Find Cavities crash

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10.dev202502060317 (2025-02-06 03:17:41 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: stack overflow

Thread 0x0000a1d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 324 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 622 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 1392 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\threading.py", line 995 in _bootstrap

Current thread 0x0000ab5c (most recent call first):
  File "C:\Users\rmatusiak\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\pyKVFinder\grid.py", line 961 in detect
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\kvfinder\cmd.py", line 56 in cmd_kvfinder
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3215 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49 in run
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\kvfinder\tool.py", line 136 in find_cavities
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202502060317\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502060317 (2025-02-06)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/223Ecol078PP_EYCTANSK_CDS_0049.pdb"

Chain information for 223Ecol078PP_EYCTANSK_CDS_0049.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> select #1: 30-458

9831 atoms, 10029 bonds, 1287 residues, 1 model selected  

> color sel forest green

> set bgColor white

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/223EcolP49.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/223Ecol078PP_EYCTANSK_CDS_0050.pdb"

Chain information for 223Ecol078PP_EYCTANSK_CDS_0050.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> ui tool show "Similar Structures"

> foldseek /A

Not saving entity_poly_seq for non-authoritative sequences  

Found 656 similar structures to 223Ecol078PP_EYCTANSK_CDS_0050.pdb #1/A in pdb
database using foldseek, name fs1  

> open 5w6h

Summary of feedback from opening 5w6h fetched from pdb  
---  
note | Fetching compressed mmCIF 5w6h from http://files.rcsb.org/download/5w6h.cif  
  
5w6h title:  
Crystal structure of Bacteriophage CBA120 tailspike protein 4 enzymatically
active domain (TSP4dN, orf213) [more info...]  
  
Chain information for 5w6h #2  
---  
Chain | Description | UniProt  
A B C | tailspike protein 4 | G3M192_9CAUD 344-1036  
  
Non-standard residues in 5w6h #2  
---  
ACT — acetate ion  
CL — chloride ion  
K — potassium ion  
NA — sodium ion  
SO4 — sulfate ion  
ZN — zinc ion  
  
92 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Deleted 2 extra chains, 150 N-terminal residues, 1822 non-polymer residues
more than 3.0 Angstroms away.  
Alignment of 5w6h chain C to query has RMSD 0.897 using 451 of 537 paired
residues within cutoff distance 2.0  

> open G3M192 fromDatabase uniprot associate #2/A,B,C

Summary of feedback from opening G3M192 fetched from uniprot  
---  
notes | Fetching compressed G3M192 UniProt info from https://www.uniprot.org/uniprot/G3M192.xml  
Alignment identifier is G3M192  
Associated 5w6h_C chain C to G3M192 with 5 mismatches  
  
Opened UniProt G3M192  

> hide #!2 models

> graphics silhouettes true

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/212Ecol018PP_DKPHSRRH_CDS_0005.pdb"

Chain information for 212Ecol018PP_DKPHSRRH_CDS_0005.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> select #1: 706-88

Nothing selected  

> color magenta

> undo

> select #1: 706-808

2439 atoms, 2490 bonds, 309 residues, 1 model selected  

> color sel magenta

> select #1: 547-705

3558 atoms, 3633 bonds, 477 residues, 1 model selected  

> select #1: 38-550

12300 atoms, 12657 bonds, 1539 residues, 1 model selected  

> color sel forest green

> select clear

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/212EcolP5.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/201Ecol019PP_TOMJBXAJ_CDS_0052.pdb"

Chain information for 201Ecol019PP_TOMJBXAJ_CDS_0052.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/201EcolP52.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/202Ecol028PP_RSMLWKBR_CDS_0004.pdb"

Chain information for 202Ecol028PP_RSMLWKBR_CDS_0004.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  
Alignment identifier is 1  

> select /A-C:1

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:1-150

3465 atoms, 3510 bonds, 450 residues, 1 model selected  

> color sel gray

> select #1: 242-588

7926 atoms, 8085 bonds, 1041 residues, 1 model selected  

> color sel forest green

> select clear

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/202EcolP4.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/211Ecol002PP_OINRNHQD_CDS_0004.pdb"

Chain information for 211Ecol002PP_OINRNHQD_CDS_0004.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  
Alignment identifier is 1  

> select /A-C:1

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:1-207

4617 atoms, 4701 bonds, 621 residues, 1 model selected  

> select /A-C:102

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select /A-C:102

27 atoms, 24 bonds, 3 residues, 1 model selected  

> select /A-C:226

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:226

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:1

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:1-183

4080 atoms, 4149 bonds, 549 residues, 1 model selected  

> color sel light gray

> color sel dark gray

> select #1: 306-814

11352 atoms, 11553 bonds, 1527 residues, 1 model selected  

> color sel forest green

> select clear

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/211EcolP4.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/208Ecol041PP_RGCOPAHN_CDS_0053.pdb"

Chain information for 208Ecol041PP_RGCOPAHN_CDS_0053.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  
Alignment identifier is 1  

> select /A-C:1

24 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A-C:1-60

1344 atoms, 1362 bonds, 180 residues, 1 model selected  

> color sel gray

> select clear

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/208EcolP53.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/213Ecol019PP_CKUOJGPZ_CDS_0013.pdb"

Chain information for 213Ecol019PP_CKUOJGPZ_CDS_0013.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/213EcolP13.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/MT653144.1_prot_QNI21770.1_34.pdb"

MT653144.1_prot_QNI21770.1_34.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
MT653144.1_prot_QNI21770.1_34 [more info...]  
  
Chain information for MT653144.1_prot_QNI21770.1_34.pdb #1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  
Non-standard residues in MT653144.1_prot_QNI21770.1_34.pdb #1  
---  
CA — (CA)  
  
Computing secondary structure  
Alignment identifier is 1/A  
Alignment identifier is 1  

> select /A:8

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:8-77

506 atoms, 514 bonds, 70 residues, 1 model selected  

> select /A:8

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:8-181

1306 atoms, 1333 bonds, 174 residues, 1 model selected  
Alignment identifier is 1/A  

> select clear

Alignment identifier is 1/A  
Alignment identifier is 1  

> select /B-C:7

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:7-64

840 atoms, 848 bonds, 116 residues, 1 model selected  

> select add #1

15281 atoms, 15592 bonds, 2034 residues, 1 model selected  
Alignment identifier is 1/A  
Alignment identifier is 1  

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/MT653144.1_prot_QNI21770.1_34.pdb"

MT653144.1_prot_QNI21770.1_34.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
MT653144.1_prot_QNI21770.1_34 [more info...]  
  
Chain information for MT653144.1_prot_QNI21770.1_34.pdb #1  
---  
Chain | Description  
A | No description available  
B C | No description available  
  
Non-standard residues in MT653144.1_prot_QNI21770.1_34.pdb #1  
---  
CA — (CA)  
  
Computing secondary structure  
Alignment identifier is 1/A  
Alignment identifier is 1  

> select /B-C:7

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select /B-C:7

16 atoms, 14 bonds, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

Alignment identifier is 1/A  
Alignment identifier is 1  

> select #1: 135-684

12489 atoms, 12735 bonds, 1650 residues, 1 model selected  

> color sel forest green

> select clear

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/208EcolP53.cxs"

> view name session-start

opened ChimeraX session  

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/201Ecol019PP_TOMJBXAJ_CDS_0052.pdb"

Chain information for 201Ecol019PP_TOMJBXAJ_CDS_0052.pdb #2  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #2 to #1 showAlignment true

Computing secondary structure  
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 208Ecol041PP_RGCOPAHN_CDS_0053.pdb, chain A (#1) with
201Ecol019PP_TOMJBXAJ_CDS_0052.pdb, chain A (#2), sequence alignment score =
2342  
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:
208Ecol041PP_RGCOPAHN_CDS_0053.pdb #1/A, 201Ecol019PP_TOMJBXAJ_CDS_0052.pdb
#2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 469 pruned atom pairs is 0.477 angstroms; (across all 504 pairs:
1.046)  
  

> color #1 white

> color #1 #a3a3a3ff

> color #2 #55ff00ff

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_identity target csab palette
> 100,red:150,white:200,blue

26499 atoms, 3549 residues, atom seq_identity range 100 to 200  

> select #1/A:362

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:362-366 #2/A:187-191

68 atoms, 68 bonds, 10 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region chain A..chain A [362-366] RMSD: 3.239  
  

> select #1/B#2/B

8833 atoms, 9023 bonds, 1183 residues, 2 models selected  

> hide sel cartoons

> select #1/C#2/C

8833 atoms, 9023 bonds, 1183 residues, 2 models selected  

> hide sel cartoons

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/OR062948.1_prot_WLY86761.1_13.pdb"

Chain information for OR062948.1_prot_WLY86761.1_13.pdb #1  
---  
Chain | Description  
A | No description available  
  
Computing secondary structure  

> select #1: 20-138

1837 atoms, 1866 bonds, 119 residues, 1 model selected  

> color sel blue

> select #1: 146-249

1646 atoms, 1680 bonds, 104 residues, 1 model selected  

> color sel orange

> select clear

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/351SaurP13.cxs"

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/OR062948.1_prot_WLY86762.1_14.pdb"

Chain information for OR062948.1_prot_WLY86762.1_14.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> select #1: 172-424

11859 atoms, 11976 bonds, 759 residues, 1 model selected  

> color sel forest green

> select #1: 462-523

2832 atoms, 2853 bonds, 186 residues, 1 model selected  

> color sel orange

> select clear

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/351SaurP14.cxs"

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/OR062948.1_prot_WLY86757.1_9.pdb"

Chain information for OR062948.1_prot_WLY86757.1_9.pdb #2  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> close session

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/OR062948.1_prot_WLY86757.1_9.pdb"

Chain information for OR062948.1_prot_WLY86757.1_9.pdb #1  
---  
Chain | Description  
A B C | No description available  
  
Computing secondary structure  

> select /A

7431 atoms, 7526 bonds, 485 residues, 1 model selected  

> select ~sel & ##selected

14862 atoms, 15052 bonds, 970 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1: 350-458

1660 atoms, 1688 bonds, 109 residues, 1 model selected  

> color sel blue

> close session

> open "C:\Users\rmatusiak\PROTEON PHARMACEUTICALS S.A\Projekt Booster -
> Dokumenty\04 Bioinformatics_data\aln\G-_Central_tail_spike_lysin.aln" format
> aln

Summary of feedback from opening C:\Users\rmatusiak\PROTEON PHARMACEUTICALS
S.A\Projekt Booster - Dokumenty\04
Bioinformatics_data\aln\G-_Central_tail_spike_lysin.aln  
---  
notes | Alignment identifier is G-_Central_tail_spike_lysin.aln  
Showing conservation header ("seq_conservation" residue attribute) for
alignment G-_Central_tail_spike_lysin.aln  
  
Opened 4 sequences from G-_Central_tail_spike_lysin.aln  

> open "C:\Users\rmatusiak\PROTEON PHARMACEUTICALS S.A\Projekt Booster -
> Dokumenty\04 Bioinformatics_data\aln\G-support.aln" format aln

Summary of feedback from opening C:\Users\rmatusiak\PROTEON PHARMACEUTICALS
S.A\Projekt Booster - Dokumenty\04 Bioinformatics_data\aln\G-support.aln  
---  
notes | Alignment identifier is G-support.aln  
Showing conservation header ("seq_conservation" residue attribute) for
alignment G-support.aln  
  
Opened 3 sequences from G-support.aln  

> open "C:\Users\rmatusiak\PROTEON PHARMACEUTICALS S.A\Projekt Booster -
> Dokumenty\04 Bioinformatics_data\aln\G-support.aln" format aln

Summary of feedback from opening C:\Users\rmatusiak\PROTEON PHARMACEUTICALS
S.A\Projekt Booster - Dokumenty\04 Bioinformatics_data\aln\G-support.aln  
---  
notes | Destroying pre-existing alignment with identifier G-support.aln  
Alignment identifier is G-support.aln  
Showing conservation header ("seq_conservation" residue attribute) for
alignment G-support.aln  
  
Opened 3 sequences from G-support.aln  

> open 4ku0 format mmcif fromDatabase pdb

4ku0 title:  
Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with T4 gp5 beta-
helix fragment [more info...]  
  
Chain information for 4ku0 #1  
---  
Chain | Description | UniProt  
A B C | Tail-associated lysozyme | VG05_BPT4 484-575  
D | Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region | Y08B_BPT4 2-97  
  
Non-standard residues in 4ku0 #1  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
ELA — 9-octadecenoic acid  
FE — Fe (III) ion  
MG — magnesium ion  
NA — sodium ion  
PLM — palmitic acid  
STE — stearic acid  
  
174 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Associated 4ku0 chain A to lcl|PP434423.1_prot_WWT49718.1_145 with 5
mismatches  
Associated 4ku0 chain B to lcl|PP434423.1_prot_WWT49718.1_145 with 5
mismatches  
Associated 4ku0 chain C to lcl|PP434423.1_prot_WWT49718.1_145 with 5
mismatches  
Associated 4ku0 chain D to lcl|PP434423.1_prot_WWT49720.1_147 with 1 mismatch  

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/OR062945.1_prot_WLY86034.1_79.pdb"

OR062945.1_prot_WLY86034.1_79.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
OR062945.1_prot_WLY86034.1_79 [more info...]  
  
Chain information for OR062945.1_prot_WLY86034.1_79.pdb #2  
---  
Chain | Description  
A C E | No description available  
  
Associated OR062945.1_prot_WLY86034.1_79.pdb chain A to
lcl|OR062945.1_prot_WLY86034.1_79 with 0 mismatches  
Associated OR062945.1_prot_WLY86034.1_79.pdb chain C to
lcl|OR062945.1_prot_WLY86034.1_79 with 0 mismatches  
Associated OR062945.1_prot_WLY86034.1_79.pdb chain E to
lcl|OR062945.1_prot_WLY86034.1_79 with 0 mismatches  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #!1 to #2 showAlignment true

Computing secondary structure  
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 OR062945.1_prot_WLY86034.1_79.pdb, chain A (#2) with 4ku0, chain A
(#1), sequence alignment score = 359.2  
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: 4ku0 #1/A,
OR062945.1_prot_WLY86034.1_79.pdb #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 92 pruned atom pairs is 0.342 angstroms; (across all 92 pairs:
0.342)  
  

> open "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04
> Bioinformatics_data/Proteins_models/OR062945.1_prot_WLY86032.1_77.pdb"

OR062945.1_prot_WLY86032.1_77.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org)
OR062945.1_prot_WLY86032.1_77 [more info...]  
  
Chain information for OR062945.1_prot_WLY86032.1_77.pdb #3  
---  
Chain | Description  
A | No description available  
  
Associated OR062945.1_prot_WLY86032.1_77.pdb chain A to
lcl|OR062945.1_prot_WLY86032.1_77 with 0 mismatches  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #3 to #1 showAlignment true

Computing secondary structure  
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 4ku0, chain D (#1) with OR062945.1_prot_WLY86032.1_77.pdb, chain A
(#3), sequence alignment score = 410.2  
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: 4ku0 #1/D,
OR062945.1_prot_WLY86032.1_77.pdb #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 96 pruned atom pairs is 0.347 angstroms; (across all 96 pairs:
0.347)  
  

> close #1

> save "C:/Users/rmatusiak/PROTEON PHARMACEUTICALS S.A/Projekt Booster -
> Dokumenty/04 Bioinformatics_data/Proteins_models/308EcolP79-P77.cxs"

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_identity target csab palette
> 100,#8d8d8d:250,white:400,red

13990 atoms, 1813 residues, atom seq_identity range 100 to 400  

> select clear

> select #3/A:26

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

> select clear

> select #2/A-E:13-14

33 atoms, 30 bonds, 6 residues, 1 model selected  

> select clear

> select #2/A-E:24

27 atoms, 24 bonds, 3 residues, 1 model selected  

> ui tool show Matchmaker

> ui tool show "Render/Select by Attribute"

> color byattribute r:seq_identity #3 target csab palette
> 100,#999999:150,white:200,red

721 atoms, 97 residues, atom seq_identity range 100 to 200  

> select clear

> select #2/A#3/A

5144 atoms, 5247 bonds, 669 residues, 2 models selected  

> select ~sel & ##selected

8846 atoms, 9022 bonds, 1144 residues, 1 model selected  

> hide sel cartoons

> undo

> select #2/C

4423 atoms, 4511 bonds, 572 residues, 1 model selected  

> select ~sel

9567 atoms, 9758 bonds, 1241 residues, 2 models selected  

> hide sel cartoons

> ui tool show "Find Cavities"

No structures chosen  
error dialog finished  

> kvfinder #2


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202502060317 (2025-02-06)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 566.14
OpenGL renderer: NVIDIA GeForce RTX 3080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: pl_PL.cp1250
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: GIGABYTE
Model: AORUS 15P YD
OS: Microsoft Windows 10 Pro for Workstations (Build 19045)
Memory: 34,089,021,440
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: pl-PL

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.8.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.18.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.2
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202502060317
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.7
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.16
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.10
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.12
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.15.4
    fonttools: 4.55.8
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.5
    joblib: 1.4.2
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.1.3
    llvmlite: 0.44.0
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.0
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.61.0
    numexpr: 2.10.2
    numpy: 2.2.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 5.24.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pyKVFinder: 0.7.2
    pynmrstar: 3.3.5
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    pytest: 8.3.4
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.2.1
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    scikit-learn: 1.6.1
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.2
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    threadpoolctl: 3.5.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    tqdm: 4.67.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    umap-learn: 0.5.7
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1