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Opened 8 months ago
Closed 8 months ago
#17203 closed defect (duplicate)
RMSD header index error when realigning
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19044
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise.cxs
Log from Tue Mar 25 20:52:17 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/Session1.cxs
Opened J80_006_volume_map_sharp2.mrc as #3, grid size 157,111,270, pixel
0.83,0.83,0.83, shown at level 0.325, step 1, values float32
Log from Tue Mar 25 18:40:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/Session1.cxs
Opened J80_006_volume_map_sharp2.mrc as #3, grid size 157,111,270, pixel
0.83,0.83,0.83, shown at level 0.325, step 1, values float32
Log from Tue Mar 25 12:51:41 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open D:\TaxolManuscript\TaxolMTMap\Session1.cxs format session
Opened J80_006_volume_map_sharp2.mrc as #3, grid size 157,111,270, pixel
0.83,0.83,0.83, shown at level 0.325, step 1, values float32
Log from Tue Mar 25 12:07:53 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:\TaxolManuscript\TaxolMTMap\TSA-GDP_Taxol_rough_model.pdb format pdb
Chain information for TSA-GDP_Taxol_rough_model.pdb #1
---
Chain | Description
A C I K | No description available
B F J N | No description available
> show cartoons
> hide atoms
> open D:/TaxolManuscript/TaxolMTMap/J80_006_volume_map_sharp.mrc
Opened J80_006_volume_map_sharp.mrc as #2, grid size 720,720,720, pixel 0.83,
shown at step 1, values float32
> volume #2 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> open D:/TaxolManuscript/TaxolMTMap/TSA-GDP_Taxol_rough_model2.pdb
Chain information for TSA-GDP_Taxol_rough_model2.pdb #3
---
Chain | Description
A C I K | No description available
B F J N | No description available
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule TSA-GDP_Taxol_rough_model2.pdb (#3) to map
J80_006_volume_map_sharp.mrc (#2) using 53628 atoms
average map value = 0.05661, steps = 28
shifted from previous position = 0.00993
rotated from previous position = 0.0134 degrees
atoms outside contour = 38914, contour level = 0.10025
Position of TSA-GDP_Taxol_rough_model2.pdb (#3) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 -0.00021371 -0.00009172 0.12561819
0.00021371 0.99999998 -0.00003144 -0.05325543
0.00009172 0.00003142 1.00000000 -0.04340107
Axis 0.13391455 -0.39083485 0.91066734
Axis point 252.71144712 588.94037667 0.00000000
Rotation angle (degrees) 0.01344592
Shift along axis -0.00188776
> hide #!1 models
> select add #3
53628 atoms, 54272 bonds, 4 pseudobonds, 3480 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> volume #2 change image level -0.03739,0 level 0.1151,0.8 level 1.182,1
> volume #2 level 0.3879
> volume #2 step 1
> hide #!2 models
> show #!2 models
> fitmap sel inMap #2
Fit molecule TSA-GDP_Taxol_rough_model2.pdb (#3) to map
J80_006_volume_map_sharp.mrc (#2) using 53628 atoms
average map value = 0.05661, steps = 40
shifted from previous position = 0.00647
rotated from previous position = 0.00822 degrees
atoms outside contour = 48975, contour level = 0.3879
Position of TSA-GDP_Taxol_rough_model2.pdb (#3) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00008601 -0.00002728 0.04802128
0.00008601 1.00000000 -0.00002012 -0.01632977
0.00002728 0.00002012 1.00000000 -0.01903402
Axis 0.21762275 -0.29507522 0.93036066
Axis point 198.24365949 564.45280976 0.00000000
Rotation angle (degrees) 0.00529717
Shift along axis -0.00243947
Average map value = 0.05661 for 53628 atoms, 48975 outside contour
> close #3
> close #1
> open D:/TaxolManuscript/TaxolMTMap/TSA-GDP_Taxol_rough_model3.pdb
Chain information for TSA-GDP_Taxol_rough_model3.pdb #1
---
Chain | Description
A C I K | No description available
B F J N | No description available
> hide atoms
> show cartoons
> fitmap #1 inMap #2
Fit molecule TSA-GDP_Taxol_rough_model3.pdb (#1) to map
J80_006_volume_map_sharp.mrc (#2) using 53628 atoms
average map value = 0.2073, steps = 28
shifted from previous position = 0.00878
rotated from previous position = 0.00699 degrees
atoms outside contour = 40777, contour level = 0.3879
Position of TSA-GDP_Taxol_rough_model3.pdb (#1) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999999 0.00001928 -0.00010506 0.02151568
-0.00001929 1.00000000 -0.00005908 0.01951427
0.00010506 0.00005908 0.99999999 -0.05219767
Axis 0.48397683 -0.86069638 -0.15801320
Axis point 494.04343631 0.00000000 196.17251403
Rotation angle (degrees) 0.00699381
Shift along axis 0.00186515
> transparency #1#2.2#!2 50
> hide (#1#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #1#2.2#!2
> show (#1#2.2#!2 & backbone) target ab
> style stick
Changed 53628 atom styles
> hide (#1#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #1#2.2#!2
> show (#1#2.2#!2 & backbone) target ab
> hide (#1#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #1#2.2#!2
> show (#1#2.2#!2 & ((protein&@ca)|(nucleic&@p))) target ab
> fitmap #1 inMap #2
Fit molecule TSA-GDP_Taxol_rough_model3.pdb (#1) to map
J80_006_volume_map_sharp.mrc (#2) using 53628 atoms
average map value = 0.2073, steps = 36
shifted from previous position = 0.00877
rotated from previous position = 0.00677 degrees
atoms outside contour = 40781, contour level = 0.3879
Position of TSA-GDP_Taxol_rough_model3.pdb (#1) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 0.00000278 -0.00000242 -0.00018015
-0.00000278 1.00000000 -0.00000305 0.00164437
0.00000242 0.00000305 1.00000000 -0.00189962
Axis 0.63779297 -0.50555963 -0.58105902
Axis point -0.00000000 592.66860737 565.12027096
Rotation angle (degrees) 0.00027406
Shift along axis 0.00015757
> save D:/TaxolManuscript/TaxolMTMap/TSA-GDP_Taxol_rough_model4.pdb
> ui tool show "Surface Zone"
> surface zone #2 nearAtoms #1 distance 8
> volume #2 level 0.2111
> save D:/TaxolManuscript/TaxolMTMap/J80_006_volume_map_sharp2.mrc models #2
"Unable to open monitor interface to \\\\\\\\.\\\DISPLAY1:" "The operation
completed successfully."
[Repeated 3 time(s)]
> open D:/TaxolManuscript/TaxolMTMap/tsaTaxol-ChainA-2pF-1.pdb
Summary of feedback from opening D:/TaxolManuscript/TaxolMTMap/tsaTaxol-
ChainA-2pF-1.pdb
---
warnings | Ignored bad PDB record found on line 23694
Ignored bad PDB record found on line 27029
Start residue of secondary structure not found: HELIX 2 2 GLY A 44 THR A 51 1
8
Start residue of secondary structure not found: HELIX 16 16 GLY B 10 HIS B 28
1 19
Start residue of secondary structure not found: HELIX 17 17 ASP B 41 ASP B 45
1 5
Start residue of secondary structure not found: HELIX 18 18 ILE B 47 VAL B 49
1 3
Start residue of secondary structure not found: HELIX 19 19 THR B 55 GLY B 57
1 3
201 messages similar to the above omitted
Chain information for tsaTaxol-ChainA-2pF-1.pdb #3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!3 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 TSA-GDP_Taxol_rough_model3.pdb, chain C (#1) with tsaTaxol-
ChainA-2pF-1.pdb, chain A (#3), sequence alignment score = 2197.6
RMSD between 429 pruned atom pairs is 0.533 angstroms; (across all 432 pairs:
4.461)
> hide (#1,3#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #1,3#2.2#!2
> show (#1,3#2.2#!2 & ((protein&@ca)|(nucleic&@p))) target ab
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #3/A to #1/N pairing ss
Parameters
---
Chain pairing | ss
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 TSA-GDP_Taxol_rough_model3.pdb, chain N (#1) with tsaTaxol-
ChainA-2pF-1.pdb, chain A (#3), sequence alignment score = 2185.9
RMSD between 428 pruned atom pairs is 0.578 angstroms; (across all 429 pairs:
0.604)
> show #!1 models
> show #!2 models
> hide #!1 models
> fitmap #3 inMap #2
Fit molecule tsaTaxol-ChainA-2pF-1.pdb (#3) to map
J80_006_volume_map_sharp.mrc (#2) using 26743 atoms
average map value = 0.3195, steps = 72
shifted from previous position = 0.804
rotated from previous position = 1.67 degrees
atoms outside contour = 10503, contour level = 0.21105
Position of tsaTaxol-ChainA-2pF-1.pdb (#3) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.64180506 0.76667969 -0.01698571 -114.14285703
0.76673665 -0.64194752 -0.00427771 263.24941567
-0.01418357 -0.01027811 -0.99984658 636.36798684
Axis -0.90603645 -0.42311227 0.00860047
Axis point 0.00000000 158.85810331 317.40268308
Rotation angle (degrees) 179.81027370
Shift along axis -2.49340441
> show #!1 models
> select add #3
26743 atoms, 27351 bonds, 3431 pseudobonds, 3432 residues, 3 models selected
> show sel cartoons
> hide #!1 models
> select subtract #3
Nothing selected
> close #2
> open D:/TaxolManuscript/TaxolMTMap/J80_006_volume_map_sharp.mrc
Opened J80_006_volume_map_sharp.mrc as #2, grid size 720,720,720, pixel 0.83,
shown at step 1, values float32
> volume #2 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #2 step 2
> transparency #3#2.2#!2 50
> save D:/TaxolManuscript/TaxolMTMap/tsaTaxol-ChainA-2pF-1.pdb models #3
> close #3
> open D:/TaxolManuscript/TaxolMTMap/tsaTaxol-ChainA-2pF-1.pdb
Chain information for tsaTaxol-ChainA-2pF-1.pdb #3
---
Chain | Description
A | No description available
> close #3
> open D:/TaxolManuscript/TaxolMTMap/tsaTaxol-ChainA-2pF-1.pdb
Chain information for tsaTaxol-ChainA-2pF-1.pdb #3
---
Chain | Description
A | No description available
> volume #2 change image level -0.03739,0 level 0.1151,0.8 level 1.182,1
> volume #2 level 0.1695
> show #!1 models
> hide #!1 models
> open D:/TaxolManuscript/TaxolMTMap/tsaTaxol-ChainA-2pF-2.pdb
Chain information for tsaTaxol-ChainA-2pF-2.pdb #4
---
Chain | Description
A | No description available
> fitmap #4 inMap #2
Fit molecule tsaTaxol-ChainA-2pF-2.pdb (#4) to map
J80_006_volume_map_sharp.mrc (#2) using 26743 atoms
average map value = 0.105, steps = 28
shifted from previous position = 0.00228
rotated from previous position = 0.00507 degrees
atoms outside contour = 19817, contour level = 0.16947
Position of tsaTaxol-ChainA-2pF-2.pdb (#4) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00006983 -0.00000770 0.03051731
0.00006983 1.00000000 -0.00005372 -0.00094130
0.00000771 0.00005372 1.00000000 -0.02422827
Axis 0.60744742 -0.08711406 0.78956873
Axis point 14.14187674 441.48770017 0.00000000
Rotation angle (degrees) 0.00506695
Shift along axis -0.00051022
> close #1
> hide #!2 models
> ui tool show Matchmaker
> open D:/TaxolManuscript/TaxolMTMap/TSA-GDP_Taxol_rough_model4.pdb
Chain information for TSA-GDP_Taxol_rough_model4.pdb #1
---
Chain | Description
A C I K | No description available
B F J N | No description available
> hide atoms
> show cartoons
> hide #!1 models
> hide #!3 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #4/A to #1/J pairing ss
Parameters
---
Chain pairing | ss
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 TSA-GDP_Taxol_rough_model4.pdb, chain J (#1) with tsaTaxol-
ChainA-2pF-2.pdb, chain A (#4), sequence alignment score = 2189.5
RMSD between 427 pruned atom pairs is 0.504 angstroms; (across all 429 pairs:
2.906)
> undo
> close #3
> close #4
> close #1
> open D:/TaxolManuscript/TaxolMTMap/tsaTaxol-ChainA-2pF-2.pdb
Chain information for tsaTaxol-ChainA-2pF-2.pdb #1
---
Chain | Description
A | No description available
> show #!2 models
Correlation = 1, Correlation about mean = 1, Overlap = 1.048e+04
Average map value = 0.105 for 26743 atoms, 19812 outside contour
[Repeated 1 time(s)]
> fitmap #1 inMap #2
Fit molecule tsaTaxol-ChainA-2pF-2.pdb (#1) to map
J80_006_volume_map_sharp.mrc (#2) using 26743 atoms
average map value = 0.105, steps = 28
shifted from previous position = 0.00228
rotated from previous position = 0.00507 degrees
atoms outside contour = 19817, contour level = 0.16947
Position of tsaTaxol-ChainA-2pF-2.pdb (#1) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00006983 -0.00000770 0.03051731
0.00006983 1.00000000 -0.00005372 -0.00094130
0.00000771 0.00005372 1.00000000 -0.02422827
Axis 0.60744742 -0.08711406 0.78956873
Axis point 14.14187674 441.48770017 0.00000000
Rotation angle (degrees) 0.00506695
Shift along axis -0.00051022
> volume #2 level 0.2486
Average map value = 0.105 for 26743 atoms, 22207 outside contour
> fitmap #1 inMap #2
Fit molecule tsaTaxol-ChainA-2pF-2.pdb (#1) to map
J80_006_volume_map_sharp.mrc (#2) using 26743 atoms
average map value = 0.1049, steps = 28
shifted from previous position = 0.0272
rotated from previous position = 0.0209 degrees
atoms outside contour = 22206, contour level = 0.24857
Position of tsaTaxol-ChainA-2pF-2.pdb (#1) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999998 0.00016262 0.00010601 -0.10585803
-0.00016264 0.99999997 0.00020286 -0.03955733
-0.00010598 -0.00020287 0.99999997 0.10916356
Axis -0.72249933 0.37750453 -0.57921071
Axis point 0.00000000 533.26568893 191.96475498
Rotation angle (degrees) 0.01608768
Shift along axis -0.00167941
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B.pdb
Summary of feedback from opening D:/TaxolManuscript/TaxolMTMap/tsa_taxol-
ChainA_B.pdb
---
warnings | Start residue of secondary structure not found: HELIX 37 37 GLY C 10 HIS C 28 1 19
Start residue of secondary structure not found: HELIX 39 39 THR C 73 THR C 80
1 8
Start residue of secondary structure not found: HELIX 40 40 TYR C 103 GLN C
128 1 26
Start residue of secondary structure not found: HELIX 41 41 GLY C 144 ASP C
160 1 17
Start residue of secondary structure not found: HELIX 42 42 GLU C 183 HIS C
197 1 15
167 messages similar to the above omitted
Chain information for tsa_taxol-ChainA_B.pdb #3
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #3/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
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 tsaTaxol-ChainA-2pF-2.pdb, chain A (#1) with tsa_taxol-
ChainA_B.pdb, chain A (#3), sequence alignment score = 2260
RMSD between 428 pruned atom pairs is 0.117 angstroms; (across all 431 pairs:
4.313)
> close #1
> open D:/TaxolManuscript/TaxolMTMap/TSA-GDP_Taxol_rough_model4.pdb
Chain information for TSA-GDP_Taxol_rough_model4.pdb #1
---
Chain | Description
A C I K | No description available
B F J N | No description available
> show cartoons
> hide atoms
> ui tool show Matchmaker
> matchmaker #3/A to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 TSA-GDP_Taxol_rough_model4.pdb, chain B (#1) with tsa_taxol-
ChainA_B.pdb, chain A (#3), sequence alignment score = 1210.4
RMSD between 403 pruned atom pairs is 0.768 angstroms; (across all 425 pairs:
1.381)
> hide #!1 models
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B.pdb models #3
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B.pdb
Chain information for tsa_taxol-ChainA_B.pdb #4
---
Chain | Description
A | No description available
B | No description available
> show #!1 models
> hide #!3 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #4/B to #1/K pairing ss
Parameters
---
Chain pairing | ss
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 TSA-GDP_Taxol_rough_model4.pdb, chain K (#1) with tsa_taxol-
ChainA_B.pdb, chain B (#4), sequence alignment score = 1178.9
RMSD between 404 pruned atom pairs is 0.746 angstroms; (across all 427 pairs:
1.293)
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2.pdb models #4
Drag select of 1728 residues, 2 pseudobonds, 318 atoms, 294 bonds
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb models
> #3-4 selectedOnly true
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb models
> #3-4 displayedOnly true
> select clear
> hide #!3 models
> show #!3 models
> show #!2 models
> fitmap #3 inMap #2
Fit molecule tsa_taxol-ChainA_B.pdb (#3) to map J80_006_volume_map_sharp.mrc
(#2) using 6853 atoms
average map value = 0.4493, steps = 68
shifted from previous position = 0.56
rotated from previous position = 1.51 degrees
atoms outside contour = 2369, contour level = 0.24857
Position of tsa_taxol-ChainA_B.pdb (#3) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.65229260 0.75790874 -0.00941886 -118.95146772
0.75795940 -0.65229207 0.00355105 266.47366841
-0.00345247 -0.00945543 -0.99994934 591.41337341
Axis -0.90892468 -0.41694531 0.00354031
Axis point -0.00000000 161.68365753 294.95134488
Rotation angle (degrees) 179.59005236
Shift along axis -0.89323612
> fitmap #4 inMap #2
Fit molecule tsa_taxol-ChainA_B.pdb (#4) to map J80_006_volume_map_sharp.mrc
(#2) using 6853 atoms
average map value = 0.4472, steps = 52
shifted from previous position = 0.409
rotated from previous position = 1.34 degrees
atoms outside contour = 2420, contour level = 0.24857
Position of tsa_taxol-ChainA_B.pdb (#4) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.90956641 -0.41538925 0.01186211 145.44717697
0.41555773 0.90925182 -0.02393536 -89.41106956
-0.00084316 0.02670019 0.99964313 -19.89879983
Axis 0.06081725 0.01526002 0.99803226
Axis point 278.33178372 291.36395367 0.00000000
Rotation angle (degrees) 24.60074685
Shift along axis -12.37836143
> close #1
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
> ui tool show "Change Chain IDs"
> hide #!2 models
Drag select of 950 residues, 1 pseudobonds
> show sel atoms
> select clear
> hide #!3 models
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2.pdb
Chain information for tsa_taxol-ChainA_B_2.pdb #1
---
Chain | Description
A | No description available
B | No description available
> show #!3 models
> ui tool show Matchmaker
> matchmaker #1/B to #3/B pairing ss
Parameters
---
Chain pairing | ss
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 tsa_taxol-ChainA_B.pdb, chain B (#3) with tsa_taxol-ChainA_B_2.pdb,
chain B (#1), sequence alignment score = 2269.3
RMSD between 429 pruned atom pairs is 0.001 angstroms; (across all 429 pairs:
0.001)
> hide #!3 models
> show #!2 models
> close #3
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2.pdb models #1
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select clear
> close #4
> ui tool show "Change Chain IDs"
> changechains A C
Chain IDs of 437 residues changed
> changechains B D
No residues specified
> changechains B D
No residues specified
> select #1/B:1-500
3340 atoms, 3415 bonds, 429 residues, 1 model selected
> changechains sel B D
Chain IDs of 429 residues changed
> select clear
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B.pdb
Chain information for tsa_taxol-ChainA_B.pdb #3
---
Chain | Description
A | No description available
B | No description available
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2.pdb models #1
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
Chain information for tsa_taxol-ChainA_B_2dimers.pdb
---
Chain | Description
4.1/A 4.2/A | No description available
4.1/B 4.2/B | No description available
> close #3
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> close #4.2
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> hide #4.1.1 models
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B.pdb models #4
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4 models
> show #!4 models
> hide #!4.1 models
> show #!4.1 models
> hide #!1 models
> show #!1 models
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B.pdb
Chain information for tsa_taxol-ChainA_B.pdb #3
---
Chain | Description
A | No description available
B | No description available
> hide #!4 models
> hide #!4.1 models
> close #4.1
> close #4
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
Chain information for tsa_taxol-ChainA_B_2dimers.pdb #4
---
Chain | Description
A C | No description available
B D | No description available
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!2 models
> fitmap #4 inMap #2
Fit molecule tsa_taxol-ChainA_B_2dimers.pdb (#4) to map
J80_006_volume_map_sharp.mrc (#2) using 13706 atoms
average map value = 0.4482, steps = 40
shifted from previous position = 0.00876
rotated from previous position = 0.0055 degrees
atoms outside contour = 4790, contour level = 0.24857
Position of tsa_taxol-ChainA_B_2dimers.pdb (#4) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00003451 0.00008795 -0.01722440
0.00003451 1.00000000 -0.00001741 -0.00222837
-0.00008795 0.00001741 1.00000000 0.00875175
Axis 0.18123629 0.91548755 0.35921574
Axis point 107.74094967 0.00000000 191.68795605
Rotation angle (degrees) 0.00550440
Shift along axis -0.00201797
> close #3
> close #1
> hide (#4#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #4#2.2#!2
> show (#4#2.2#!2 & ((protein&@ca)|(nucleic&@p))) target ab
> volume #2 step 1
> show atoms
> hide (#4#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #4#2.2#!2
> show (#4#2.2#!2 & backbone) target ab
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
Chain information for tsa_taxol-ChainA_B_2dimers.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
> close #4
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
Chain information for tsa_taxol-ChainA_B_2dimers.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
> open D:/TaxolManuscript/TaxolMTMap/TSA-GDP_Taxol_rough_model4.pdb
Chain information for TSA-GDP_Taxol_rough_model4.pdb #4
---
Chain | Description
A C I K | No description available
B F J N | No description available
> hide atoms
> show cartoons
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #3/A to #4/N pairing ss
Parameters
---
Chain pairing | ss
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 TSA-GDP_Taxol_rough_model4.pdb, chain N (#4) with tsa_taxol-
ChainA_B_2dimers.pdb, chain A (#3), sequence alignment score = 1222.5
RMSD between 409 pruned atom pairs is 0.757 angstroms; (across all 425 pairs:
1.187)
> show #!3 models
> hide #!1 models
> show #!1 models
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_3.pdb models #3
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #1/B to #4/I pairing ss
Parameters
---
Chain pairing | ss
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 TSA-GDP_Taxol_rough_model4.pdb, chain I (#4) with tsa_taxol-
ChainA_B_2dimers.pdb, chain B (#1), sequence alignment score = 1208.9
RMSD between 405 pruned atom pairs is 0.835 angstroms; (across all 427 pairs:
1.333)
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_4.pdb models #1
> hide #!1 models
> hide #!4 models
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-2PF.pdb
Chain information for tsa_taxol-2PF.pdb #5
---
Chain | Description
A C H I | No description available
B D F G | No description available
> hide #!5 atoms
> show #!5 cartoons
> show #!2 models
> close #4
> close #3
> close #1
> show atoms
> style stick
Changed 27412 atom styles
> color #2 #dfdfdf80 models
> color #2 #eaeaea80 models
> color #2 #f9f9f980 models
> fitmap #5 inMap #2
Fit molecule tsa_taxol-2PF.pdb (#5) to map J80_006_volume_map_sharp.mrc (#2)
using 27412 atoms
average map value = 0.3373, steps = 48
shifted from previous position = 0.114
rotated from previous position = 0.387 degrees
atoms outside contour = 11650, contour level = 0.24857
Position of tsa_taxol-2PF.pdb (#5) relative to J80_006_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.99998622 -0.00523751 -0.00034774 2.29216834
0.00523598 0.99997726 -0.00424943 0.11284188
0.00036999 0.00424755 0.99999091 -1.87188523
Axis 0.62913377 -0.05314209 0.77547831
Axis point -19.48492615 439.56063425 0.00000000
Rotation angle (degrees) 0.38691698
Shift along axis -0.01552254
> lighting shadows false
> hide (#5#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #5#2.2#!2
> show (#5#2.2#!2 & backbone) target ab
> hide (#5#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #5#2.2#!2
> show (#5#2.2#!2 & ((protein&@ca)|(nucleic&@p))) target ab
> size stickRadius 0.2
Changed 28056 bond radii
> size pseudobondRadius 0.2
Changed 3448 pseudobond radii
> size pseudobondRadius 0.25
Changed 3448 pseudobond radii
> hide #!2 models
> ui tool show "Color Actions"
> set bgColor white
> set bgColor #ffffff00
> select #5/B,D,G,F
13360 atoms, 13660 bonds, 1712 pseudobonds, 1716 residues, 2 models selected
> ui tool show "Color Actions"
> set bgColor turquoise
> set bgColor #40e0d000
> set bgColor white
> set bgColor #ffffff00
> color sel turquoise target acsp
> color sel cyan target acsp
> select clear
> select #5/B,D,G,F
13360 atoms, 13660 bonds, 1712 pseudobonds, 1716 residues, 2 models selected
> color sel medium aquamarine target acsp
> select clear
> show #!2 models
> ui tool show "Color Zone"
> select add #2
3 models selected
> select add #2
3 models selected
> select add #2
3 models selected
> select clear
> select add #5
27412 atoms, 28056 bonds, 3448 pseudobonds, 3472 residues, 3 models selected
> color zone #2 near #5 distance 4.98
> select clear
> hide #!2 models
> select #5/A,C
6846 atoms, 7002 bonds, 868 pseudobonds, 874 residues, 3 models selected
> ui tool show "Fit in Map"
> fitmap sel inMap #2
Fit molecule tsa_taxol-2PF.pdb (#5) to map J80_006_volume_map_sharp.mrc (#2)
using 6846 atoms
average map value = 0.3589, steps = 68
shifted from previous position = 0.679
rotated from previous position = 2.1 degrees
atoms outside contour = 2409, contour level = 0.24857
Position of tsa_taxol-2PF.pdb (#5) relative to J80_006_volume_map_sharp.mrc
(#2) coordinates:
Matrix rotation and translation
0.99913617 -0.04115036 0.00579365 15.74794318
0.04119690 0.99911774 -0.00815788 -8.11561059
-0.00545284 0.00838952 0.99994994 -1.35564968
Axis 0.19526577 0.13271299 0.97172966
Axis point 207.22162237 375.11285557 0.00000000
Rotation angle (degrees) 2.42843442
Shift along axis 0.68066231
> show #!2 models
> hide #!5 models
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_2dimers.pdb
> D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_3.pdb
> D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_4.pdb
Chain information for tsa_taxol-ChainA_B_2dimers.pdb #1
---
Chain | Description
A C | No description available
B D | No description available
Chain information for tsa_taxol-ChainA_B_3.pdb #3
---
Chain | Description
A C | No description available
B D | No description available
Chain information for tsa_taxol-ChainA_B_4.pdb #4
---
Chain | Description
A C | No description available
B D | No description available
> fitmap #4 inMap #2
Fit molecule tsa_taxol-ChainA_B_4.pdb (#4) to map J80_006_volume_map_sharp.mrc
(#2) using 13706 atoms
average map value = 0.245, steps = 56
shifted from previous position = 1.48
rotated from previous position = 2.06 degrees
atoms outside contour = 8122, contour level = 0.24857
Position of tsa_taxol-ChainA_B_4.pdb (#4) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99957520 0.02826312 0.00711404 -14.44397242
-0.02840680 0.99937627 0.02097903 -0.41623328
-0.00651667 -0.02117220 0.99975461 9.19990764
Axis -0.58599916 0.18949813 -0.78784227
Axis point -32.93135448 486.98038143 0.00000000
Rotation angle (degrees) 2.06110249
Shift along axis 1.13720412
> fitmap #3 inMap #2
Fit molecule tsa_taxol-ChainA_B_3.pdb (#3) to map J80_006_volume_map_sharp.mrc
(#2) using 13706 atoms
average map value = 0.2816, steps = 72
shifted from previous position = 1.09
rotated from previous position = 2.45 degrees
atoms outside contour = 7082, contour level = 0.24857
Position of tsa_taxol-ChainA_B_3.pdb (#3) relative to
J80_006_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99912879 -0.04124342 0.00637536 15.60773779
0.04129968 0.99910662 -0.00896125 -7.91208075
-0.00600008 0.00921674 0.99993952 -1.42703453
Axis 0.21280169 0.14487379 0.96629552
Axis point 202.37486674 370.04698555 0.00000000
Rotation angle (degrees) 2.44791066
Shift along axis 0.79616284
> volume #2 level 0.1436
> select add #5
27412 atoms, 28056 bonds, 3448 pseudobonds, 3472 residues, 3 models selected
> select subtract #5
Nothing selected
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_3.pdb models #3
> save D:/TaxolManuscript/TaxolMTMap/tsa_taxol-ChainA_B_4.pdb models #4
> close #5
> close #4
> close #3
> close #1
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-2PF.pdb
Chain information for tsa_taxol-2PF.pdb #1
---
Chain | Description
A C H I | No description available
B D F G | No description available
> hide atoms
> show cartoons
[Repeated 1 time(s)]
> volume #2 level 0.3793
> hide #!1 models
> show #!1 models
> hide (#1#2.2#!2 & (protein|nucleic)) target a
> cartoon hide #1#2.2#!2
> show (#1#2.2#!2 & ((protein&@ca)|(nucleic&@p))) target ab
> show atoms
> hide atoms
> style stick
Changed 27412 atom styles
> hide #!2 models
> hide #!1 models
> show #!1 models
> show atoms
> hide (#1 & (protein|nucleic)) target a
> cartoon hide #1
> show (#1 & ((protein&@ca)|(nucleic&@p))) target ab
> size pseudobondRadius 0.25
Changed 3448 pseudobond radii
> show #!2 models
> transparency #1#2.2#!2 50
> volume #2 level 0.2186
> hide #!2 models
> open D:/TaxolManuscript/TaxolMTMap/J80_006_volume_map_sharp2.mrc
Opened J80_006_volume_map_sharp2.mrc as #3, grid size 157,111,270, pixel
0.83,0.83,0.83, shown at level 0.625, step 1, values float32
> volume #3 level 0.2714
> volume #3 level 0.2017
> close #2
> select clear
> hide #!3 models
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> ui tool show "Fit in Map"
> show #!3 models
> fitmap sel inMap #3
Fit molecule tsa_taxol-2PF.pdb (#1) to map J80_006_volume_map_sharp2.mrc (#3)
using 248 atoms
average map value = 0.236, steps = 60
shifted from previous position = 0.32
rotated from previous position = 0.363 degrees
atoms outside contour = 122, contour level = 0.20171
Position of tsa_taxol-2PF.pdb (#1) relative to J80_006_volume_map_sharp2.mrc
(#3) coordinates:
Matrix rotation and translation
0.99998024 0.00606982 -0.00163401 -1.79342463
-0.00607120 0.99998121 -0.00084492 1.83639323
0.00162885 0.00085483 0.99999831 -0.59143603
Axis 0.13398399 -0.25719793 -0.95702535
Axis point 295.35870827 293.19158600 0.00000000
Rotation angle (degrees) 0.36343551
Shift along axis -0.14658745
> volume #3 level 0.2767
> ui tool show "Hide Dust"
> select clear
> transparency 50
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> color sel light gray
> select clear
> color byhetero
> hide #!3 models
> select #1/I,P
3535 atoms, 3621 bonds, 434 pseudobonds, 441 residues, 3 models selected
> select clear
> select #1/I,P: GDP
112 atoms, 120 bonds, 4 residues, 1 model selected
> color sel light gray
> select clear
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> color sel light gray
> select clear
> select #1/H,I: GTP
64 atoms, 68 bonds, 2 residues, 1 model selected
> select #1/H,C,A,I: GTP
128 atoms, 136 bonds, 4 residues, 1 model selected
> color sel light gray
> select clear
> select #1/B,D,G,F
13360 atoms, 13660 bonds, 1712 pseudobonds, 1716 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium aquamarine target acsp
> select clear
> show #!3 models
> select #1/B,D,G,F
13360 atoms, 13660 bonds, 1712 pseudobonds, 1716 residues, 2 models selected
> select clear
> hide #!1 models
> show #!1 models
> hide #!3 models
Drag select of 3948 atoms, 528 bonds, 3444 pseudobonds
> show #!3 models
> ui tool show "Color Zone"
> color zone #3 near #1 distance 4.98
> hide #!3 models
> select #1/H,C,A,I
13692 atoms, 14004 bonds, 1736 pseudobonds, 1748 residues, 3 models selected
> ui tool show "Color Actions"
> color sel pale green target acsp
> select clear
> color zone #3 near #1 distance 4.98
> show #!3 models
> select #1/H,C,A,I:GTP
128 atoms, 136 bonds, 4 residues, 1 model selected
> color sel pale green target acsp
> select #1/B,D,G,F:GDP
Nothing selected
> ui tool show "Color Actions"
> color pale turquoise target acsp
> hide #!3 models
> select #1/H,C,A,I
13692 atoms, 14004 bonds, 1736 pseudobonds, 1748 residues, 3 models selected
> ui tool show "Color Actions"
> color sel pale green target acsp
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> color sel light gray
> select clear
> color zone #3 near #1 distance 4.98
> show #!3 models
> transparency 50
> select clear
> ui tool show "Hide Dust"
> size stickRadius 0.3
Changed 28056 bond radii
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> color sel byhetero
> select clear
> surface dust #3 size 4.98
> save D:/TaxolManuscript/TaxolMTMap/Session1.cxs
> select #1/B,D,G,F:GDP
Nothing selected
> color light gray
> select #1/B,D,G,F:GDP
Nothing selected
> hide #!3 models
> show atoms
> select #1/B,D,G,F:GDP
Nothing selected
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> select #1/B,D,G,F:GDP
Nothing selected
> select #1/H,C,A,I:GTP
128 atoms, 136 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 128 atom styles
> style sel stick
Changed 128 atom styles
> color sel light gray
> color sel byhetero
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> size pseudobondRadius 0.3
Changed 3448 pseudobond radii
> hide #!3 models
> select #1/GDP
Nothing selected
> select #1/P:GDP
112 atoms, 120 bonds, 4 residues, 1 model selected
> color sel light gray
> color sel byhetero
> select clear
> show #!3 models
> select #1/P:GDP
112 atoms, 120 bonds, 4 residues, 1 model selected
> ui tool show "Color Zone"
> color zone #3 near sel distance 4.98
> undo
> hide #!3 models
> select #1/P:GDP
112 atoms, 120 bonds, 4 residues, 1 model selected
> select #1/P:GDP
112 atoms, 120 bonds, 4 residues, 1 model selected
> color sel light gray
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> color sel light gray
> select clear
> select #1/H,C,A,I:GTP
128 atoms, 136 bonds, 4 residues, 1 model selected
> color sel light gray
> color zone #3 near #1 distance 4.12
> show #!3 models
> volume #3 level 0.5178
> transparency sel 50
[Repeated 2 time(s)]
> select add #1
27412 atoms, 28056 bonds, 3448 pseudobonds, 3472 residues, 3 models selected
> select subtract #1
Nothing selected
> transparency 50
> volume #3 level 0.3249
> ui tool show "Color Zone"
> color zone #3 near #1 distance 4
> transparency 50
> select #1/H,C,A,I:GTP
128 atoms, 136 bonds, 4 residues, 1 model selected
> color sel byhetero
> select #1/E
248 atoms, 272 bonds, 4 residues, 1 model selected
> color sel byhetero
> select #1/P:GDP
112 atoms, 120 bonds, 4 residues, 1 model selected
> color sel byhetero
> select clear
> save D:/TaxolManuscript/TaxolMTMap/Session1.cxs
——— End of log from Tue Mar 25 12:07:53 2025 ———
opened ChimeraX session
> transparency 50
> size pseudobondRadius 0.3
Changed 3448 pseudobond radii
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #1 distance 4.98
> ui tool show "Hide Dust"
> surface dust #3 size 4.98
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/Session1.cxs
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/MapModel1.tif width
> 2000 height 1258 supersample 3
> graphics silhouettes true
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/MapModel1.tif width
> 2000 height 1258 supersample 3
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/Session1.cxs
——— End of log from Tue Mar 25 12:51:41 2025 ———
opened ChimeraX session
> select clear
[Repeated 1 time(s)]
> size pseudobondRadius 0.3
Changed 3448 pseudobond radii
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/MapModel1.tif width
> 3000 height 1836 supersample 3
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/MapModel1.tif width
> 3000 height 3265 supersample 3
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/Session1.cxs
——— End of log from Tue Mar 25 18:40:41 2025 ———
opened ChimeraX session
> hide #!3 models
> open D:/TaxolManuscript/TaxolMTMap/b3gdp.cif
> D:/TaxolManuscript/TaxolMTMap/tsagdp.cif
Summary of feedback from opening D:/TaxolManuscript/TaxolMTMap/b3gdp.cif
---
warnings | Unknown polymer entity '3' on line 26928
Missing or incomplete sequence information. Inferred polymer connectivity.
note | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
Summary of feedback from opening D:/TaxolManuscript/TaxolMTMap/tsagdp.cif
---
warnings | Unknown polymer entity '5' on line 26867
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for b3gdp.cif #2
---
Chain | Description
A B C D | No description available
E F G I | No description available
Chain information for tsagdp.cif #4
---
Chain | Description
A E G | No description available
B F | No description available
C | No description available
D H | No description available
> style stick
Changed 81728 atom styles
> hide (#1-2,4 & (protein|nucleic)) target a
> cartoon hide #1-2,4
> show (#1-2,4 & ((protein&@ca)|(nucleic&@p))) target ab
> close #3
> hide #!2 models
> hide #!4 models
> select #1/C,F,H,D
13526 atoms, 13832 bonds, 1724 pseudobonds, 1732 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
Drag select of 180 atoms, 196 bonds
> hide sel atoms
> select add #1
27412 atoms, 28056 bonds, 1726 pseudobonds, 3472 residues, 3 models selected
> select subtract #1
Nothing selected
> show #!2 models
> ui tool show "Side View"
> select #2/A,I,B,E
13547 atoms, 13857 bonds, 1718 pseudobonds, 1728 residues, 3 models selected
> hide sel atoms
Drag select of 5 atoms
> hide sel atoms
> show #!4 models
> hide #!4 models
> show #!4 models
> select add #2
27102 atoms, 27707 bonds, 1720 pseudobonds, 3471 residues, 3 models selected
> select subtract #2
Nothing selected
> select #3/A,B,C,D
Nothing selected
> select #3/A,B,C,D
Nothing selected
> select #4/A,B,C,D
13513 atoms, 13823 bonds, 1718 pseudobonds, 1728 residues, 3 models selected
> hide sel atoms
Drag select of 97 atoms
> select clear
Drag select of 110 atoms
> hide sel atoms
> select add #2
27211 atoms, 27707 bonds, 1720 pseudobonds, 3580 residues, 4 models selected
> select add #4
54316 atoms, 55331 bonds, 3439 pseudobonds, 7136 residues, 6 models selected
> select subtract #4
27102 atoms, 27707 bonds, 1720 pseudobonds, 3471 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!4 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> open D:/TaxolManuscript/TaxolMTMap/tsa_taxol-2PF-2.pdb
Chain information for tsa_taxol-2PF-2.pdb #3
---
Chain | Description
A C H I L M | No description available
B D F G J K | No description available
> show #!1,3 atoms
> style #!1,3 stick
Changed 68530 atom styles
> hide (#1,3 & (protein|nucleic)) target a
> cartoon hide #1,3
> show (#1,3 & ((protein&@ca)|(nucleic&@p))) target ab
> hide #!1 models
> select #1/C,F,H,D,L
13526 atoms, 13832 bonds, 1724 pseudobonds, 1732 residues, 3 models selected
> select add #1
27412 atoms, 28056 bonds, 3448 pseudobonds, 3472 residues, 3 models selected
> select subtract #1
Nothing selected
> select #3/C,F,H,D,L
16949 atoms, 17333 bonds, 2158 pseudobonds, 2169 residues, 3 models selected
> hide sel atoms
> select #3/C,F,H,K,L
16949 atoms, 17333 bonds, 431 pseudobonds, 2169 residues, 3 models selected
> hide sel atoms
Drag select of 270 atoms, 294 bonds
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> select add #3
41118 atoms, 42084 bonds, 2589 pseudobonds, 5208 residues, 3 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #2/C to #3/M pairing ss
Parameters
---
Chain pairing | ss
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 tsa_taxol-2PF-2.pdb, chain M (#3) with b3gdp.cif, chain C (#2),
sequence alignment score = 2167.7
RMSD between 427 pruned atom pairs is 0.655 angstroms; (across all 431 pairs:
0.727)
> show #!1 models
> hide #!2 models
> hide #!3 models
> show #!2 models
> show #!3 models
> hide #!1 models
> select #3/A
3423 atoms, 3501 bonds, 434 pseudobonds, 437 residues, 3 models selected
> hide sel atoms
> show #!4 models
> hide #!3 models
> hide #!2 models
> select add #3
41118 atoms, 42084 bonds, 2156 pseudobonds, 5208 residues, 3 models selected
> select subtract #3
Nothing selected
> show #!3 models
> select add #3
41118 atoms, 42084 bonds, 2156 pseudobonds, 5208 residues, 3 models selected
> select subtract #3
Nothing selected
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #4/H to #3/M pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsa_taxol-2PF-2.pdb, chain M (#3) with tsagdp.cif, chain H (#4),
sequence alignment score = 1232
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol-2PF-2.pdb #3/M,
tsagdp.cif #4/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 399 pruned atom pairs is 0.812 angstroms; (across all 426 pairs:
1.375)
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #4/H to #3/M pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsa_taxol-2PF-2.pdb, chain M (#3) with tsagdp.cif, chain H (#4),
sequence alignment score = 1232
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol-2PF-2.pdb #3/M,
tsagdp.cif #4/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 399 pruned atom pairs is 0.812 angstroms; (across all 426 pairs:
1.375)
> show #!4 models
> hide #!4 models
> select #3/A
3423 atoms, 3501 bonds, 1 pseudobond, 437 residues, 2 models selected
> show sel atoms
> hide (#!3 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!3 & sel-residues)
> show (#!3 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> show #!4 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #4/H to #3/B pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsa_taxol-2PF-2.pdb, chain B (#3) with tsagdp.cif, chain H (#4),
sequence alignment score = 1860.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol-2PF-2.pdb #3/B,
tsagdp.cif #4/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 428 pruned atom pairs is 0.553 angstroms; (across all 429 pairs:
0.574)
> show #!3 models
> select #3/M
3423 atoms, 3501 bonds, 434 pseudobonds, 437 residues, 3 models selected
> hide sel atoms
> select add #3
41118 atoms, 42084 bonds, 2156 pseudobonds, 5208 residues, 3 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #2/C to #4/H pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsagdp.cif, chain H (#4) with b3gdp.cif, chain C (#2), sequence
alignment score = 1239.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: b3gdp.cif #2/C, tsagdp.cif
#4/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 396 pruned atom pairs is 0.801 angstroms; (across all 422 pairs:
1.682)
> show #!2 models
> show #!3 models
> save D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise.cxs
——— End of log from Tue Mar 25 20:52:17 2025 ———
opened ChimeraX session
> close #1
> hide #!3 models
> hide #!4 models
> close
> open
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
53 messages similar to the above omitted
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 GLN D 43 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
245 messages similar to the above omitted
PDB SEQRES record for chain H is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for tsa_taxol_ChainB.pdb #1
---
Chain | Description
B | No description available
J | No description available
Chain information for tsaGDP-ChainH.pdb #2
---
Chain | Description
H | No description available
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> ui tool show "Side View"
> ui tool show Matchmaker
> matchmaker #1/B to #2/H pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsaGDP-ChainH.pdb, chain H (#2) with tsa_taxol_ChainB.pdb, chain B
(#1), sequence alignment score = 8374.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 1656 pruned atom pairs is 1.086 angstroms; (across all 1718
pairs: 1.165)
> select #1/B:1-500
3340 atoms, 3415 bonds, 428 pseudobonds, 429 residues, 2 models selected
> select #1/B:1-500, #2/H:1-500
Expected an objects specifier or a keyword
> select #1/B:1-500, select #2/H:1-500
6678 atoms, 6828 bonds, 857 pseudobonds, 859 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #2/H & sel to #1/B & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H
(#2), sequence alignment score = 1860.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs:
0.574)
> close #1-2
> open
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
53 messages similar to the above omitted
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDP-ChainH.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 GLN D 43 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
245 messages similar to the above omitted
PDB SEQRES record for chain H is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for tsa_taxol_ChainB.pdb #1
---
Chain | Description
B | No description available
J | No description available
Chain information for tsaGDP-ChainH.pdb #2
---
Chain | Description
H | No description available
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> select #1/B:1-500, select #2/H:1-500
6673 atoms, 6823 bonds, 856 pseudobonds, 858 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #2/H & sel to #1/B & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H
(#2), sequence alignment score = 1860.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs:
0.574)
> close #1
> open
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
53 messages similar to the above omitted
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for tsa_taxol_ChainB.pdb #1
---
Chain | Description
B | No description available
J | No description available
> hide (#!2 & sel-residues & (protein|nucleic)) target a
> cartoon hide (#!2 & sel-residues)
> show (#!2 & sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select clear
> hide (protein|nucleic) target a
> cartoon hide
> show ((protein&@ca)|(nucleic&@p)) target ab
> select #1/B:1-500, select #2/H:1-500
6673 atoms, 6823 bonds, 856 pseudobonds, 858 residues, 4 models selected
> ui tool show Matchmaker
> matchmaker #2/H & sel to #1/B & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 tsa_taxol_ChainB.pdb, chain B (#1) with tsaGDP-ChainH.pdb, chain H
(#2), sequence alignment score = 1860.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 428 pruned atom pairs is 0.554 angstroms; (across all 429 pairs:
0.574)
> select #1/B:1501
32 atoms, 34 bonds, 1 residue, 1 model selected
> select #1/B:1501 #2/H:2001
37 atoms, 38 bonds, 2 residues, 2 models selected
MatchMaker Alignment [ID: 1] region tsa_taxol_ChainB.pdb, chain B..tsaGDP-
ChainH.pdb, chain H [860] RMSD: 22.198
> select #1/B:1501
32 atoms, 34 bonds, 1 residue, 1 model selected
> select #1/B:1501
32 atoms, 34 bonds, 1 residue, 1 model selected
> sequence align 1 program clustalOmega
Alignment identifier is 2
Associated tsaGDP-ChainH.pdb chain H to tsaGDP-ChainH.pdb, chain H with 0
mismatches
Associated tsa_taxol_ChainB.pdb chain B to tsa_taxol_ChainB.pdb, chain B with
0 mismatches
Associated tsa_taxol_ChainB.pdb chain J to tsaGDP-ChainH.pdb, chain H with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Webservices job id: M6CYALN3YUZWKJPA
> sequence align 1 program muscle replace true
Webservices job id: 5BVBW795IK3IVBOU
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!1 target csab palette
> 0.0502306,blue:0.0502306,white:7.88071,red
16808 atoms, 2151 residues, atom seq_rmsd range 0.0502 to 58
> color #2 #e4ebe6ff
> color #2 #d3dad6ff
> size pseudobondRadius 0.2
Changed 3861 pseudobond radii
> save
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDPvsTaxol.cxs
> size pseudobondRadius 0.3
Changed 3861 pseudobond radii
> color #1 #ced2cbff
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!1 target csab palette
> 0.0502306,blue:0.0502306,white:8,red
16808 atoms, 2151 residues, atom seq_rmsd range 0.0502 to 58
> save
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsaGDPvsTaxol.cxs
> hide #!1 models
> hide #!2 models
> select add #1
16808 atoms, 17189 bonds, 2146 pseudobonds, 2151 residues, 4 models selected
> select subtract #1
Nothing selected
> open D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/b3gdp-
> ChainC.pdb
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB-
> for_b3.pdb
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/b3gdp-ChainC.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY E 10 HIS E 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP E 41 GLN E 43 1
3
Start residue of secondary structure not found: HELIX 3 3 ILE E 47 VAL E 49 1
3
Start residue of secondary structure not found: HELIX 4 4 GLY E 71 SER E 78 1
8
Start residue of secondary structure not found: HELIX 5 5 GLY E 82 LEU E 84 1
3
249 messages similar to the above omitted
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainB-
for_b3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
53 messages similar to the above omitted
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for b3gdp-ChainC.pdb #3
---
Chain | Description
C | No description available
Chain information for tsa_taxol_ChainB-for_b3.pdb #4
---
Chain | Description
B | No description available
J | No description available
Associated tsa_taxol_ChainB-for_b3.pdb chain B to tsa_taxol_ChainB.pdb, chain
B with 0 mismatches
Associated tsa_taxol_ChainB-for_b3.pdb chain J to tsaGDP-ChainH.pdb, chain H
with 0 mismatches
Chains used in RMSD evaluation for alignment 1: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H, tsa_taxol_ChainB-for_b3.pdb #4/B
> hide (#3-4 & (protein|nucleic)) target a
> cartoon hide #3-4
> show (#3-4 & ((protein&@ca)|(nucleic&@p))) target ab
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #4
Chains used in RMSD evaluation for alignment 1: tsa_taxol_ChainB.pdb #1/B,
tsaGDP-ChainH.pdb #2/H
> show #!3 models
> open
> D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainM-
> for_b3.pdb
Summary of feedback from opening
D:/TaxolManuscript/TaxolMTMap/StructuralFigure1/DimerRise/tsa_taxol_ChainM-
for_b3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY D 10 HIS D 28 1 19
Start residue of secondary structure not found: HELIX 2 2 ASP D 41 ASP D 45 1
5
Start residue of secondary structure not found: HELIX 3 3 ILE D 47 VAL D 49 1
3
Start residue of secondary structure not found: HELIX 4 4 THR D 55 GLY D 57 1
3
Start residue of secondary structure not found: HELIX 5 5 GLY D 71 SER D 78 1
8
53 messages similar to the above omitted
Chain information for tsa_taxol_ChainM-for_b3.pdb #4
---
Chain | Description
M | No description available
> hide (#3-4 & (protein|nucleic)) target a
> cartoon hide #3-4
> show (#3-4 & ((protein&@ca)|(nucleic&@p))) target ab
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> select #3/C:1-500, select #4/M:1-500
6754 atoms, 6908 bonds, 864 pseudobonds, 866 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #4/M & sel to #3/C & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 b3gdp-ChainC.pdb, chain C (#3) with tsa_taxol_ChainM-for_b3.pdb,
chain M (#4), sequence alignment score = 2167.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: b3gdp-ChainC.pdb #3/C,
tsa_taxol_ChainM-for_b3.pdb #4/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 427 pruned atom pairs is 0.655 angstroms; (across all 431 pairs:
0.727)
> sequence align 2 program muscle
Alignment identifier is 3
Associated tsa_taxol_ChainB.pdb chain J to tsa_taxol_ChainM-for_b3.pdb, chain
M with 0 mismatches
Associated b3gdp-ChainC.pdb chain C to b3gdp-ChainC.pdb, chain C with 0
mismatches
Associated tsa_taxol_ChainM-for_b3.pdb chain M to tsa_taxol_ChainM-for_b3.pdb,
chain M with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Webservices job id: 74ASA3SJD6IHQIC5
> select #3/C:3346 #4/M:3346
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/C:3346 #4/M:3346
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/C:3346 #4/M:3346
14 atoms, 14 bonds, 2 residues, 2 models selected
> select #3/C:1-500, select #4/M:1-500
6754 atoms, 6908 bonds, 864 pseudobonds, 866 residues, 6 models selected
> ui tool show Matchmaker
> matchmaker #4/M & sel to #3/C & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 b3gdp-ChainC.pdb, chain C (#3) with tsa_taxol_ChainM-for_b3.pdb,
chain M (#4), sequence alignment score = 2167.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: b3gdp-ChainC.pdb #3/C,
tsa_taxol_ChainM-for_b3.pdb #4/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 427 pruned atom pairs is 0.655 angstroms; (across all 431 pairs:
0.727)
> sequence align 2 program muscle
Alignment identifier is 3
Associated tsa_taxol_ChainB.pdb chain J to tsa_taxol_ChainM-for_b3.pdb, chain
M with 0 mismatches
Associated b3gdp-ChainC.pdb chain C to b3gdp-ChainC.pdb, chain C with 0
mismatches
Associated tsa_taxol_ChainM-for_b3.pdb chain M to tsa_taxol_ChainM-for_b3.pdb,
chain M with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Webservices job id: FD5NJOW2QUUGKUHB
> sequence align 2 program muscle replace true
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 550, in <lambda>
unparse=StringArg.unparse, cmd_text=cmd_text: run(self.session,
^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 370, in seqalign_align
seq_source._set_realigned(realigned)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 905, in _set_realigned
self._notify_observers(self.NOTE_REALIGNMENT, prev_seqs)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 482, in alignment_notification
self.seq_canvas.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1063, in
alignment_notification
self._reformat()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat
self.lead_block = SeqBlock(label_scene, self.main_scene,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[Previous line repeated 112 more times]
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__
self.layout_lines(headers, self.header_label_color)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines
self._layout_line(line, label_color, bli, end)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line
item = self.make_item(line, self.seq_offset + i, xs[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item
info = line.depiction_val(offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
See log for complete Python traceback.
Webservices job id: 2ZENAY298LXHYCH5
QGraphicsScene::removeItem: item 0x23f5c33efa0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33f000's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33f540's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f8c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fc20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fa60's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f7a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33ef20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33ef40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33efc0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33efe0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33f020's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fd20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fb40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fea0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f8e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f8a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fe40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f880's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fa40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fec0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f7c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fd80's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f900's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fcc0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f960's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fb00's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fc40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f9a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f7e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f9e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fe20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fe60's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fa00's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fbe0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fba0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fc00's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fd40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ff80's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3304a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330580's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3306c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330360's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ff60's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330500's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3305c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3305e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ffa0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330640's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330540's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3303c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ffc0's scene (0x0) is different from
this scene (0x23f7e538490)
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 252, in _actually_resize
self._reformat()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat
self.lead_block = SeqBlock(label_scene, self.main_scene,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[Previous line repeated 54 more times]
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__
self.layout_lines(headers, self.header_label_color)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines
self._layout_line(line, label_color, bli, end)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line
item = self.make_item(line, self.seq_offset + i, xs[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item
info = line.depiction_val(offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
See log for complete Python traceback.
QGraphicsScene::removeItem: item 0x23f5c33efa0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33f000's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33f540's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f8c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fc20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fa60's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f7a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33ef20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33ef40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33efc0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33efe0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c33f020's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fd20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fb40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fea0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f8e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f8a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fe40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f880's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fa40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fec0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f7c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fd80's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f900's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fcc0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f960's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fb00's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fc40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f9a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f7e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32f9e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fe20's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fe60's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fa00's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fbe0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fba0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fc00's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32fd40's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ff80's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3304a0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330580's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3306c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330360's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ff60's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330500's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3305c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3305e0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ffa0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330640's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c330540's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c3303c0's scene (0x0) is different from
this scene (0x23f7e538490)
QGraphicsScene::removeItem: item 0x23f5c32ffc0's scene (0x0) is different from
this scene (0x23f7e538490)
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 252, in _actually_resize
self._reformat()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat
self.lead_block = SeqBlock(label_scene, self.main_scene,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[Previous line repeated 35 more times]
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__
self.layout_lines(headers, self.header_label_color)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines
self._layout_line(line, label_color, bli, end)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line
item = self.make_item(line, self.seq_offset + i, xs[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item
info = line.depiction_val(offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
See log for complete Python traceback.
> ui tool show Matchmaker
> matchmaker #4/M & sel to #3/C & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
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 b3gdp-ChainC.pdb, chain C (#3) with tsa_taxol_ChainM-for_b3.pdb,
chain M (#4), sequence alignment score = 2167.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: b3gdp-ChainC.pdb #3/C,
tsa_taxol_ChainM-for_b3.pdb #4/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 427 pruned atom pairs is 0.655 angstroms; (across all 431 pairs:
0.727)
> select #3/C:3422 #4/M:3417
20 atoms, 19 bonds, 2 residues, 2 models selected
> sequence align 2 program muscle replace true
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 550, in <lambda>
unparse=StringArg.unparse, cmd_text=cmd_text: run(self.session,
^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\cmd.py", line 370, in seqalign_align
seq_source._set_realigned(realigned)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 905, in _set_realigned
self._notify_observers(self.NOTE_REALIGNMENT, prev_seqs)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seqalign\alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\tool.py", line 482, in alignment_notification
self.seq_canvas.alignment_notification(note_name, note_data)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1063, in
alignment_notification
self._reformat()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1027, in _reformat
self.lead_block = SeqBlock(label_scene, self.main_scene,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1651, in __init__
self.next_block = SeqBlock(label_scene, main_scene, self, self.font,
self.emphasis_font,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[Previous line repeated 112 more times]
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1645, in __init__
self.layout_lines(headers, self.header_label_color)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2342, in layout_lines
self._layout_line(line, label_color, bli, end)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2319, in _layout_line
item = self.make_item(line, self.seq_offset + i, xs[i],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 2400, in make_item
info = line.depiction_val(offset)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
IndexError: list index out of range
IndexError: list index out of range
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\alignment_headers\rmsd.py", line 70, in depiction_val
val = self[pos]
~~~~^^^^^
See log for complete Python traceback.
Webservices job id: 1TT6JXE0AEW99I2K
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_rmsd #!4 target csab palette
> 0.0940649,blue:0.0940649,white:18.4029,red
13526 atoms, 1732 residues, atom seq_rmsd range 0.0941 to 66.3
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select add #4
13538 atoms, 13844 bonds, 1731 pseudobonds, 1733 residues, 5 models selected
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 1775, in _sel_change_cb
self.show_chimerax_selection()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 1197, in
show_chimerax_selection
sel_region.add_blocks(blocks)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 90, in add_blocks
for x1, y1, x2, y2 in self.seq_canvas.bbox_list(cover_gaps=self.cover_gaps,
*block):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 444, in bbox_list
return self.lead_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)
^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'bbox_list'
Error processing trigger "selection changed":
AttributeError: 'NoneType' object has no attribute 'bbox_list'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1769, in bbox_list
return self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)
^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select add #3
27066 atoms, 27682 bonds, 3451 pseudobonds, 3460 residues, 8 models selected
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
AttributeError: 'SeqBlock' object has no attribute 'next_block'
Error processing trigger "changes done":
AttributeError: 'SeqBlock' object has no attribute 'next_block'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1895, in update_swatches
block = block.next_block
^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 1775, in _sel_change_cb
self.show_chimerax_selection()
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 1197, in
show_chimerax_selection
sel_region.add_blocks(blocks)
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\region_browser.py", line 90, in add_blocks
for x1, y1, x2, y2 in self.seq_canvas.bbox_list(cover_gaps=self.cover_gaps,
*block):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 444, in bbox_list
return self.lead_block.bbox_list(line1, line2, pos1, pos2, cover_gaps)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1796, in bbox_list
bboxes.extend(self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps))
^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'bbox_list'
Error processing trigger "selection changed":
AttributeError: 'NoneType' object has no attribute 'bbox_list'
File "C:\Users\mahalingank2\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\seq_view\seq_canvas.py", line 1796, in bbox_list
bboxes.extend(self.next_block.bbox_list(line1, line2, pos1, pos2, cover_gaps))
^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 27.20.100.9126
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Dell Inc.
Model: Precision 3540
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,985,317,376
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Sequence |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → RMSD header index error when realigning |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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