Docked sequence viewer panels made main window 16000 pixels high

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number__1.zip

Unrecognized file suffix '.zip'  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_1/number__1/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 1 [more info...]  
  
Chain information for model.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_2/number__2/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #2  
---  
Chain | Description  
A C D | No description available  
B | No description available  
  

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_3/number__3/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 3 [more info...]  
  
Chain information for model.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  

> hide #2 models

> show #2 models

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_4/number__4/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 4 [more info...]  
  
Chain information for model.pdb #4  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_5/number__5/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 5 [more info...]  
  
Chain information for model.pdb #5  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_6/number__6/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 6 [more info...]  
  
Chain information for model.pdb #6  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_7/number__7/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 7 [more info...]  
  
Chain information for model.pdb #7  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_8/number__8/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for model.pdb #8  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_9/number__9/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 9 [more info...]  
  
Chain information for model.pdb #9  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_10/number__10/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 10 [more info...]  
  
Chain information for model.pdb #10  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_11/number__11/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 11 [more info...]  
  
Chain information for model.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_12/number__12/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 12 [more info...]  
  
Chain information for model.pdb #12  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_13/number__13/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 13 [more info...]  
  
Chain information for model.pdb #13  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_14/number__14/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 14 [more info...]  
  
Chain information for model.pdb #14  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_15/number__15/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 15 [more info...]  
  
Chain information for model.pdb #15  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_16/number__16/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 16 [more info...]  
  
Chain information for model.pdb #16  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_17/number_17/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number #17 [more info...]  
  
Chain information for model.pdb #17  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_18/number__18/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) model # 18 [more info...]  
  
Chain information for model.pdb #18  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_19/number__19/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 19 [more info...]  
  
Chain information for model.pdb #19  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/1_20_mode/number_20/number__20/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 20 [more info...]  
  
Chain information for model.pdb #20  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_21/number__21/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 21 [more info...]  
  
Chain information for model.pdb #21  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_22/number__22/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 22 [more info...]  
  
Chain information for model.pdb #22  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_23/number__23/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 23 [more info...]  
  
Chain information for model.pdb #23  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_24/number__24/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 24 [more info...]  
  
Chain information for model.pdb #24  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_25/number__25/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 25 [more info...]  
  
Chain information for model.pdb #25  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_26/number__26/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 26 [more info...]  
  
Chain information for model.pdb #26  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_27/number__27/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 27 [more info...]  
  
Chain information for model.pdb #27  
---  
Chain | Description  
A C | No description available  
B D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_28/number__28/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 28 [more info...]  
  
Chain information for model.pdb #28  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_29/number__29/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 29 [more info...]  
  
Chain information for model.pdb #29  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_30/number__30/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 30 [more info...]  
  
Chain information for model.pdb #30  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_31/number__31/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 31 [more info...]  
  
Chain information for model.pdb #31  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_32/number__32/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 32 [more info...]  
  
Chain information for model.pdb #32  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_33/number__33/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 33 [more info...]  
  
Chain information for model.pdb #33  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_34/number__34/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 34 [more info...]  
  
Chain information for model.pdb #34  
---  
Chain | Description  
A B C D | No description available  
  

> open
> /Users/naeymaislam/Desktop/Projects/Bile_Acid_conjugation/SWISS_MODEL/21_35_model/number_35/number__35/models/01/model.pdb

model.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) number # 35 [more info...]  
  
Chain information for model.pdb #35  
---  
Chain | Description  
A B C D | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-35 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 model.pdb, chain D (#1) with model.pdb, chain C (#2), sequence
alignment score = 441.1  
RMSD between 173 pruned atom pairs is 1.061 angstroms; (across all 285 pairs:
7.262)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#3), sequence
alignment score = 711.3  
RMSD between 230 pruned atom pairs is 0.909 angstroms; (across all 308 pairs:
2.534)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain B (#4), sequence
alignment score = 660.9  
RMSD between 222 pruned atom pairs is 1.025 angstroms; (across all 299 pairs:
2.645)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain D (#5), sequence
alignment score = 1431.6  
RMSD between 310 pruned atom pairs is 0.268 angstroms; (across all 314 pairs:
0.478)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#6), sequence
alignment score = 1007.5  
RMSD between 298 pruned atom pairs is 0.325 angstroms; (across all 313 pairs:
1.126)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#7), sequence
alignment score = 659.4  
RMSD between 226 pruned atom pairs is 0.877 angstroms; (across all 306 pairs:
2.755)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#8), sequence
alignment score = 1080.5  
RMSD between 308 pruned atom pairs is 0.322 angstroms; (across all 313 pairs:
0.858)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#9), sequence
alignment score = 1064.7  
RMSD between 296 pruned atom pairs is 0.302 angstroms; (across all 311 pairs:
0.912)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain D (#10), sequence
alignment score = 667.9  
RMSD between 280 pruned atom pairs is 0.366 angstroms; (across all 306 pairs:
1.830)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain C (#11), sequence
alignment score = 447.5  
RMSD between 183 pruned atom pairs is 1.059 angstroms; (across all 282 pairs:
3.752)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain A (#12), sequence
alignment score = 632.5  
RMSD between 171 pruned atom pairs is 0.891 angstroms; (across all 195 pairs:
1.642)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain D (#13), sequence
alignment score = 348.7  
RMSD between 184 pruned atom pairs is 0.324 angstroms; (across all 252 pairs:
4.420)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#14), sequence
alignment score = 1396.9  
RMSD between 309 pruned atom pairs is 0.274 angstroms; (across all 314 pairs:
0.501)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#15), sequence
alignment score = 1059.5  
RMSD between 306 pruned atom pairs is 0.317 angstroms; (across all 313 pairs:
0.614)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#16), sequence
alignment score = 693.8  
RMSD between 228 pruned atom pairs is 0.888 angstroms; (across all 308 pairs:
2.543)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain D (#17), sequence
alignment score = 613.2  
RMSD between 289 pruned atom pairs is 0.244 angstroms; (across all 309 pairs:
1.716)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain B (#18), sequence
alignment score = 709.8  
RMSD between 231 pruned atom pairs is 1.029 angstroms; (across all 311 pairs:
2.623)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#19), sequence
alignment score = 711.3  
RMSD between 230 pruned atom pairs is 0.909 angstroms; (across all 308 pairs:
2.534)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#20), sequence
alignment score = 1295.7  
RMSD between 310 pruned atom pairs is 0.301 angstroms; (across all 312 pairs:
0.364)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain C (#21), sequence
alignment score = 574  
RMSD between 265 pruned atom pairs is 0.335 angstroms; (across all 305 pairs:
2.051)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#22), sequence
alignment score = 656.8  
RMSD between 266 pruned atom pairs is 0.793 angstroms; (across all 300 pairs:
2.339)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#23), sequence
alignment score = 684.7  
RMSD between 225 pruned atom pairs is 0.871 angstroms; (across all 308 pairs:
2.541)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#24), sequence
alignment score = 816.9  
RMSD between 304 pruned atom pairs is 0.268 angstroms; (across all 312 pairs:
0.606)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#25), sequence
alignment score = 1396.9  
RMSD between 309 pruned atom pairs is 0.274 angstroms; (across all 314 pairs:
0.501)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#26), sequence
alignment score = 1065.8  
RMSD between 298 pruned atom pairs is 0.338 angstroms; (across all 309 pairs:
0.894)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#27), sequence
alignment score = 689  
RMSD between 246 pruned atom pairs is 0.935 angstroms; (across all 310 pairs:
2.509)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain D (#28), sequence
alignment score = 631.9  
RMSD between 274 pruned atom pairs is 0.365 angstroms; (across all 306 pairs:
1.910)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain C (#29), sequence
alignment score = 1005.3  
RMSD between 229 pruned atom pairs is 0.199 angstroms; (across all 230 pairs:
0.254)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#30), sequence
alignment score = 1073.5  
RMSD between 306 pruned atom pairs is 0.308 angstroms; (across all 313 pairs:
0.595)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain B (#31), sequence
alignment score = 333  
RMSD between 150 pruned atom pairs is 0.897 angstroms; (across all 249 pairs:
5.669)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#32), sequence
alignment score = 593  
RMSD between 185 pruned atom pairs is 0.853 angstroms; (across all 271 pairs:
3.876)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#33), sequence
alignment score = 694.5  
RMSD between 228 pruned atom pairs is 0.888 angstroms; (across all 308 pairs:
2.544)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain B (#34), sequence
alignment score = 333  
RMSD between 150 pruned atom pairs is 0.897 angstroms; (across all 249 pairs:
5.669)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#35), sequence
alignment score = 1073.5  
RMSD between 306 pruned atom pairs is 0.308 angstroms; (across all 313 pairs:
0.595)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #8/A #8/B #8/C #8/D

Alignment identifier is 1  

> ui tool show "Modeller Comparative"

<QNSWindow: 0x7fe1010ef1e0; contentView=<QNSView: 0x7fe1010eef20;
QCocoaWindow(0x60000c0837b0, window=QWidgetWindow(0x600001181200,
name="AlignSeqMenuButtonClassWindow"))>> has active key-value observers (KVO)!
These will stop working now that the window is recreated, and will result in
exceptions when the observers are removed. Break in
QCocoaWindow::recreateWindowIfNeeded to debug.  

> ui tool show Matchmaker

> matchmaker #2-35 to #1 showAlignment true

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 model.pdb, chain D (#1) with model.pdb, chain C (#2), sequence
alignment score = 441.1  
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: model.pdb #1/D, model.pdb #2/C  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 173 pruned atom pairs is 1.061 angstroms; (across all 285 pairs:
7.262)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#3), sequence
alignment score = 711.3  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3: model.pdb #1/A, model.pdb #3/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 230 pruned atom pairs is 0.909 angstroms; (across all 308 pairs:
2.534)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain B (#4), sequence
alignment score = 660.9  
Alignment identifier is 4  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4  
Hiding conservation header for alignment 4  
Chains used in RMSD evaluation for alignment 4: model.pdb #1/B, model.pdb #4/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4  
RMSD between 222 pruned atom pairs is 1.025 angstroms; (across all 299 pairs:
2.645)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain D (#5), sequence
alignment score = 1431.6  
Alignment identifier is 5  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5  
Hiding conservation header for alignment 5  
Chains used in RMSD evaluation for alignment 5: model.pdb #1/A, model.pdb #5/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5  
RMSD between 310 pruned atom pairs is 0.268 angstroms; (across all 314 pairs:
0.478)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#6), sequence
alignment score = 1007.5  
Alignment identifier is 6  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6  
Hiding conservation header for alignment 6  
Chains used in RMSD evaluation for alignment 6: model.pdb #1/B, model.pdb #6/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6  
RMSD between 298 pruned atom pairs is 0.325 angstroms; (across all 313 pairs:
1.126)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#7), sequence
alignment score = 659.4  
Alignment identifier is 7  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7  
Hiding conservation header for alignment 7  
Chains used in RMSD evaluation for alignment 7: model.pdb #1/A, model.pdb #7/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7  
RMSD between 226 pruned atom pairs is 0.877 angstroms; (across all 306 pairs:
2.755)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#8), sequence
alignment score = 1080.5  
Alignment identifier is 8  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 8  
Hiding conservation header for alignment 8  
Chains used in RMSD evaluation for alignment 8: model.pdb #1/A, model.pdb #8/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 8  
RMSD between 308 pruned atom pairs is 0.322 angstroms; (across all 313 pairs:
0.858)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#9), sequence
alignment score = 1064.7  
Alignment identifier is 9  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 9  
Hiding conservation header for alignment 9  
Chains used in RMSD evaluation for alignment 9: model.pdb #1/A, model.pdb #9/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 9  
RMSD between 296 pruned atom pairs is 0.302 angstroms; (across all 311 pairs:
0.912)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain D (#10), sequence
alignment score = 667.9  
Alignment identifier is 10  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 10  
Hiding conservation header for alignment 10  
Chains used in RMSD evaluation for alignment 10: model.pdb #1/B, model.pdb
#10/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 10  
RMSD between 280 pruned atom pairs is 0.366 angstroms; (across all 306 pairs:
1.830)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain C (#11), sequence
alignment score = 447.5  
Alignment identifier is 11  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 11  
Hiding conservation header for alignment 11  
Chains used in RMSD evaluation for alignment 11: model.pdb #1/D, model.pdb
#11/C  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 11  
RMSD between 183 pruned atom pairs is 1.059 angstroms; (across all 282 pairs:
3.752)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain A (#12), sequence
alignment score = 632.5  
Alignment identifier is 12  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 12  
Hiding conservation header for alignment 12  
Chains used in RMSD evaluation for alignment 12: model.pdb #1/D, model.pdb
#12/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 12  
RMSD between 171 pruned atom pairs is 0.891 angstroms; (across all 195 pairs:
1.642)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain D (#13), sequence
alignment score = 348.7  
Alignment identifier is 13  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 13  
Hiding conservation header for alignment 13  
Chains used in RMSD evaluation for alignment 13: model.pdb #1/B, model.pdb
#13/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 13  
RMSD between 184 pruned atom pairs is 0.324 angstroms; (across all 252 pairs:
4.420)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#14), sequence
alignment score = 1396.9  
Alignment identifier is 14  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 14  
Hiding conservation header for alignment 14  
Chains used in RMSD evaluation for alignment 14: model.pdb #1/B, model.pdb
#14/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 14  
RMSD between 309 pruned atom pairs is 0.274 angstroms; (across all 314 pairs:
0.501)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#15), sequence
alignment score = 1059.5  
Alignment identifier is 15  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 15  
Hiding conservation header for alignment 15  
Chains used in RMSD evaluation for alignment 15: model.pdb #1/B, model.pdb
#15/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 15  
RMSD between 306 pruned atom pairs is 0.317 angstroms; (across all 313 pairs:
0.614)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#16), sequence
alignment score = 693.8  
Alignment identifier is 16  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 16  
Hiding conservation header for alignment 16  
Chains used in RMSD evaluation for alignment 16: model.pdb #1/A, model.pdb
#16/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 16  
RMSD between 228 pruned atom pairs is 0.888 angstroms; (across all 308 pairs:
2.543)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain D (#17), sequence
alignment score = 613.2  
Alignment identifier is 17  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 17  
Hiding conservation header for alignment 17  
Chains used in RMSD evaluation for alignment 17: model.pdb #1/A, model.pdb
#17/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 17  
RMSD between 289 pruned atom pairs is 0.244 angstroms; (across all 309 pairs:
1.716)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain B (#18), sequence
alignment score = 709.8  
Alignment identifier is 18  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 18  
Hiding conservation header for alignment 18  
Chains used in RMSD evaluation for alignment 18: model.pdb #1/B, model.pdb
#18/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 18  
RMSD between 231 pruned atom pairs is 1.029 angstroms; (across all 311 pairs:
2.623)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#19), sequence
alignment score = 711.3  
Alignment identifier is 19  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 19  
Hiding conservation header for alignment 19  
Chains used in RMSD evaluation for alignment 19: model.pdb #1/A, model.pdb
#19/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 19  
RMSD between 230 pruned atom pairs is 0.909 angstroms; (across all 308 pairs:
2.534)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#20), sequence
alignment score = 1295.7  
Alignment identifier is 20  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 20  
Hiding conservation header for alignment 20  
Chains used in RMSD evaluation for alignment 20: model.pdb #1/B, model.pdb
#20/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 20  
RMSD between 310 pruned atom pairs is 0.301 angstroms; (across all 312 pairs:
0.364)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain C (#21), sequence
alignment score = 574  
Alignment identifier is 21  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 21  
Hiding conservation header for alignment 21  
Chains used in RMSD evaluation for alignment 21: model.pdb #1/B, model.pdb
#21/C  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 21  
RMSD between 265 pruned atom pairs is 0.335 angstroms; (across all 305 pairs:
2.051)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#22), sequence
alignment score = 656.8  
Alignment identifier is 22  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 22  
Hiding conservation header for alignment 22  
Chains used in RMSD evaluation for alignment 22: model.pdb #1/B, model.pdb
#22/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 22  
RMSD between 266 pruned atom pairs is 0.793 angstroms; (across all 300 pairs:
2.339)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#23), sequence
alignment score = 684.7  
Alignment identifier is 23  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 23  
Hiding conservation header for alignment 23  
Chains used in RMSD evaluation for alignment 23: model.pdb #1/A, model.pdb
#23/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 23  
RMSD between 225 pruned atom pairs is 0.871 angstroms; (across all 308 pairs:
2.541)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#24), sequence
alignment score = 816.9  
Alignment identifier is 24  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 24  
Hiding conservation header for alignment 24  
Chains used in RMSD evaluation for alignment 24: model.pdb #1/B, model.pdb
#24/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 24  
RMSD between 304 pruned atom pairs is 0.268 angstroms; (across all 312 pairs:
0.606)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#25), sequence
alignment score = 1396.9  
Alignment identifier is 25  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 25  
Hiding conservation header for alignment 25  
Chains used in RMSD evaluation for alignment 25: model.pdb #1/B, model.pdb
#25/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 25  
RMSD between 309 pruned atom pairs is 0.274 angstroms; (across all 314 pairs:
0.501)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain A (#26), sequence
alignment score = 1065.8  
Alignment identifier is 26  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 26  
Hiding conservation header for alignment 26  
Chains used in RMSD evaluation for alignment 26: model.pdb #1/A, model.pdb
#26/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 26  
RMSD between 298 pruned atom pairs is 0.338 angstroms; (across all 309 pairs:
0.894)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#27), sequence
alignment score = 689  
Alignment identifier is 27  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 27  
Hiding conservation header for alignment 27  
Chains used in RMSD evaluation for alignment 27: model.pdb #1/B, model.pdb
#27/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 27  
RMSD between 246 pruned atom pairs is 0.935 angstroms; (across all 310 pairs:
2.509)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain D (#28), sequence
alignment score = 631.9  
Alignment identifier is 28  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 28  
Hiding conservation header for alignment 28  
Chains used in RMSD evaluation for alignment 28: model.pdb #1/B, model.pdb
#28/D  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 28  
RMSD between 274 pruned atom pairs is 0.365 angstroms; (across all 306 pairs:
1.910)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain C (#29), sequence
alignment score = 1005.3  
Alignment identifier is 29  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 29  
Hiding conservation header for alignment 29  
Chains used in RMSD evaluation for alignment 29: model.pdb #1/A, model.pdb
#29/C  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 29  
RMSD between 229 pruned atom pairs is 0.199 angstroms; (across all 230 pairs:
0.254)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#30), sequence
alignment score = 1073.5  
Alignment identifier is 30  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 30  
Hiding conservation header for alignment 30  
Chains used in RMSD evaluation for alignment 30: model.pdb #1/B, model.pdb
#30/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 30  
RMSD between 306 pruned atom pairs is 0.308 angstroms; (across all 313 pairs:
0.595)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain B (#31), sequence
alignment score = 333  
Alignment identifier is 31  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 31  
Hiding conservation header for alignment 31  
Chains used in RMSD evaluation for alignment 31: model.pdb #1/D, model.pdb
#31/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 31  
RMSD between 150 pruned atom pairs is 0.897 angstroms; (across all 249 pairs:
5.669)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#32), sequence
alignment score = 593  
Alignment identifier is 32  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 32  
Hiding conservation header for alignment 32  
Chains used in RMSD evaluation for alignment 32: model.pdb #1/A, model.pdb
#32/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 32  
RMSD between 185 pruned atom pairs is 0.853 angstroms; (across all 271 pairs:
3.876)  
  
Matchmaker model.pdb, chain A (#1) with model.pdb, chain B (#33), sequence
alignment score = 694.5  
Alignment identifier is 33  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 33  
Hiding conservation header for alignment 33  
Chains used in RMSD evaluation for alignment 33: model.pdb #1/A, model.pdb
#33/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 33  
RMSD between 228 pruned atom pairs is 0.888 angstroms; (across all 308 pairs:
2.544)  
  
Matchmaker model.pdb, chain D (#1) with model.pdb, chain B (#34), sequence
alignment score = 333  
Alignment identifier is 34  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 34  
Hiding conservation header for alignment 34  
Chains used in RMSD evaluation for alignment 34: model.pdb #1/D, model.pdb
#34/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 34  
RMSD between 150 pruned atom pairs is 0.897 angstroms; (across all 249 pairs:
5.669)  
  
Matchmaker model.pdb, chain B (#1) with model.pdb, chain A (#35), sequence
alignment score = 1073.5  
Alignment identifier is 35  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 35  
Hiding conservation header for alignment 35  
Chains used in RMSD evaluation for alignment 35: model.pdb #1/B, model.pdb
#35/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 35  
RMSD between 306 pruned atom pairs is 0.308 angstroms; (across all 313 pairs:
0.595)  
  

> ui tool show Log

> show cartoons

> hide atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> sequence chain #1/C

Alignment identifier is 1/C  

> sequence chain #1/D

Alignment identifier is 1/D  

> select #1/A:11

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:11-136

1013 atoms, 1040 bonds, 126 residues, 1 model selected  

> select #1/A:103-111,117-126,180-190,215-217,226-239,246-260

526 atoms, 536 bonds, 62 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> sequence chain #1/B

Alignment identifier is 1/B  

> sequence chain #1/C

Alignment identifier is 1/C  

> sequence chain #1/D

Alignment identifier is 1/D  

> sequence chain #2/A

Alignment identifier is 2/A  

> sequence chain #2/B

Alignment identifier is 2/B  

> sequence chain #2/C

Alignment identifier is 2/C  

> sequence chain #2/D

Alignment identifier is 2/D  

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #3/B

Alignment identifier is 3/B  

> sequence chain #3/C

Alignment identifier is 3/C  

> sequence chain #3/D

Alignment identifier is 3/D  

> sequence chain #4/A

Alignment identifier is 4/A  

> sequence chain #4/B

Alignment identifier is 4/B  

> sequence chain #4/C

Alignment identifier is 4/C  

> sequence chain #4/D

Alignment identifier is 4/D  

> sequence chain #5/A

Alignment identifier is 5/A  

> sequence chain #5/B

Alignment identifier is 5/B  

> sequence chain #5/C

Alignment identifier is 5/C  

> sequence chain #5/D

Alignment identifier is 5/D  

> sequence chain #6/A

Alignment identifier is 6/A  

> sequence chain #6/B

Alignment identifier is 6/B  

> sequence chain #6/C

Alignment identifier is 6/C  

> sequence chain #6/D

Alignment identifier is 6/D  

> sequence chain #7/A

Alignment identifier is 7/A  

> sequence chain #7/B

Alignment identifier is 7/B  

> sequence chain #7/C

Alignment identifier is 7/C  

> sequence chain #7/D

Alignment identifier is 7/D  

> sequence chain #8/A

Alignment identifier is 8/A  

> sequence chain #8/B

Alignment identifier is 8/B  

> sequence chain #8/C

Alignment identifier is 8/C  

> sequence chain #8/D

Alignment identifier is 8/D  

> sequence chain #9/A

Alignment identifier is 9/A  

> sequence chain #9/B

Alignment identifier is 9/B  

> sequence chain #9/C

Alignment identifier is 9/C  

> sequence chain #9/D

Alignment identifier is 9/D  

> sequence chain #10/A

Alignment identifier is 10/A  

> sequence chain #10/B

Alignment identifier is 10/B  

> sequence chain #10/C

Alignment identifier is 10/C  

> sequence chain #10/D

Alignment identifier is 10/D  

> sequence chain #11/A

Alignment identifier is 11/A  

> sequence chain #11/B

Alignment identifier is 11/B  

> sequence chain #11/C

Alignment identifier is 11/C  

> sequence chain #11/D

Alignment identifier is 11/D  

> sequence chain #12/A

Alignment identifier is 12/A  

> sequence chain #12/B

Alignment identifier is 12/B  

> sequence chain #12/C

Alignment identifier is 12/C  

> sequence chain #12/D

Alignment identifier is 12/D  

> sequence chain #13/A

Alignment identifier is 13/A  

> sequence chain #13/B

Alignment identifier is 13/B  

> sequence chain #13/C

Alignment identifier is 13/C  

> sequence chain #13/D

Alignment identifier is 13/D  

> sequence chain #14/A

Alignment identifier is 14/A  

> sequence chain #14/B

Alignment identifier is 14/B  

> sequence chain #14/C

Alignment identifier is 14/C  

> sequence chain #14/D

Alignment identifier is 14/D  

> sequence chain #15/A

Alignment identifier is 15/A  

> sequence chain #15/B

Alignment identifier is 15/B  

> sequence chain #15/C

Alignment identifier is 15/C  

> sequence chain #15/D

Alignment identifier is 15/D  

> sequence chain #16/A

Alignment identifier is 16/A  

> sequence chain #16/B

Alignment identifier is 16/B  

> sequence chain #16/C

Alignment identifier is 16/C  

> sequence chain #16/D

Alignment identifier is 16/D  

> sequence chain #17/A

Alignment identifier is 17/A  

> sequence chain #17/B

Alignment identifier is 17/B  

> sequence chain #17/C

Alignment identifier is 17/C  

> sequence chain #17/D

Alignment identifier is 17/D  

> sequence chain #18/A

Alignment identifier is 18/A  

> sequence chain #18/B

Alignment identifier is 18/B  

> sequence chain #18/C

Alignment identifier is 18/C  

> sequence chain #18/D

Alignment identifier is 18/D  

> sequence chain #19/A

Alignment identifier is 19/A  

> sequence chain #19/B

Alignment identifier is 19/B  

> sequence chain #19/C

Alignment identifier is 19/C  

> sequence chain #19/D

Alignment identifier is 19/D  

> sequence chain #20/A

Alignment identifier is 20/A  

> sequence chain #20/B

Alignment identifier is 20/B  

> sequence chain #20/C

Alignment identifier is 20/C  

> sequence chain #20/D

Alignment identifier is 20/D  

> sequence chain #21/A

Alignment identifier is 21/A  

> sequence chain #21/B

Alignment identifier is 21/B  

> sequence chain #21/C

Alignment identifier is 21/C  

> sequence chain #21/D

Alignment identifier is 21/D  

> sequence chain #22/A

Alignment identifier is 22/A  

> sequence chain #22/B

Alignment identifier is 22/B  

> sequence chain #22/C

Alignment identifier is 22/C  

> sequence chain #22/D

Alignment identifier is 22/D  

> sequence chain #23/A

Alignment identifier is 23/A  

> sequence chain #23/B

Alignment identifier is 23/B  

> sequence chain #23/C

Alignment identifier is 23/C  

> sequence chain #23/D

Alignment identifier is 23/D  

> sequence chain #24/A

Alignment identifier is 24/A  

> sequence chain #24/B

Alignment identifier is 24/B  

> sequence chain #24/C

Alignment identifier is 24/C  

> sequence chain #24/D

Alignment identifier is 24/D  

> sequence chain #25/A

Alignment identifier is 25/A  

> sequence chain #25/B

Alignment identifier is 25/B  

> sequence chain #25/C

Alignment identifier is 25/C  

> sequence chain #25/D

Alignment identifier is 25/D  

> sequence chain #26/A

Alignment identifier is 26/A  

> sequence chain #26/B

Alignment identifier is 26/B  

> sequence chain #26/C

Alignment identifier is 26/C  

> sequence chain #26/D

Alignment identifier is 26/D  

> sequence chain #27/A

Alignment identifier is 27/A  

> sequence chain #27/B

Alignment identifier is 27/B  

> sequence chain #27/C

Alignment identifier is 27/C  

> sequence chain #27/D

Alignment identifier is 27/D  

> sequence chain #28/A

Alignment identifier is 28/A  

> sequence chain #28/B

Alignment identifier is 28/B  

> sequence chain #28/C

Alignment identifier is 28/C  

> sequence chain #28/D

Alignment identifier is 28/D  

> sequence chain #29/A

Alignment identifier is 29/A  

> sequence chain #29/B

Alignment identifier is 29/B  

> sequence chain #29/C

Alignment identifier is 29/C  

> sequence chain #29/D

Alignment identifier is 29/D  

> sequence chain #30/A

Alignment identifier is 30/A  

> sequence chain #30/B

Alignment identifier is 30/B  

> sequence chain #30/C

Alignment identifier is 30/C  

> sequence chain #30/D

Alignment identifier is 30/D  

> sequence chain #31/A

Alignment identifier is 31/A  

> sequence chain #31/B

Alignment identifier is 31/B  

> sequence chain #31/C

Alignment identifier is 31/C  

> sequence chain #31/D

Alignment identifier is 31/D  

> sequence chain #32/A

Alignment identifier is 32/A  

> sequence chain #32/B

Alignment identifier is 32/B  

> sequence chain #32/C

Alignment identifier is 32/C  

> sequence chain #32/D

Alignment identifier is 32/D  

> sequence chain #33/A

Alignment identifier is 33/A  

> sequence chain #33/B

Alignment identifier is 33/B  

> sequence chain #33/C

Alignment identifier is 33/C  

> sequence chain #33/D

Alignment identifier is 33/D  

> sequence chain #34/A

Alignment identifier is 34/A  

> sequence chain #34/B

Alignment identifier is 34/B  

> sequence chain #34/C

Alignment identifier is 34/C  

> sequence chain #34/D

Alignment identifier is 34/D  

> sequence chain #35/A

Alignment identifier is 35/A  

> sequence chain #35/B

Alignment identifier is 35/B  

> sequence chain #35/C

Alignment identifier is 35/C  

> sequence chain #35/D

Alignment identifier is 35/D  
An OpenGL graphics error occurred. Most often this is caused by a graphics
driver bug. The only way to fix such bugs is to update your graphics driver.
Redrawing graphics is now stopped to avoid a continuous stream of error
messages. To restart graphics use the command "graphics restart" after
changing the settings that caused the error.  
  
Texture size (2522,16496) exceeds OpenGL driver maximum 16384  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 237, in _draw_scene  
r.outline.set_outline_mask() # copy depth to outline framebuffer  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1837, in set_outline_mask  
mfb = self._mask_framebuffer()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1898, in _mask_framebuffer  
t.initialize_8_bit(size)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2904, in initialize_8_bit  
self.initialize_texture(size, format, iformat, tdtype, ncomp)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2925, in initialize_texture  
self._check_maximum_texture_size(size)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2998, in
_check_maximum_texture_size  
raise OpenGLError('Texture size (%s) exceeds OpenGL driver maximum %d' %  
chimerax.graphics.opengl.OpenGLError: Texture size (2522,16496) exceeds OpenGL
driver maximum 16384  
  
Exception ignored in: <function Texture.__del__ at 0x7fe0fb152f70>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 3003, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  

QMainWindowLayout::tabPosition called with out-of-bounds value '0'  

Window position QRect(2223,4597 100x30) outside any known screen, using
primary screen  




OpenGL version: 4.1 ATI-4.7.103
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      System Firmware Version: 447.80.3.0.0
      OS Loader Version: 540.80.2~11
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 12 days 7:34

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2415:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: CFV9N6543CCL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: Yes

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Tom Goddard]

The user showed about 100 sequence viewers of separate chains that I guess all tried to dock in the main window and made the window taller than 16000 pixels which made the graphics window taller than 16000 pixels and that exceeded the maximum OpenGL framebuffer size of 16384 for the graphics driver on this machine.

Making the ChimeraX window 16000 pixels high by docking a hundred panels more or less cripples the program. This has happened to me quite a few times.

Maybe we should consider new rules to handle docking tools that end up stacking the tool on maybe the largest or top tool panel if it would cause the window to become higher than the screen. Basically we should have a layout solution that prevents the main window from becoming taller than the screen.

Reassigning to Eric to consider ways to avoid docked panels making the main window become taller than the screen.

[Eric Pettersen]

There should be some code to try to prevent the window from becoming too tall, though it might be difficult to determine how much taller the window will get from docking a tool. But we should really try to prevent 100 windows from being creating at once, because there are no good solutions for that (and is almost certainly not desired by the user): 100 floating windows is bad, 100 docked windows are bad, and 100 tabs are bad (might force the window too wide!).

[Eric Pettersen]

Changes made in response to #6386 prevents this scenario. If some other way to add a zillion docked windows shows up, will consider at that time whether to fix that specific problem or try to add some generic code to the main window to prevent the general behavior (somewhat difficult because these requests come in one at a time).