx
derivatives
No presets found in custom preset folder D:/Pseudo/MyPDB\240912 TPS uptake
No presets found in custom preset folder D:/Pseudo/MyPDB\240912 AF3 FhaB
No presets found in custom preset folder D:/Pseudo/MyPDB\240912 AF3 HP
derivatives
No presets found in custom preset folder D:/Pseudo/MyPDB\241209 AF3 RP06-14
x1-to-x5
No presets found in custom preset folder D:/Pseudo/MyPDB\240911 AF3 HMW1a &
PdtA
No presets found in custom preset folder D:/Pseudo/MyPDB\240505 AFmulti ExlA
x4-to-7 by Leandro
No presets found in custom preset folder D:/Pseudo/MyPDB\240902 AF3 dRP
No presets found in custom preset folder D:/Pseudo/MyPDB\240912 AF3 C-trunc
No presets found in custom preset folder D:/Pseudo/MyPDB\250210 AF3 RobVar
> ui tool show CliX
> select :35-261
84743 atoms, 85814 bonds, 11577 residues, 51 models selected
> ui tool show Matchmaker
> matchmaker #2-51 & sel to #1 & sel
Computing secondary structure
[Repeated 50 time(s)] 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 ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0811_model_0.cif, chain A (#2), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.668 angstroms; (across all 227 pairs:
2.033)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0811_model_1.cif, chain A (#3), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.695 angstroms; (across all 227 pairs:
2.069)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0811_model_2.cif, chain A (#4), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.668 angstroms; (across all 227 pairs:
1.998)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0811_model_3.cif, chain A (#5), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.693 angstroms; (across all 227 pairs:
2.013)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0811_model_4.cif, chain A (#6), sequence alignment score =
1074.8
RMSD between 203 pruned atom pairs is 0.690 angstroms; (across all 227 pairs:
1.500)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0833_model_0.cif, chain A (#7), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.667 angstroms; (across all 227 pairs:
1.999)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0833_model_1.cif, chain A (#8), sequence alignment score =
1074.8
RMSD between 203 pruned atom pairs is 0.669 angstroms; (across all 227 pairs:
1.655)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0833_model_2.cif, chain A (#9), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.667 angstroms; (across all 227 pairs:
1.973)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0833_model_3.cif, chain A (#10), sequence alignment score =
1083.8
RMSD between 204 pruned atom pairs is 0.701 angstroms; (across all 227 pairs:
1.665)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0833_model_4.cif, chain A (#11), sequence alignment score =
1074.8
RMSD between 203 pruned atom pairs is 0.683 angstroms; (across all 227 pairs:
1.591)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0931_model_0.cif, chain A (#12), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.684 angstroms; (across all 227 pairs:
2.057)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0931_model_1.cif, chain A (#13), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.676 angstroms; (across all 227 pairs:
2.030)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0931_model_2.cif, chain A (#14), sequence alignment score =
1065.8
RMSD between 203 pruned atom pairs is 0.695 angstroms; (across all 227 pairs:
2.067)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0931_model_3.cif, chain A (#15), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.678 angstroms; (across all 227 pairs:
1.994)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0931_model_4.cif, chain A (#16), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.691 angstroms; (across all 227 pairs:
2.064)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1023_model_0.cif, chain A (#17), sequence alignment score =
1056.8
RMSD between 201 pruned atom pairs is 0.689 angstroms; (across all 227 pairs:
2.025)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1023_model_1.cif, chain A (#18), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.687 angstroms; (across all 227 pairs:
2.044)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1023_model_2.cif, chain A (#19), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.661 angstroms; (across all 227 pairs:
1.978)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1023_model_3.cif, chain A (#20), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.691 angstroms; (across all 227 pairs:
2.040)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1023_model_4.cif, chain A (#21), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.675 angstroms; (across all 227 pairs:
1.996)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1119_unrelaxed_rank_001_alphafold2_ptm_model_3.pdb, chain A
(#22), sequence alignment score = 1076.6
RMSD between 209 pruned atom pairs is 0.712 angstroms; (across all 227 pairs:
1.340)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1119_unrelaxed_rank_002_alphafold2_ptm_model_5.pdb, chain A
(#23), sequence alignment score = 1095.8
RMSD between 205 pruned atom pairs is 0.710 angstroms; (across all 227 pairs:
1.596)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1119_unrelaxed_rank_003_alphafold2_ptm_model_2.pdb, chain A
(#24), sequence alignment score = 1086.8
RMSD between 203 pruned atom pairs is 0.715 angstroms; (across all 227 pairs:
1.657)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1119_unrelaxed_rank_004_alphafold2_ptm_model_4.pdb, chain A
(#25), sequence alignment score = 1080.8
RMSD between 205 pruned atom pairs is 0.706 angstroms; (across all 227 pairs:
1.486)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1119_unrelaxed_rank_005_alphafold2_ptm_model_1.pdb, chain A
(#26), sequence alignment score = 1085.6
RMSD between 205 pruned atom pairs is 0.710 angstroms; (across all 227 pairs:
1.486)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1218_model_0.cif, chain A (#27), sequence alignment score =
1065.8
RMSD between 203 pruned atom pairs is 0.707 angstroms; (across all 227 pairs:
1.990)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1218_model_1.cif, chain A (#28), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.675 angstroms; (across all 227 pairs:
1.948)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1218_model_2.cif, chain A (#29), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.662 angstroms; (across all 227 pairs:
1.955)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1218_model_3.cif, chain A (#30), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.673 angstroms; (across all 227 pairs:
1.925)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1218_model_4.cif, chain A (#31), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.684 angstroms; (across all 227 pairs:
1.965)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1317_model_0.cif, chain A (#32), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.656 angstroms; (across all 227 pairs:
1.931)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1317_model_1.cif, chain A (#33), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.660 angstroms; (across all 227 pairs:
2.017)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1317_model_2.cif, chain A (#34), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.660 angstroms; (across all 227 pairs:
1.957)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1317_model_3.cif, chain A (#35), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.678 angstroms; (across all 227 pairs:
1.980)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1317_model_4.cif, chain A (#36), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.673 angstroms; (across all 227 pairs:
1.936)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1548_model_0.cif, chain A (#37), sequence alignment score =
1083.8
RMSD between 205 pruned atom pairs is 0.677 angstroms; (across all 227 pairs:
1.605)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1548_model_1.cif, chain A (#38), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.666 angstroms; (across all 227 pairs:
2.034)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1548_model_2.cif, chain A (#39), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.674 angstroms; (across all 227 pairs:
1.916)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1548_model_3.cif, chain A (#40), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.673 angstroms; (across all 227 pairs:
1.979)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1548_model_4.cif, chain A (#41), sequence alignment score =
1083.8
RMSD between 203 pruned atom pairs is 0.687 angstroms; (across all 227 pairs:
1.564)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1600_model_0.cif, chain A (#42), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.670 angstroms; (across all 227 pairs:
1.981)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1600_model_1.cif, chain A (#43), sequence alignment score =
1065.8
RMSD between 203 pruned atom pairs is 0.683 angstroms; (across all 227 pairs:
1.934)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1600_model_2.cif, chain A (#44), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.663 angstroms; (across all 227 pairs:
1.890)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1600_model_3.cif, chain A (#45), sequence alignment score =
1065.8
RMSD between 203 pruned atom pairs is 0.703 angstroms; (across all 227 pairs:
2.050)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1600_model_4.cif, chain A (#46), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.674 angstroms; (across all 227 pairs:
1.927)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1618_model_0.cif, chain A (#47), sequence alignment score =
1083.8
RMSD between 204 pruned atom pairs is 0.713 angstroms; (across all 227 pairs:
1.604)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1618_model_1.cif, chain A (#48), sequence alignment score =
1065.8
RMSD between 203 pruned atom pairs is 0.685 angstroms; (across all 227 pairs:
1.919)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1618_model_2.cif, chain A (#49), sequence alignment score =
1083.8
RMSD between 203 pruned atom pairs is 0.687 angstroms; (across all 227 pairs:
1.730)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1618_model_3.cif, chain A (#50), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.669 angstroms; (across all 227 pairs:
1.934)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c1618_model_4.cif, chain A (#51), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.684 angstroms; (across all 227 pairs:
2.023)
> save "D:/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA C-trunc.cxs"
> open "D:/Pseudo/MyPDB/240901 AF3 working/ExlA models AF3/exlA_15.cif"
Chain information for exlA_15.cif #52
---
Chain | Description
A | .
Computing secondary structure
> select :35-261
86395 atoms, 87484 bonds, 11804 residues, 52 models selected
> ui tool show Matchmaker
> matchmaker #52 & sel to #1 & sel
Computing secondary structure
[Repeated 1 time(s)] 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 ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with exlA_15.cif, chain A (#52), sequence alignment score = 908.4
RMSD between 173 pruned atom pairs is 0.657 angstroms; (across all 193 pairs:
1.816)
> save "D:/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA C-trunc.cxs"
> show #2 target m
> hide #2-52 target m
> hide #1 models
> show #2 target m
> show #3 target m
> hide #2 target m
> show #4 target m
> hide #3 target m
> show #5 target m
> hide #4 target m
> show #6 target m
> hide #5 target m
> hide #6 models
> show #2 models
> show #7 models
> hide #2 models
> show #8 target m
> hide #7 target m
> show #9 target m
> hide #8 target m
> show #10 target m
> hide #9 target m
> show #11 target m
> hide #10 target m
> show #7 models
> hide #11 target m
> show #8 target m
> hide #7 target m
> show #9 target m
> hide #8 target m
> show #10 target m
> hide #9 target m
> show #11 target m
> hide #10 target m
> hide #11 models
> show #12 models
> show #13 target m
> hide #12 target m
> show #12 target m
> hide #13 target m
> show #13 target m
> hide #12 target m
> show #14 target m
> hide #13 target m
> show #15 target m
> hide #14 target m
> show #16 target m
> hide #15 target m
> hide #16 models
> show #17 models
> show #18 target m
> hide #17 target m
> show #19 target m
> hide #18 target m
> show #20 target m
> hide #19 target m
> show #21 target m
> hide #20 target m
> show #22 target m
> hide #21 target m
> show #23 target m
> hide #22 target m
> show #24 target m
> hide #23 target m
> show #25 target m
> hide #24 target m
> show #26 target m
> hide #25 target m
> show #27 target m
> hide #26 target m
> show #28 target m
> hide #27 target m
> show #27 target m
> hide #28 target m
> show #28 target m
> hide #27 target m
> show #29 target m
> hide #28 target m
> show #30 target m
> hide #29 target m
> show #31 target m
> hide #30 target m
> show #32 target m
> hide #31 target m
> show #33 target m
> hide #32 target m
> show #34 target m
> hide #33 target m
> show #35 target m
> hide #34 target m
> show #36 target m
> hide #35 target m
> show #37 target m
> hide #36 target m
> show #38 target m
> hide #37 target m
> show #39 target m
> hide #38 target m
> show #40 target m
> hide #39 target m
> show #41 target m
> hide #40 target m
> show #37 models
> hide #41 models
> show #38 target m
> hide #37 target m
> show #39 target m
> hide #38 target m
> show #40 target m
> hide #39 target m
> show #41 target m
> hide #40 target m
> show #42 target m
> hide #41 target m
> show #43 target m
> hide #42 target m
> show #44 target m
> hide #43 target m
> show #45 target m
> hide #44 target m
> show #46 target m
> hide #45 target m
> show #43 models
> show #42 models
> hide #43,46 target m
> show #43 target m
> hide #42 target m
> show #44 target m
> hide #43 target m
> show #45 target m
> hide #44 target m
> show #46 target m
> hide #45 target m
> hide #46 models
> show #42 models
> hide #42 models
> show #47 models
> show #48 target m
> hide #47 target m
> show #49 target m
> hide #48 target m
> show #50 target m
> hide #49 target m
> show #51 target m
> hide #50 target m
> select clear
> mlp #51
Map values for surface "fold_c1618_model_4.cif_A SES surface": minimum -28.71,
mean -7.459, maximum 22.44
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!51 models
> save "D:/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA C-trunc.cxs"
To also show corresponding color key, enter the above mlp command and add key
true
To also show corresponding color key, enter the above mlp command and add key
true
To also show corresponding color key, enter the above mlp command and add key
true
> show #2-50,52#!51 target m
> mlp #2-50,52#!51
Map values for surface "fold_c1548_model_1.cif_A SES surface": minimum -28.89,
mean -7.463, maximum 25.55
Map values for surface "fold_c1548_model_3.cif_A SES surface": minimum -28.51,
mean -7.506, maximum 24.63
Map values for surface "fold_c1548_model_4.cif_A SES surface": minimum -29.17,
mean -7.521, maximum 23.13
Map values for surface "fold_c1548_model_2.cif_A SES surface": minimum -27.66,
mean -7.525, maximum 23.03
Map values for surface "fold_c1023_model_3.cif_A SES surface": minimum -29.74,
mean -7.887, maximum 25.4
Map values for surface "fold_c0833_model_4.cif_A SES surface": minimum -27.51,
mean -8.002, maximum 23.61
Map values for surface "fold_c1023_model_4.cif_A SES surface": minimum -29.71,
mean -7.91, maximum 22.34
Map values for surface
"fold_c1119_unrelaxed_rank_001_alphafold2_ptm_model_3.pdb_A SES surface":
minimum -27.49, mean -8.026, maximum 24.85
Map values for surface "fold_c0931_model_2.cif_A SES surface": minimum -27,
mean -7.89, maximum 23.77
Map values for surface
"fold_c1119_unrelaxed_rank_003_alphafold2_ptm_model_2.pdb_A SES surface":
minimum -27.99, mean -7.925, maximum 23.63
Map values for surface
"fold_c1119_unrelaxed_rank_005_alphafold2_ptm_model_1.pdb_A SES surface":
minimum -30.19, mean -8.072, maximum 24.94
Map values for surface "fold_c0931_model_4.cif_A SES surface": minimum -27.92,
mean -7.848, maximum 23.16
Map values for surface "fold_c1218_model_0.cif_A SES surface": minimum -28.64,
mean -8.112, maximum 24.02
Map values for surface "fold_c1218_model_3.cif_A SES surface": minimum -29.68,
mean -8.084, maximum 23.79
Map values for surface "fold_c0833_model_0.cif_A SES surface": minimum -27.73,
mean -8.096, maximum 23.37
Map values for surface "fold_c1218_model_4.cif_A SES surface": minimum -30.75,
mean -8.118, maximum 24.76
Map values for surface "fold_c1317_model_1.cif_A SES surface": minimum -28.09,
mean -8.076, maximum 24.09
Map values for surface "fold_c1317_model_2.cif_A SES surface": minimum -27.52,
mean -8.09, maximum 22.94
Map values for surface "fold_c0833_model_1.cif_A SES surface": minimum -26.82,
mean -8.057, maximum 24.22
Map values for surface "fold_c0931_model_3.cif_A SES surface": minimum -27.69,
mean -7.764, maximum 24.48
Map values for surface
"fold_c1119_unrelaxed_rank_004_alphafold2_ptm_model_4.pdb_A SES surface":
minimum -28.64, mean -8.052, maximum 24.84
Map values for surface "fold_c0833_model_3.cif_A SES surface": minimum -27.47,
mean -8.027, maximum 22.74
Map values for surface "fold_c1023_model_2.cif_A SES surface": minimum -29.04,
mean -7.987, maximum 22.65
Map values for surface
"fold_c1119_unrelaxed_rank_002_alphafold2_ptm_model_5.pdb_A SES surface":
minimum -29.9, mean -8.056, maximum 26.53
Map values for surface "fold_c1218_model_1.cif_A SES surface": minimum -28.14,
mean -8.121, maximum 25.81
Map values for surface "fold_c1218_model_2.cif_A SES surface": minimum -27.67,
mean -8.091, maximum 22.95
Map values for surface "fold_c0811_model_4.cif_A SES surface": minimum -27.52,
mean -8.028, maximum 22.86
Map values for surface "fold_c1317_model_0.cif_A SES surface": minimum -28.46,
mean -8.1, maximum 23.69
Map values for surface "fold_c1317_model_3.cif_A SES surface": minimum -28.67,
mean -8.195, maximum 22.96
Map values for surface "fold_c1317_model_4.cif_A SES surface": minimum -28.3,
mean -8.128, maximum 23.46
Map values for surface "fold_c1548_model_0.cif_A SES surface": minimum -29.15,
mean -7.507, maximum 24.77
Map values for surface "fold_c0811_model_1.cif_A SES surface": minimum -27.26,
mean -7.941, maximum 23.57
Map values for surface "fold_c1023_model_1.cif_A SES surface": minimum -28.62,
mean -7.944, maximum 23.17
Map values for surface "fold_c0811_model_0.cif_A SES surface": minimum -27.86,
mean -8.025, maximum 23.49
Map values for surface "fold_c0833_model_2.cif_A SES surface": minimum -27.02,
mean -8.062, maximum 25.56
Map values for surface "fold_c0811_model_3.cif_A SES surface": minimum -27.32,
mean -7.974, maximum 24.22
Map values for surface "fold_c0931_model_1.cif_A SES surface": minimum -26.85,
mean -7.847, maximum 23.14
Map values for surface "fold_c1023_model_0.cif_A SES surface": minimum -28.95,
mean -7.975, maximum 22.28
Map values for surface "fold_c0811_model_2.cif_A SES surface": minimum -26.97,
mean -7.988, maximum 24.22
Map values for surface "fold_c0931_model_0.cif_A SES surface": minimum -26.95,
mean -7.881, maximum 22.76
Map values for surface "fold_c1600_model_3.cif_A SES surface": minimum -29.38,
mean -7.505, maximum 23.12
Map values for surface "fold_c1618_model_2.cif_A SES surface": minimum -29.37,
mean -7.441, maximum 23.58
Map values for surface "fold_c1600_model_0.cif_A SES surface": minimum -28.81,
mean -7.544, maximum 22.86
Map values for surface "fold_c1618_model_3.cif_A SES surface": minimum -29.73,
mean -7.477, maximum 24.87
Map values for surface "fold_c1600_model_4.cif_A SES surface": minimum -30.51,
mean -7.5, maximum 23.07
Map values for surface "fold_c1600_model_1.cif_A SES surface": minimum -28.4,
mean -7.513, maximum 22.97
Map values for surface "fold_c1618_model_4.cif_A SES surface": minimum -28.71,
mean -7.459, maximum 22.44
Map values for surface "fold_c1600_model_2.cif_A SES surface": minimum -29.34,
mean -7.507, maximum 23.5
Map values for surface "fold_c1618_model_1.cif_A SES surface": minimum -28.6,
mean -7.438, maximum 23.12
Map values for surface "fold_c1618_model_0.cif_A SES surface": minimum -29.99,
mean -7.457, maximum 23.44
Map values for surface "exlA_15.cif_A SES surface": minimum -28.88, mean
-7.456, maximum 25.69
To also show corresponding color key, enter the above mlp command and add key
true
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!13 models
> hide #!14 models
> hide #!15 models
> hide #!16 models
> hide #!18 models
> hide #!19 models
> hide #!20 models
> hide #!21 models
> hide #!23 models
> hide #!24 models
> hide #!25 models
> hide #!26 models
> hide #!28 models
> hide #!29 models
> hide #!30 models
> hide #!31 models
> hide #!33 models
> hide #!34 models
> hide #!35 models
> hide #!36 models
> hide #!38 models
> hide #!39 models
> hide #!40 models
> hide #!41 models
> hide #!43 models
> hide #!44 models
> hide #!45 models
> hide #!46 models
> hide #!48 models
> hide #!49 models
> hide #!50 models
> hide #!51 models
> save "D:/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA C-trunc.cxs"
> close #3-6,8-11,13-16,18-21,23-26,28-31,33-36,38-41,43-46,48-51
> show #!2 target m
> hide #!7,12,17,22,27,32,37,42,47,52 target m
> show #!7 target m
> hide #!2 target m
> show #!2 target m
> hide #!7 target m
> show #!7 target m
> hide #!2 target m
> show #!12 target m
> hide #!7 target m
> show #!7 target m
> hide #!12 target m
> show #!2 target m
> hide #!7 models
> save "D:/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA C-trunc.cxs"
——— End of log from Wed Feb 12 18:32:30 2025 ———
opened ChimeraX session
> show #!52 models
> hide #!2 models
> cd "D:/Pseudo/MyPDB/240912 AF3 C-trunc/captions"
Current working directory is: D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie1.mp4"
Movie saved to \D:Pseudo\\...\captions\movie1.mp4
> show #!47 target m
> hide #!52 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie2.mp4"
Movie saved to \D:Pseudo\\...\captions\movie2.mp4
> show #!42 target m
> hide #!47 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie3.mp4"
Movie saved to \D:Pseudo\\...\captions\movie3.mp4
> show #!37 target m
> hide #!42 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie4.mp4"
Movie saved to \D:Pseudo\\...\captions\movie4.mp4
> show #!32 target m
> hide #!37 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie5.mp4"
Movie saved to \D:Pseudo\\...\captions\movie5.mp4
> show #!27 target m
> hide #!32 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie6.mp4"
Movie saved to \D:Pseudo\\...\captions\movie6.mp4
> show #!22 target m
> hide #!27 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie7.mp4"
Movie saved to \D:Pseudo\\...\captions\movie7.mp4
> show #!17 target m
> hide #!22 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie8.mp4"
Movie saved to \D:Pseudo\\...\captions\movie8.mp4
> show #!12 target m
> hide #!17 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie9.mp4"
Movie saved to \D:Pseudo\\...\captions\movie9.mp4
> show #!7 target m
> hide #!12 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie10.mp4"
Movie saved to \D:Pseudo\\...\captions\movie10.mp4
> show #!2 target m
> hide #!7 target m
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie11.mp4"
Movie saved to \D:Pseudo\\...\captions\movie11.mp4
> open "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0720_model_0.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0720_model_1.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0720_model_2.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0720_model_3.cif"
> "D:/Pseudo/MyPDB/240912 AF3 C-trunc/fold_c0720_model_4.cif"
Chain information for fold_c0720_model_0.cif #3
---
Chain | Description
A | .
Chain information for fold_c0720_model_1.cif #4
---
Chain | Description
A | .
Chain information for fold_c0720_model_2.cif #5
---
Chain | Description
A | .
Chain information for fold_c0720_model_3.cif #6
---
Chain | Description
A | .
Chain information for fold_c0720_model_4.cif #8
---
Chain | Description
A | .
Computing secondary structure
[Repeated 4 time(s)]
> ui tool show "Renumber Residues"
> renumber #3/A #4/A #5/A #6/A #8/A seqStart 35
3430 residues renumbered
> select :35-261
29345 atoms, 29699 bonds, 3859 residues, 17 models selected
> ui tool show Matchmaker
> matchmaker #3-6,8 & sel to #1 & sel
Computing secondary structure
[Repeated 4 time(s)] 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 ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0720_model_0.cif, chain A (#3), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.687 angstroms; (across all 227 pairs:
2.051)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0720_model_1.cif, chain A (#4), sequence alignment score =
1065.8
RMSD between 202 pruned atom pairs is 0.685 angstroms; (across all 227 pairs:
2.035)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0720_model_2.cif, chain A (#5), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.677 angstroms; (across all 227 pairs:
2.018)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0720_model_3.cif, chain A (#6), sequence alignment score =
1068.8
RMSD between 202 pruned atom pairs is 0.694 angstroms; (across all 227 pairs:
1.767)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#1) with fold_c0720_model_4.cif, chain A (#8), sequence alignment score =
1065.8
RMSD between 201 pruned atom pairs is 0.685 angstroms; (across all 227 pairs:
2.047)
> hide #!2 models
> hide #4 models
> hide #5 models
> hide #6 models
> hide #8 models
> help help:index.html
> select clear
> close #4-6,8
> mlp #3
Map values for surface "fold_c0720_model_0.cif_A SES surface": minimum -27.22,
mean -7.815, maximum 23.44
To also show corresponding color key, enter the above mlp command and add key
true
> movie record
> turn y 2 180
> wait 180
> movie encode "D:\Pseudo\MyPDB\240912 AF3 C-trunc\captions\movie1.mp4"
Movie saved to \D:Pseudo\\...\captions\movie1.mp4
> rename #1 id #50
> rename #3 id #1
> rename #7 id #3
> rename #12 id #4
> rename #17 id #5
> rename #22 id #6
> rename #27 id #7
> rename #32 id #8
> rename #37 id #9
> rename #42 id #10
> rename #47 id #11
> rename #52 id #12
> save "D:/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA C-trunc.cxs"
——— End of log from Thu Feb 13 12:56:46 2025 ———
opened ChimeraX session
> show #!2 target m
> hide #!1 target m
> show #!1 target m
> hide #!2 target m
> show #!2 target m
> hide #!1 target m
> show #!3 target m
> hide #!2 target m
> show #!4 target m
> hide #!3 target m
> show #!5 target m
> hide #!4 target m
> show #!6 target m
> hide #!5 target m
> show #!5 target m
> hide #!6 target m
> log metadata #5
No models had metadata
> log chains #5
Chain information for fold_c1023_model_0.cif #5
---
Chain | Description
A | .
> show #!6 models
> hide #!5 models
> show #!7 target m
> hide #!6 target m
> show #!8 models
> hide #!7 models
> show #!9 target m
> hide #!8 target m
> show #!10 target m
> hide #!9 target m
> show #!9 target m
> hide #!10 target m
> show #!10 target m
> hide #!9 target m
> show #!9 target m
> hide #!10 target m
> hide #9.1 models
> hide #10.1 models
> show #!10 target m
> hide #!9 target m
> show #!9 target m
> hide #!10 target m
> hide #8.1 models
> show #!8 target m
> hide #!9 target m
> show #!9 target m
> hide #!8 target m
> show #!8 target m
> hide #!9 target m
> show #!9 target m
> hide #!8 target m
> show #!8 target m
> hide #!9 target m
> show #!4 models
> hide #!8 models
> show #8.1 models
> show #9.1 models
> show #10.1 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> show #!5 target m
> hide #!4 target m
> show #!4 target m
> hide #!5 target m
> show #!3 target m
> hide #!4 target m
> show #!4 target m
> hide #!3 target m
> show #!3 target m
> hide #!4 target m
> show #!2 target m
> hide #!3 target m
> show #!3 target m
> hide #!2 target m
> show #!4 target m
> hide #!3 target m
> show #!5 target m
> hide #!4 target m
> show #!4 target m
> hide #!5 target m
> show #!5 target m
> hide #!4 target m
> show #!4 target m
> hide #!5 target m
> select clear
> transparency #4 30
> show #!3 target m
> hide #!4 target m
> show #!1-12 target m
> transparency #1-12 30
> hide #!1-12 target m
> show #!5 models
> show #!4 target m
> hide #!5 target m
> show #!5 target m
> hide #!4 target m
> show #!6 target m
> hide #!5 target m
> show #!7 target m
> hide #!6 target m
> show #!8 target m
> hide #!7 target m
> show #!9 target m
> hide #!8 target m
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
> save "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA
> C-trunc.cxs"
——— End of log from Wed Mar 12 18:25:35 2025 ———
opened ChimeraX session
> select #1:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1904.7
> select up
451 atoms, 459 bonds, 54 residues, 2 models selected
> select up
5031 atoms, 5083 bonds, 686 residues, 2 models selected
> open "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c993_model_0.cif"
> "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1044_model_0.cif"
> "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1138_model_0.cif"
> "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3
> C-trunc/fold_c1224_model_0.cif"
Chain information for fold_c993_model_0.cif #13
---
Chain | Description
A | .
Chain information for fold_c1044_model_0.cif #14
---
Chain | Description
A | .
Chain information for fold_c1138_model_0.cif #15
---
Chain | Description
A | .
Chain information for fold_c1224_model_0.cif #16
---
Chain | Description
A | .
Computing secondary structure
[Repeated 3 time(s)]
> ui tool show Matchmaker
> matchmaker #13-16 to #50
Computing secondary structure
[Repeated 3 time(s)] 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 ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#50) with fold_c993_model_0.cif, chain A (#13), sequence alignment score =
4650.4
RMSD between 681 pruned atom pairs is 1.010 angstroms; (across all 959 pairs:
7.164)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#50) with fold_c1044_model_0.cif, chain A (#14), sequence alignment score =
4941.7
RMSD between 705 pruned atom pairs is 0.953 angstroms; (across all 1010 pairs:
6.697)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#50) with fold_c1138_model_0.cif, chain A (#15), sequence alignment score =
5346.1
RMSD between 732 pruned atom pairs is 0.953 angstroms; (across all 1104 pairs:
7.134)
Matchmaker ExlA 35-1651_robetta_models_comb 620-621_min 607-625.pdb, chain A
(#50) with fold_c1224_model_0.cif, chain A (#16), sequence alignment score =
5756.5
RMSD between 747 pruned atom pairs is 0.944 angstroms; (across all 1190 pairs:
7.543)
> hide #!9 models
> mlp #13-16
Map values for surface "fold_c993_model_0.cif_A SES surface": minimum -27.69,
mean -7.935, maximum 23.78
Map values for surface "fold_c1044_model_0.cif_A SES surface": minimum -29.47,
mean -7.949, maximum 23.38
Map values for surface "fold_c1138_model_0.cif_A SES surface": minimum -28.36,
mean -8.133, maximum 22.24
Map values for surface "fold_c1224_model_0.cif_A SES surface": minimum -28.85,
mean -8.153, maximum 23.98
To also show corresponding color key, enter the above mlp command and add key
true
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
[Repeated 1 time(s)]
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
[Repeated 1 time(s)]
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
> save "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA
> C-trunc.cxs"
> select up
5031 atoms, 5083 bonds, 686 residues, 2 models selected
> select up
156452 atoms, 157830 bonds, 19868 residues, 18 models selected
> select #1:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> select #1:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1904.7
> select #2:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1897.5
> select #3:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1901.7
> select #4:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> hide #!13 models
> hide #!14 models
> hide #!16 models
> hide #!15 models
> show #!1 target m
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1901.3
> select #13:366,371,373,375,378,451,455
54 atoms, 47 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (54 atoms) = 1800.9
> select #5:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1901.6
> select #6:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1873.8
> select #15:366,371,373,375,378,451,455
54 atoms, 47 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (54 atoms) = 1799.5
> select #14:366,371,373,375,378,451,455
54 atoms, 47 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (54 atoms) = 1800.5
> select #7:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1899.9
> select #16:366,371,373,375,378,451,455
54 atoms, 47 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (54 atoms) = 1798
> select #8:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1900.6
> select #9:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1896.7
> select #10:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1898.7
> select #11:366,371,373,375,378,451,455
84 atoms, 86 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (84 atoms) = 1894.1
> select #12:366,371,373,375,378,451,455
54 atoms, 47 bonds, 7 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (54 atoms) = 1799
> select #1:450,522,523,527,528,601,602,604
75 atoms, 74 bonds, 8 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (75 atoms) = 1512.3
> select #1:678,698,696,773,775
30 atoms, 29 bonds, 3 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (30 atoms) = 685.73
> ui tool show "Renumber Residues"
> renumber #1/A #2/A #3/A #4/A #5/A #6/A #7/A #8/A #9/A #10/A #11/A #12/A
> #13/A #14/A #15/A #16/A #50/A seqStart 35
13683 residues renumbered
> select clear
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\AF - ExlA C-trunc.cxs
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\confidence
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc\captions
SHGetFileInfo() timed out for C:\Users\amaillard\Documents\Pseudo\MyPDB\240912
AF3 C-trunc
> save "C:/Users/amaillard/Documents/Pseudo/MyPDB/240912 AF3 C-trunc/AF - ExlA
> C-trunc.cxs"
——— End of log from Mon Mar 24 16:56:36 2025 ———
opened ChimeraX session
> select #7:450,522,523,527,528,601,602,604
67 atoms, 65 bonds, 8 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (67 atoms) = 1480
> select #7:678,698,696,773,775
35 atoms, 31 bonds, 5 residues, 1 model selected
> measure sasa sel
Solvent accessible area for sel (35 atoms) = 971.3
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #5/A
Alignment identifier is 5/A
> sequence chain #6/A
Alignment identifier is 6/A
> sequence chain #7/A
Alignment identifier is 7/A
> sequence chain #8/A
Alignment identifier is 8/A
> sequence chain #9/A
Alignment identifier is 9/A
> sequence chain #10/A
Alignment identifier is 10/A
> sequence chain #11/A
Alignment identifier is 11/A
> sequence chain #13/A
Alignment identifier is 13/A
> sequence chain #14/A
Alignment identifier is 14/A
> sequence chain #15/A
Alignment identifier is 15/A
> sequence chain #16/A
Alignment identifier is 16/A
> ui tool show "Renumber Residues"
> renumber #3/A seqStart 34
800 residues renumbered
> renumber #7/A seqStart 34
1185 residues renumbered
> renumber #7/A seqStart 34
0 residues renumbered
> renumber #2/A seqStart 34
778 residues renumbered
> renumber #11/A seqStart 34
1585 residues renumbered
> renumber #10/A seqStart 34
1567 residues renumbered
> renumber #4/A seqStart 34
898 residues renumbered
> renumber #5/A seqStart 34
990 residues renumbered
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop
[Repeated 2 time(s)]
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Cable
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Calculus
SHGetFileInfo() timed out for
C:\Users\amaillard\Desktop\docear-1.2.0.0_stable_build291
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\ExlA models for
Viviana
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Fiji.app
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop
[Repeated 1 time(s)]
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Cable
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Calculus
SHGetFileInfo() timed out for
C:\Users\amaillard\Desktop\docear-1.2.0.0_stable_build291
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\ExlA models for
Viviana
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Fiji.app
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop
[Repeated 1 time(s)]
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Cable
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Calculus
SHGetFileInfo() timed out for
C:\Users\amaillard\Desktop\docear-1.2.0.0_stable_build291
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\ExlA models for
Viviana
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop\Fiji.app
SHGetFileInfo() timed out for C:\Users\amaillard\Desktop
OpenGL version: 3.3.0 NVIDIA 377.83
OpenGL renderer: Quadro 600/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: fr_FR.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: OptiPlex 7010
OS: Microsoft Windows 10 Entreprise (Build 19045)
Memory: 17,132,265,472
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
OSLanguage: fr-FR
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2024.8.30
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-clix: 0.1.10
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
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: 1.2.1
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
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
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
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: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.18.1
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
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: 1.41
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.5
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pywin32: 306
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
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: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
WMI: 1.5.1
Attachments (1)
Change History (6)
comment:1 by , 7 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Input/Output |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Save dialog slow on Windows |
comment:2 by , 7 months ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
email2trac barfed on my response, so I'm reproducing it here:
Hi Antoine,
Please try getting tomorrow's daily build (it should be dated March 26th or later). Before opening the save dialog, run the attached Python script (simply by opening it, e.g. "open native_save.py"). Does the save dialog then open any faster? If it does open, the resulting save dialog will be less functional then the normal version since it will be using a "native" save dialog that we won't be able to customize with additional widgets, so for instance you won't be able to specify supersampling amount for images, which models to save as PDB, and so on. You will always get the default save behavior.
So it's really to see if it's the use of the non-native dialog that's causing the problem for you.
--Eric
by , 7 months ago
| Attachment: | native_save.py added |
|---|
Python script needed to switch to native save dialog
comment:3 by , 7 months ago
| Status: | assigned → feedback |
|---|
comment:4 by , 7 months ago
Antoine's response went just to me, so reproducing it here:
Hello Eric,
Restoring the native save dialog works great!
Your description of what I will be missing lets me understand that the save dialog in ChimeraX offers similar options to what you developped in Chimera: this I could not figure out so far because the dialog was so impractical :-)
Probably the trouble is with my aging computer. I am happy that you could feature this fix.
Whether it is pertinent to enable the switch between the original or the native 'save dialog' in eg 'preferences' is up to you.
I understand that patches for rare issues may add little value.
Anyway, thank you soooo much!
Have a nice day,
Antoine
comment:5 by , 7 months ago
| Resolution: | → limitation |
|---|---|
| Status: | feedback → closed |
I guess I'll leave my code changes in so that using the script can activate the native save dialog, but since it's not really a fix and is a downgrade in functionality I'm not strongly inclined to make it easier to access. For people (like you) who run into this behavior, I'll give them the script and advise them to put it in their startup commands, and to try removing the command when new versions of ChimeraX come out in order to check if the normal behavior has improved.
Note:
See TracTickets
for help on using tickets.
It seems that using a non-native save dialog (which we need to do in order to add additional controls) can be very slow on Windows depending on what other software is installed (possibly data encryption) as per: https://bugreports.qt.io/browse/QTBUG-106870
Reported by Antoine.