sym: Tried to get the position of deleted drawing

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "C:/Users/consc842/OneDrive/Dokumente/PhD/CbA5H/CbA5H structure.cxs"

Not registering illegal selector name "SLBB domain"  

Log from Mon Feb 27 12:30:20 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\consc842\Downloads\6ttl.pdb format pdb

6ttl.pdb title:  
Crystal structure of [fefe]-hydrogenase CBA5H (partial) from clostridium
beijerinckii In hinact state [more info...]  
  
Chain information for 6ttl.pdb #1  
---  
Chain | Description  
A B | [fefe]-hydrogenase  
  
Non-standard residues in 6ttl.pdb #1  
---  
402 — dicarbonyl[bis(cyanide-
kappac)]-μ-(iminodimethanethiolatato-1KAPPAS:2KAPPAS)-μ-(oxomethylidene)diiron(2+)  
SF4 — iron/sulfur cluster  
  

> select /A:108-640

3799 atoms, 3859 bonds, 3 pseudobonds, 479 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

Drag select of 25 atoms, 10 pseudobonds, 21 bonds  

> hide sel atoms

> select /A:108-640

3799 atoms, 3859 bonds, 3 pseudobonds, 479 residues, 2 models selected  

> select /B:108-640

3799 atoms, 3859 bonds, 3 pseudobonds, 479 residues, 2 models selected  
Alignment identifier is 1/B  

> select /B:330

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

> select /B:330-331

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select
> /B:113-131,134-138,140-156,161-175,187-201,272-282,293-296,298-304,311-323,329-351,370-379,391-403,424-434,449-459,479-484,489-505,541-555,569-574,583-601,606-620,626-634

2088 atoms, 2096 bonds, 261 residues, 1 model selected  

> select /B:360-361

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

> select /B:360-361

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

> select /B:362

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

> select /B:361-362

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select
> /B:113-131,134-138,140-156,161-175,187-201,272-282,293-296,298-304,311-323,329-351,370-379,391-403,424-434,449-459,479-484,489-505,541-555,569-574,583-601,606-620,626-634

2088 atoms, 2096 bonds, 261 residues, 1 model selected  

> select /B:360

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

> select /B:350-360

47 atoms, 46 bonds, 1 pseudobond, 5 residues, 2 models selected  

> select /B:272

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

> select /B:272-349

601 atoms, 610 bonds, 78 residues, 1 model selected  

> select /B:411

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /B:411-412

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

> select /B:365

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

> select /B:365-367

19 atoms, 18 bonds, 3 residues, 1 model selected  

> select /B:108

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

> select /B:108-124

152 atoms, 155 bonds, 17 residues, 1 model selected  

> select /B:108

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

> select /B:108-218

909 atoms, 921 bonds, 1 pseudobond, 108 residues, 2 models selected  

> select /B:213

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

> select /B:108-213

870 atoms, 882 bonds, 1 pseudobond, 103 residues, 2 models selected  

> name frozen "SLBB domain" sel

Not registering illegal selector name "SLBB domain"  

> create SLBB domain

Unknown command: create SLBB domain  

> select

7648 atoms, 7760 bonds, 36 pseudobonds, 962 residues, 3 models selected  

> selcect residue 108

Unknown command: selcect residue 108  

> selcect [residue 108]

Unknown command: selcect [residue 108]  

> select /B:172

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

> select /B:172-173

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /B:108

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

> select /B:108-177

582 atoms, 589 bonds, 70 residues, 1 model selected  

> select /B:108

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

> select /B:108-211

852 atoms, 863 bonds, 1 pseudobond, 101 residues, 2 models selected  

> log metadata #1

Metadata for 6ttl.pdb #1  
---  
Title | Crystal structure of [fefe]-hydrogenase CBA5H (partial) from
clostridium beijerinckii In hinact state  
Citation | A safety cap protects hydrogenase from oxygen attack. PMID:
33531463  
Non-standard residues | 402 — dicarbonyl[bis(cyanide-
kappac)]-μ-(iminodimethanethiolatato-1KAPPAS:2KAPPAS)-μ-(oxomethylidene)diiron(2+)  
SF4 — iron/sulfur cluster  
Gene source | Clostridium beijerinckii  
Experimental method | X-ray diffraction  
Resolution | 2.90Å  
  
> log chains #1

Chain information for 6ttl.pdb #1  
---  
Chain | Description  
A B | [fefe]-hydrogenase  
  

> log metadata #1

Metadata for 6ttl.pdb #1  
---  
Title | Crystal structure of [fefe]-hydrogenase CBA5H (partial) from
clostridium beijerinckii In hinact state  
Citation | A safety cap protects hydrogenase from oxygen attack. PMID:
33531463  
Non-standard residues | 402 — dicarbonyl[bis(cyanide-
kappac)]-μ-(iminodimethanethiolatato-1KAPPAS:2KAPPAS)-μ-(oxomethylidene)diiron(2+)  
SF4 — iron/sulfur cluster  
Gene source | Clostridium beijerinckii  
Experimental method | X-ray diffraction  
Resolution | 2.90Å  
  
> log chains #1

Chain information for 6ttl.pdb #1  
---  
Chain | Description  
A B | [fefe]-hydrogenase  
  

> ui tool show "Selection Inspector"

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> help

> name frozen "SLBB domain" sel

Not registering illegal selector name "SLBB domain"  

> name frozen SLBB sel

> view clip false

> log metadata #1

Metadata for 6ttl.pdb #1  
---  
Title | Crystal structure of [fefe]-hydrogenase CBA5H (partial) from
clostridium beijerinckii In hinact state  
Citation | A safety cap protects hydrogenase from oxygen attack. PMID:
33531463  
Non-standard residues | 402 — dicarbonyl[bis(cyanide-
kappac)]-μ-(iminodimethanethiolatato-1KAPPAS:2KAPPAS)-μ-(oxomethylidene)diiron(2+)  
SF4 — iron/sulfur cluster  
Gene source | Clostridium beijerinckii  
Experimental method | X-ray diffraction  
Resolution | 2.90Å  
  
> log chains #1

Chain information for 6ttl.pdb #1  
---  
Chain | Description  
A B | [fefe]-hydrogenase  
  

> color (#!1 & sel) lime

> color (#!1 & sel) forest green

> select /B:216

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

> select /B:216

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

> name list

SLBB [852 atoms, 1726 bonds, 2 models]  

> select /B:108

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

> select /B:108-110

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select /B:178-179

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /B:178-180

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

> help

> select SLBB

852 atoms, 863 bonds, 1 pseudobond, 101 residues, 2 models selected  

> name SLBB sel

> select add #1

7648 atoms, 7760 bonds, 36 pseudobonds, 962 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select ::name="SF4"

16 atoms, 24 bonds, 2 residues, 1 model selected  

> select up

7648 atoms, 7760 bonds, 962 residues, 1 model selected  

> select down

16 atoms, 24 bonds, 2 residues, 1 model selected  

> select down

16 atoms, 24 bonds, 2 residues, 1 model selected  

> select down

16 atoms, 24 bonds, 2 residues, 1 model selected  

> select down

16 atoms, 24 bonds, 2 residues, 1 model selected  

> select up

7648 atoms, 7760 bonds, 962 residues, 1 model selected  

> select up

7648 atoms, 7760 bonds, 962 residues, 1 model selected  

> select up

7648 atoms, 7760 bonds, 962 residues, 1 model selected  

> select down

16 atoms, 24 bonds, 2 residues, 1 model selected  

> select down

16 atoms, 24 bonds, 2 residues, 1 model selected  

> help

> save "C:/Users/consc842/OneDrive/Dokumente/PhD/CbA5H/CbA5H structure.cxs"

——— End of log from Mon Feb 27 12:30:20 2023 ———

opened ChimeraX session  

> open "C:\Users\consc842\Downloads\CpI with adt-bridged cofactor.pdb" format
> pdb

CpI with adt-bridged cofactor.pdb title:  
Active semisynthetic [fefe]-hydrogenase cpi with aza-dithiolato- bridged [2FE]
cofactor [more info...]  
  
Chain information for CpI with adt-bridged cofactor.pdb #2  
---  
Chain | Description | UniProt  
A B | iron hydrogenase 1 | PHF1_CLOPA  
  
Non-standard residues in CpI with adt-bridged cofactor.pdb #2  
---  
402 — dicarbonyl[bis(cyanide-
kappac)]-μ-(iminodimethanethiolatato-1KAPPAS:2KAPPAS)-μ-(oxomethylidene)diiron(2+)  
FES — FE2/S2 (inorganic) cluster  
MG — magnesium ion  
SF4 — iron/sulfur cluster  
  

> select #2/A:1-581

8994 atoms, 9071 bonds, 581 residues, 1 model selected  

> hide sel atoms

> hide sel cartoons

Drag select of 50 atoms, 2 residues, 15 pseudobonds, 48 bonds  
Drag select of 60 atoms, 15 pseudobonds, 61 bonds  

> hide sel cartoons

> hide sel atoms

> help

> select #2/A:1-581

8994 atoms, 9071 bonds, 581 residues, 1 model selected  

> select #2/A:1-581

8994 atoms, 9071 bonds, 581 residues, 1 model selected  

> select #2/B:2-579

8943 atoms, 9019 bonds, 578 residues, 1 model selected  

> delete A

Missing or invalid "atoms" argument: invalid atoms specifier  

> help

> ui tool show "Side View"

> close session

> open 6ttl

Summary of feedback from opening 6ttl fetched from pdb  
---  
notes | Fetching compressed mmCIF 6ttl from
http://files.rcsb.org/download/6ttl.cif  
Fetching CCD 402 from http://ligand-expo.rcsb.org/reports/4/402/402.cif  
Fetching CCD SF4 from http://ligand-expo.rcsb.org/reports/S/SF4/SF4.cif  
  
6ttl title:  
crystal structure of [FeFe]-hydrogenase CbA5H (partial) from Clostridium
beijerinckii in Hinact state [more info...]  
  
Chain information for 6ttl #1  
---  
Chain | Description | UniProt  
A B | [FeFe]-hydrogenase | A0A1I9RYV3_CLOBE  
  
Non-standard residues in 6ttl #1  
---  
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)  
SF4 — iron/sulfur cluster  
  

> delete /b

> view ligand

> label ligand

> hide #1.3 models

> open 4xdc

Summary of feedback from opening 4xdc fetched from pdb  
---  
notes | Fetching compressed mmCIF 4xdc from
http://files.rcsb.org/download/4xdc.cif  
Fetching CCD FES from http://ligand-expo.rcsb.org/reports/F/FES/FES.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
  
4xdc title:  
Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe]
cofactor [more info...]  
  
Chain information for 4xdc #2  
---  
Chain | Description | UniProt  
A B | Iron hydrogenase 1 | PHF1_CLOPA  
  
Non-standard residues in 4xdc #2  
---  
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)  
FES — FE2/S2 (inorganic) cluster  
MG — magnesium ion  
SF4 — iron/sulfur cluster  
  
4xdc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> delete /B

> ui tool show "Model Panel"

> mmaker #2 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 6ttl, chain A (#1) with 4xdc, chain A (#2), sequence alignment
score = 955.7  
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: 6ttl #1/A, 4xdc #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 288 pruned atom pairs is 1.019 angstroms; (across all 436 pairs:
17.107)  
  

> select #2/A:575-581

104 atoms, 107 bonds, 7 residues, 1 model selected  

> select #2/A:511-581

1184 atoms, 1200 bonds, 71 residues, 1 model selected  

> select #2/A:1-66

999 atoms, 1001 bonds, 66 residues, 1 model selected  

> select #2/A:1-66

999 atoms, 1001 bonds, 66 residues, 1 model selected  

> select #2/A:67

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #2/A:67-82

231 atoms, 230 bonds, 16 residues, 1 model selected  

> select #2/A:1-141

2227 atoms, 2238 bonds, 141 residues, 1 model selected  

> select #1/A:429-640 #2/A:361-581

5087 atoms, 5144 bonds, 433 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [451-699]
RMSD: 2.059  
  

> select #2/A:360

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select #1/A:418-428 #2/A:350-360

260 atoms, 262 bonds, 22 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [440-450]
RMSD: 0.625  
  

> select #1/A:449 #2/A:381

21 atoms, 19 bonds, 2 residues, 2 models selected  

> select #1/A:404

14 atoms, 15 bonds, 1 residue, 1 model selected  

> select #1/A:404-640 #2/A:336-581

5673 atoms, 5740 bonds, 483 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [426-699]
RMSD: 1.991  
  

> select #1/A:379-640 #2/A:311-581

6247 atoms, 6323 bonds, 533 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [426-699] + 1
other block RMSD: 1.950  
  

> select #1/A:360-640 #2/A:292-581

6694 atoms, 6783 bonds, 571 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [426-699] + 2
other blocks RMSD: 1.948  
  

> name H-domain sel

> select SLBB

6694 atoms, 6783 bonds, 571 residues, 2 models selected  

> hide sel atoms

> undo

> select add #1

8319 atoms, 8426 bonds, 18 pseudobonds, 771 residues, 5 models selected  

> select subtract #1

4495 atoms, 4546 bonds, 290 residues, 1 model selected  

> select add #2

9693 atoms, 9132 bonds, 49 pseudobonds, 1233 residues, 2 models selected  

> select subtract #2

Nothing selected  

> select SLBB

Nothing selected  

> select H-domain

Nothing selected  

> select #1/A:406-640 #2/A:338-581

5619 atoms, 5682 bonds, 479 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [428-699]
RMSD: 1.995  
  

> name frozen H-domain sel

> select add #2

11531 atoms, 10997 bonds, 49 pseudobonds, 1468 residues, 3 models selected  

> select subtract #2

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select up

1857 atoms, 1886 bonds, 237 residues, 1 model selected  

> select up

2199 atoms, 2237 bonds, 281 residues, 1 model selected  

> select down

1857 atoms, 1886 bonds, 237 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select up

1857 atoms, 1886 bonds, 237 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select down

1838 atoms, 1865 bonds, 235 residues, 1 model selected  

> select up

1857 atoms, 1886 bonds, 237 residues, 1 model selected  

> select up

2199 atoms, 2237 bonds, 281 residues, 1 model selected  

> select up

2217 atoms, 2255 bonds, 283 residues, 1 model selected  

> select up

2874 atoms, 2922 bonds, 369 residues, 1 model selected  

> select up

2890 atoms, 2937 bonds, 371 residues, 1 model selected  

> select up

3173 atoms, 3225 bonds, 404 residues, 1 model selected  

> select up

3232 atoms, 3284 bonds, 411 residues, 1 model selected  

> select up

3799 atoms, 3859 bonds, 479 residues, 1 model selected  

> select up

3824 atoms, 3880 bonds, 481 residues, 1 model selected  

> select up

13517 atoms, 13012 bonds, 1714 residues, 2 models selected  

> select up

13517 atoms, 13012 bonds, 1714 residues, 2 models selected  

> select up

13517 atoms, 13012 bonds, 1714 residues, 2 models selected  

> select #1/A:429-640 #2/A:361-581

5087 atoms, 5144 bonds, 433 residues, 2 models selected  

> select #1/A:429-640 #2/A:361-581

5087 atoms, 5144 bonds, 433 residues, 2 models selected  

> select #1/A:429-640 #2/A:361-581

5087 atoms, 5144 bonds, 433 residues, 2 models selected  

> select #1/A:429-640 #2/A:361-581

5087 atoms, 5144 bonds, 433 residues, 2 models selected  

> select add #2

11354 atoms, 10818 bonds, 49 pseudobonds, 1445 residues, 3 models selected  

> select subtract #2

1661 atoms, 1686 bonds, 212 residues, 1 model selected  

> name frozen H-domain_CpI sel

[Repeated 3 time(s)]

> select H-domain

5619 atoms, 5682 bonds, 479 residues, 2 models selected  

> select H-domain_CpI

1661 atoms, 1686 bonds, 212 residues, 1 model selected  

> select #1/A:429-640 #2/A:361-581

5087 atoms, 5144 bonds, 433 residues, 2 models selected  

> select #2/A:361-581

3426 atoms, 3458 bonds, 221 residues, 1 model selected  

> select #2/A:311-581

4202 atoms, 4245 bonds, 271 residues, 1 model selected  

> select #2/A:292-581

4495 atoms, 4546 bonds, 290 residues, 1 model selected  

> select #2/A:267-581

4870 atoms, 4922 bonds, 315 residues, 1 model selected  

> select #2/A:252-581

5135 atoms, 5190 bonds, 330 residues, 1 model selected  

> select #2/A:242-581

5265 atoms, 5321 bonds, 340 residues, 1 model selected  

> select #2/A:217-581

5640 atoms, 5700 bonds, 365 residues, 1 model selected  

> select #2/A:205-581

5840 atoms, 5901 bonds, 377 residues, 1 model selected  

> select #2/A:205-581

5840 atoms, 5901 bonds, 377 residues, 1 model selected  

> select #2/A:211

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #2/A:211-213

53 atoms, 52 bonds, 3 residues, 1 model selected  

> select #2/A:208

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #2/A:208-581

5795 atoms, 5856 bonds, 374 residues, 1 model selected  

> name frozen H-domain_CbA5H sel

> select #1/A:270

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:270-640

2850 atoms, 2898 bonds, 1 pseudobond, 365 residues, 2 models selected  

> name frozen H-domain_CpI sel

> transparency H-domain 80

> transparency H-domain 80 [target c]

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency H-domain 80 target c

> select #1/A:270-640 #2/A:208-581

8645 atoms, 8754 bonds, 1 pseudobond, 739 residues, 3 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [292-699]
RMSD: 1.941  
  

> name H-domain sel

> select down

2850 atoms, 2898 bonds, 1 pseudobond, 365 residues, 2 models selected  

> transparency H-domain 80 target c

> select add #1

3824 atoms, 3880 bonds, 18 pseudobonds, 481 residues, 4 models selected  

> select subtract #1

Nothing selected  

> select H-domain_CpI

2850 atoms, 2898 bonds, 1 pseudobond, 365 residues, 2 models selected  

> select H-domain_CbA5H

5795 atoms, 5856 bonds, 374 residues, 1 model selected  

> transparency sel 80 target c

> set bgColor white

> set bgColor #ffffff00

> select add #2

9693 atoms, 9132 bonds, 49 pseudobonds, 1233 residues, 2 models selected  

> select subtract #2

Nothing selected  

> hide #!1 models

> show #!1 models

> save "C:/Users/consc842/OneDrive/Dokumente/PhD/CbA5H/CpI and CbA5H
> alignment.cxs"

> set bgColor white

> set bgColor black

> set bgColor transparent

> ui tool show Angles/Torsions

> ui tool show "Side View"

> hide #!2 models

> show #!2 models

> select #1/A:365

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

> select #1/A:365-367

19 atoms, 18 bonds, 3 residues, 1 model selected  

> select #2/A:299

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:364-367 #2/A:296-299

83 atoms, 82 bonds, 8 residues, 2 models selected  
MatchMaker Alignment [ID: 1] region 6ttl, chain A..4xdc, chain A [386-389]
RMSD: 2.312  
  

> select :SF4

40 atoms, 60 bonds, 5 residues, 2 models selected  

> select :MG

3 atoms, 3 residues, 1 model selected  

> select :FES

4 atoms, 4 bonds, 1 residue, 1 model selected  

> select :FES

4 atoms, 4 bonds, 1 residue, 1 model selected  

> select ::name="402"

34 atoms, 18 bonds, 20 pseudobonds, 2 residues, 4 models selected  

> hide sel atoms

> undo

> sym #2 assembly 1

Associated 4xdc (3.1) chain A to 4xdc, chain A with 0 mismatches  
Chains used in RMSD evaluation for alignment 1: 6ttl #1/A, 4xdc #2/A, 4xdc
#3.1/A  

> view

> sym #2 assembly 2

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\log\tool.py",
line 206, in link_intercept  
chimerax_intercept(request_info, *args, session=self.session, view=self, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 364, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\sym.py", line 122, in sym  
a.show_copies(m, surface_only, resolution, grid_spacing, session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\sym.py", line 407, in show_copies  
g = session.models.add_group(mlist)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 890, in add_group  
self.add([group], parent=parent)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 721, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1246, in added_to_session  
super().added_to_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 179, in added_to_session  
if not self.scene_position.is_identity():  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 508, in _get_scene_position  
return product([d.position for d in self.drawing_lineage])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 508, in <listcomp>  
return product([d.position for d in self.drawing_lineage])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 491, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "4xdc"  
  
RuntimeError: Tried to get the position of deleted drawing "4xdc"  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 491, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  
An error occurred in drawing the scene. 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.  
  
object of type 'NoneType' has no len()  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 177, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 201, in _draw_scene  
highlight_drawings, on_top_drawings) = self._drawings_by_pass(mdraw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 272, in _drawings_by_pass  
d.drawings_for_each_pass(pass_drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 755, in drawings_for_each_pass  
d.drawings_for_each_pass(pass_drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 755, in drawings_for_each_pass  
d.drawings_for_each_pass(pass_drawings)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 733, in drawings_for_each_pass  
if not self.display:  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 113, in _redraw  
self.render()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\sideview\tool.py", line 166, in render  
near, far = main_view.near_far_distances(main_camera, view_num)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 931, in near_far_distances  
near, far = self._near_far_bounds(cp, vd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 944, in _near_far_bounds  
b = self.drawing_bounds(allow_drawing_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 638, in drawing_bounds  
dm.cached_drawing_bounds = b = self.drawing.bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in <listcomp>  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 965, in <listcomp>  
if d.display and not d.skip_bounds]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "frame drawn":  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 813, in picked_object  
xyz1, xyz2 = self.clip_plane_points(win_x, win_y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 971, in clip_plane_points  
near, far = self.near_far_distances(c, view_num, include_clipping = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 931, in near_far_distances  
near, far = self._near_far_bounds(cp, vd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 944, in _near_far_bounds  
b = self.drawing_bounds(allow_drawing_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 638, in drawing_bounds  
dm.cached_drawing_bounds = b = self.drawing.bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in <listcomp>  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 965, in <listcomp>  
if d.display and not d.skip_bounds]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  

> undo

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\undo.py",
line 185, in undo  
inst.undo()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py", line 612, in undo  
view(self._session, objects=self._before,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py", line 69, in view  
show_view(session, objects, frames)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\std_commands\view.py", line 216, in show_view  
v1 = NamedView(v, v.center_of_rotation, models)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 694, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 721, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 780, in _front_center_cofr  
b = self.drawing_bounds(allow_drawing_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 638, in drawing_bounds  
dm.cached_drawing_bounds = b = self.drawing.bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in <listcomp>  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 965, in <listcomp>  
if d.display and not d.skip_bounds]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
undo failed: object of type 'NoneType' has no len():  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 297, in mouse_drag  
self._rotate(axis, angle)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 381, in _rotate  
self.view.rotate(saxis, angle, self.models())  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 1013, in rotate  
center = self.center_of_rotation  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 694, in _get_cofr  
cofr = self._compute_center_of_rotation()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 721, in _compute_center_of_rotation  
p = self._front_center_cofr()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 780, in _front_center_cofr  
b = self.drawing_bounds(allow_drawing_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 638, in drawing_bounds  
dm.cached_drawing_bounds = b = self.drawing.bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in <listcomp>  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 965, in <listcomp>  
if d.display and not d.skip_bounds]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  

> open "C:\Users\consc842\OneDrive\Dokumente\PhD\CbA5H\CpI and CbA5H
> alignment.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 619, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 940, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 910, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 190, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 335, in _graphics_updater  
return structure_graphics_updater(self.session)  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 619, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 940, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 910, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 190, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 335, in _graphics_updater  
return structure_graphics_updater(self.session)  
AttributeError: 'AtomicStructure' object has no attribute 'session'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 364, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1004, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 742, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 619, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 940, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 910, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 190, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1765, in remove_structure  
self._structures.remove(s)  
KeyError: <chimerax.atomic.structure.AtomicStructure object at
0x000001D5876CE550>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1765, in remove_structure  
self._structures.remove(s)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\updateloop.py", line 140, in _redraw_timer_callback  
self.session.ui.mouse_modes.mouse_pause_tracking()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 493, in
mouse_pause_tracking  
self._mouse_pause()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py", line 628, in _mouse_pause  
m.pause(self._mouse_pause_position)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\std_modes.py", line 779, in pause  
p = self.view.picked_object(x, y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 813, in picked_object  
xyz1, xyz2 = self.clip_plane_points(win_x, win_y)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 971, in clip_plane_points  
near, far = self.near_far_distances(c, view_num, include_clipping = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 931, in near_far_distances  
near, far = self._near_far_bounds(cp, vd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 944, in _near_far_bounds  
b = self.drawing_bounds(allow_drawing_changes = False)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\view.py", line 638, in drawing_bounds  
dm.cached_drawing_bounds = b = self.drawing.bounds()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in <listcomp>  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 964, in bounds  
dbounds = [d.bounds() for d in self.child_drawings()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 965, in <listcomp>  
if d.display and not d.skip_bounds]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 377, in get_display  
return self._any_displayed_positions and len(self._positions) > 0  
  
See log for complete Python traceback.  
  

> open "C:\Users\consc842\OneDrive\Dokumente\PhD\CbA5H\CpI and CbA5H
> alignment.cxs" format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 619, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 940, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 910, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 190, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1765, in remove_structure  
self._structures.remove(s)  
KeyError: <chimerax.atomic.structure.AtomicStructure object at
0x000001D5876CE550>  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 700, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 619, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 940, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 910, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 190, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1765, in remove_structure  
self._structures.remove(s)  
KeyError: <chimerax.atomic.structure.AtomicStructure object at
0x000001D5876CE550>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest  
self._callback(info)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 353, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 455, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 364, in thread_safe  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 446, in defer  
cxcmd(session, topic)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ui\widgets\htmlview.py", line 464, in cxcmd  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 458, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open  
return cxs_open(session, data, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 1004, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 742, in restore  
self.reset()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 541, in reset  
sm.reset_state(container, self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 619, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 940, in close  
self.remove(mopen)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 910, in remove  
m.removed_from_session(session)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 190, in removed_from_session  
self._graphics_updater.remove_structure(self)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1765, in remove_structure  
self._structures.remove(s)  
KeyError: <chimerax.atomic.structure.AtomicStructure object at
0x000001D5876CE550>  
  
KeyError:  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\structure.py", line 1765, in remove_structure  
self._structures.remove(s)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.3616
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: sv_SE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: Latitude 7430
OS: Microsoft Windows 10 Education (Build 19045)
Memory: 16,579,715,072
MaxProcessMemory: 137,438,953,344
CPU: 16 12th Gen Intel(R) Core(TM) i7-1270P
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0