Device loss detected in Present()

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.13.dev202605050228 (2026-05-05 02:28:15 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.13.dev202605050228 (2026-05-05)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\hp\Downloads\3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
> format pdb

Summary of feedback from opening C:\Users\hp\Downloads\3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM AT Tue May 5 18:56:57 2026  
  
Chain information for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Computing secondary structure  

> combine #1.1 #1.2 modelId 2

Remapping chain ID 'A' in 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.2
to 'B'  
Computing secondary structure  
[Repeated 1 time(s)]Drag select of 8 residues  
Drag select of 16 residues  

> undo

[Repeated 1 time(s)]Drag select of 16 residues  

> undo

> select add #1.2/A:1@@serial_number=3

1 atom, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=3

Nothing selected  

> select add #1.2/A:1@@serial_number=3

1 atom, 1 residue, 1 model selected  
Drag select of 4 residues, 2 bonds  

> select #1.1/A:76

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

> select #1.1/A:76

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

> select subtract #1.1/A:76

Nothing selected  
Drag select of 2 residues, 2 bonds  

> select subtract #1.1/A:3

6 atoms, 2 bonds, 1 residue, 2 models selected  

> select add #1.2/A:1@@serial_number=2

7 atoms, 2 bonds, 2 residues, 2 models selected  

> select subtract #1.2/A:1@@serial_number=2

6 atoms, 1 bond, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=5

7 atoms, 1 bond, 2 residues, 2 models selected  

> select #1.1/A:196

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

> select subtract #1.1/A:196

Nothing selected  

> select add #1.2/A:1@@serial_number=3

1 atom, 4 bonds, 1 residue, 1 model selected  

> name frozen Ligand sel

> select clear

> color medium blue

> select Ligand

1 atom, 13 bonds, 1 residue, 1 model selected  

> color sel magenta

> select Ligand

1 atom, 13 bonds, 1 residue, 1 model selected  

> color sel magenta

> color sel byelement

> select clear

> color byelement

> select

4906 atoms, 5038 bonds, 616 residues, 4 models selected  

> color sel byhetero

> select clear

> select add #1.1

2436 atoms, 2502 bonds, 307 residues, 1 model selected  

> select add #1.2

2453 atoms, 2519 bonds, 308 residues, 2 models selected  

> select add #2

4906 atoms, 5038 bonds, 616 residues, 3 models selected  

> select clear

> select Ligand

1 atom, 13 bonds, 1 residue, 1 model selected  

> select sel @< 5

46 atoms, 38 bonds, 12 residues, 3 models selected  

> show sel target ab

> select Ligand

1 atom, 13 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> ui tool show "Add Hydrogens"

> addh #2#1.1-2

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for combination (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #2/A ASN 307  
309 hydrogen bonds  
combination #2/A ASN 307 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
(#1.1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ASN 307  
303 hydrogen bonds  
3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.1/A ASN 307 is not terminus,
removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4722 hydrogens added  
  

> ui tool show H-Bonds

> hbonds sel saveFile "C:/Users/hp/Desktop/h bonds tester 2" color #00ff00
> showDist true select true reveal true

0 hydrogen bonds found  

> select clear

> select Ligand

1 atom, 13 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel saveFile "C:/Users/hp/Desktop/h bonds tester 3" color #aa557f
> showDist true select true reveal true

0 hydrogen bonds found  

> \

Unknown command: \  

> close session

> open C:/Users/hp/Downloads/3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb

Summary of feedback from opening C:/Users/hp/Downloads/3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM AT Tue May 5 18:56:57 2026  
  
Chain information for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Computing secondary structure  

> combine #1.1 #1.2 modelId 2

Remapping chain ID 'A' in 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.2
to 'B'  
Computing secondary structure  
[Repeated 1 time(s)]

> ui tool show "Add Hydrogens"

> addh #2#1.1-2

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for combination (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #2/A ASN 307  
309 hydrogen bonds  
combination #2/A ASN 307 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
(#1.1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ASN 307  
303 hydrogen bonds  
3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.1/A ASN 307 is not terminus,
removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4722 hydrogens added  
  
Drag select of 4 residues  

> undo

> select add #1.2/A:1@@serial_number=2

1 atom, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=2

Nothing selected  

> select add #1.2/A:1@@serial_number=2

1 atom, 1 residue, 1 model selected  
Drag select of 2 residues, 4 atoms, 10 bonds  

> select subtract #1.1/A:50

24 atoms, 10 bonds, 3 residues, 2 models selected  

> select add #1.1/A:50

43 atoms, 28 bonds, 4 residues, 3 models selected  

> select #1.1/A:50

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select subtract #1.1/A:50

Nothing selected  

> select add #1.2/A:1@@serial_number=2

1 atom, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=2

Nothing selected  

> select add #1.2/A:1@@serial_number=2

1 atom, 1 residue, 1 model selected  

> X

Unknown command: X  

> X

Unknown command: X  

> X

Unknown command: X  

> X

Unknown command: X  
Drag select of 6 residues  

> undo

[Repeated 1 time(s)]

> select add #1.1/A:51

23 atoms, 24 bonds, 2 residues, 2 models selected  

> undo

> select add #1.2/A:1@@serial_number=7

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

> select add #1.2/A:1@@serial_number=9

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

> select add #1.2/A:1@@serial_number=11

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

> select add #1.2/A:1@@serial_number=3

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

> select add #1.2/A:1@@serial_number=7

1 atom, 3 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=8

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

> name frozen Ligand sel

> ui tool show H-Bonds

> hbonds sel saveFile "C:/Users/hp/Downloads/h bonds final" color #aa557f
> showDist true select true reveal true

0 hydrogen bonds found  

> select add #1.2/A:1@@serial_number=14

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=15

2 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@HC

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

> select add #1.1/A:248

24 atoms, 35 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:248

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

> select add #1.2/A:1@@serial_number=3

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

> select add #1.2/A:1@@serial_number=13

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

> select add #1.2/A:1@HC1

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

> select add #1.2/A:1@HC2

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

> select add #1.2/A:1@@serial_number=12

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

> select add #1.2/A:1@@serial_number=17

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

> select add #1.2/A:1@HN1

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

> select add #1.2/A:1@HC3

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

> select add #1.2/A:1@@serial_number=16

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

> select add #1.2/A:1@HC4

13 atoms, 23 bonds, 1 residue, 1 model selected  

> name frozen Ligand sel

> ui tool show H-Bonds

> hbonds sel saveFile "C:/Users/hp/Downloads/h bonds" color #aa557f showDist
> true select true reveal true

2 hydrogen bonds found  

> select

9628 atoms, 9760 bonds, 2 pseudobonds, 616 residues, 6 models selected  

> show (#2#1.1-2 & sel) target ab

> undo

> select clear

> select Ligand

13 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel target ab

> color sel byhetero

> undo

> select

9628 atoms, 9760 bonds, 2 pseudobonds, 616 residues, 6 models selected  

> color (#2#1.1-2 & sel) byhetero

> select clear

> hide cartoons

> select add #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=13

2 atoms, 1 residue, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select add #2/A:248@HH

3 atoms, 2 residues, 2 models selected  

> select add #2/A:255@H

4 atoms, 3 residues, 2 models selected  

> undo

[Repeated 1 time(s)]

> select #2/A:248@HH

1 atom, 1 residue, 1 model selected  

> select subtract #2/A:248@HH

Nothing selected  
Drag select of 2 atoms  

> select add #1.2/A:1@@serial_number=12

3 atoms, 2 residues, 2 models selected  

> select subtract #1.2/A:1@@serial_number=12

2 atoms, 2 residues, 2 models selected  

> select add #1.2/A:1@@serial_number=12

3 atoms, 2 residues, 2 models selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> undo

[Repeated 5 time(s)]

> select subtract #1.2/A:1@@serial_number=13

1 atom, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=13

2 atoms, 2 residues, 2 models selected  

> select clear

> select add #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=13

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

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select ~sel & ##selected

21 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #3

21 atoms, 19 bonds, 2 pseudobonds, 1 residue, 3 models selected  

> select subtract #3

21 atoms, 19 bonds, 1 residue, 1 model selected  

> close session

> open C:\Users\hp\Downloads\3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
> format pdb

Summary of feedback from opening C:\Users\hp\Downloads\3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM AT Tue May 5 18:56:57 2026  
  
Chain information for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Computing secondary structure  

> combine #1.1 #1.2 modelId 2

Remapping chain ID 'A' in 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.2
to 'B'  
Computing secondary structure  
[Repeated 1 time(s)]

> select add #1.2/A:1@@serial_number=17

1 atom, 3 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=4

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

> select add #1.2/A:1@@serial_number=7

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

> select add #1.2/A:1@@serial_number=9

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

> select add #1.2/A:1@@serial_number=11

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

> select add #1.2/A:1@@serial_number=10

6 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=14

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

> select add #1.2/A:1@@serial_number=15

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

> select add #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=13

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

> select add #1.1/A:22

18 atoms, 24 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:22

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

> select add #1.2/A:1@@serial_number=12

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

> name frozen Ligand sel

> color sel red

> select clear

> color orange

> color cyan

> select Ligand

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

> color sel red

> ui tool show H-Bonds

> ui tool show "Add Hydrogens"

> addh #2#1.1-2

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for combination (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #2/A ASN 307  
309 hydrogen bonds  
combination #2/A ASN 307 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
(#1.1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ASN 307  
303 hydrogen bonds  
3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.1/A ASN 307 is not terminus,
removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4722 hydrogens added  
  

> select Ligand

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

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/hp/Downloads/again color #aa557f showDist true
> select true reveal true

4 hydrogen bonds found  

> select clear

> select

9628 atoms, 9760 bonds, 4 pseudobonds, 616 residues, 6 models selected  

> color (#2#1.1-2 & sel) byhetero

> select clear

> hide cartoons

> select add #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=13

2 atoms, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=4

3 atoms, 1 residue, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select clear

> close session

> open C:\Users\hp\Downloads\3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
> format pdb

Summary of feedback from opening C:\Users\hp\Downloads\3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM AT Tue May 5 18:56:57 2026  
  
Chain information for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Computing secondary structure  

> combine #1.1 #1.2 modelId 2

Remapping chain ID 'A' in 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.2
to 'B'  
Computing secondary structure  
[Repeated 1 time(s)]

> select add #1.1/A:178

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

> undo

> ui tool show "Build Structure"

> select add #1.1/A:36

8 atoms, 8 bonds, 1 residue, 2 models selected  

> undo

Drag select of 2 residues, 4 atoms, 6 bonds  
Drag select of 12 residues, 2 atoms, 4 bonds  

> undo

[Repeated 1 time(s)]Drag select of 2 residues, 2 atoms, 2 bonds  

> undo

> select add #1.2/A:1@@serial_number=15

1 atom, 3 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=14

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

> select add #1.2/A:1@N

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=7

5 atoms, 7 bonds, 1 residue, 1 model selected  
Drag select of 2 bonds  

> select add #1.2/A:1@@serial_number=16

6 atoms, 9 bonds, 1 residue, 2 models selected  

> select subtract #1.2/A:1@@serial_number=16

5 atoms, 9 bonds, 1 residue, 2 models selected  

> select add #1.2/A:1@@serial_number=16

6 atoms, 9 bonds, 1 residue, 2 models selected  

> select add #1.2/A:1@@serial_number=12

7 atoms, 9 bonds, 1 residue, 2 models selected  

> select subtract #1.2/A:1@@serial_number=16

6 atoms, 9 bonds, 1 residue, 2 models selected  

> select add #1.2/A:1@@serial_number=16

7 atoms, 9 bonds, 1 residue, 2 models selected  

> select subtract #1.2/A:1@@serial_number=16

6 atoms, 9 bonds, 1 residue, 2 models selected  

> select add #1.2/A:1@@serial_number=4

7 atoms, 10 bonds, 1 residue, 2 models selected  

> select add #1.1/A:119

14 atoms, 17 bonds, 2 residues, 3 models selected  

> select subtract #1.1/A:119

7 atoms, 11 bonds, 1 residue, 2 models selected  
Drag select of 2 residues  

> select subtract #1.1/A:120

17 atoms, 12 bonds, 2 residues, 2 models selected  

> select #1.1/A:120

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

> select subtract #1.1/A:120

Nothing selected  

> select add #1.2/A:1@@serial_number=17

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=13

2 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=4

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

> select add #1.2/A:1@N

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

> select add #1.2/A:1@@serial_number=5

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

> select subtract #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=2

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

> select subtract #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=5

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

> select subtract #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=9

6 atoms, 13 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=10

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

> select add #1.2/A:1@@serial_number=8

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

> select add #1.2/A:1@@serial_number=11

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

> select add #1.2/A:1@@serial_number=12

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

> select add #1.1/A:255

18 atoms, 24 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:255

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

> select add #1.2/A:1@@serial_number=16

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

> select add #1.2/A:1@@serial_number=7

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

> select add #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=15

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

> select add #1.2/A:1@@serial_number=14

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

> color sel orange red

> select add #1.2/A:1@@serial_number=6

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

> select subtract #1.2/A:1@@serial_number=6

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

> select add #1.2/A:1@@serial_number=6

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

> select subtract #1.2/A:1@@serial_number=6

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

> select add #1.2/A:1@@serial_number=6

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

> select subtract #1.2/A:1@@serial_number=6

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

> select add #1.2/A:1@@serial_number=6

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

> color sel red

> select add #1.2/A:1@@serial_number=3

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

> select subtract #1.2/A:1@@serial_number=3

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

> select #1.2/A:1@@serial_number=3

1 atom, 1 residue, 1 model selected  

> color sel red

> select add #1.2/A:1@@serial_number=16

2 atoms, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=12

3 atoms, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=16

2 atoms, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=16

3 atoms, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=16

2 atoms, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=10

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

> select add #1.2/A:1@@serial_number=8

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

> select add #1.2/A:1@@serial_number=16

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

> select add #1.2/A:1@@serial_number=12

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

> select add #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=15

7 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=14

8 atoms, 13 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=4

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

> select add #1.2/A:1@@serial_number=13

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

> select add #1.2/A:1@@serial_number=17

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

> select add #1.2/A:1@@serial_number=7

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

> select add #1.2/A:1@@serial_number=9

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

> name frozen Ligand sel

> show sel target ab

> select sel @< 5

150 atoms, 114 bonds, 36 residues, 3 models selected  

> select clear

> select Ligand

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

> ui tool show "Add Hydrogens"

> addh #2#1.1-2

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for combination (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #2/A ASN 307  
309 hydrogen bonds  
combination #2/A ASN 307 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb
(#1.1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 3CPA_TYR_ideal_fitdock-
out_5.-6.2.complex.pdb #1.1/A ASN 307  
303 hydrogen bonds  
3CPA_TYR_ideal_fitdock-out_5.-6.2.complex.pdb #1.1/A ASN 307 is not terminus,
removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4722 hydrogens added  
  

> select clear

> select Ligand

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

> select add #1.2/A:1@HN1

14 atoms, 18 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@HC2

15 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@HC4

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

> select add #1.2/A:1@HC3

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

> select add #1.2/A:1@HC1

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

> select subtract #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@HC

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

> select add #1.2/A:1@@serial_number=5

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

> select add #1.1/A:176

35 atoms, 38 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:176

19 atoms, 23 bonds, 1 residue, 1 model selected  

> name frozen Ligand sel

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/hp/Downloads/again2 color #aa557f showDist true
> select true reveal true

4 hydrogen bonds found  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select down

7 atoms, 5 residues, 2 models selected  

> select clear

> select

9628 atoms, 9760 bonds, 4 pseudobonds, 616 residues, 6 models selected  

> color (#2#1.1-2 & sel) byhetero

> select clear

> select Ligand

19 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> hide cartoons

> select add #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select clear

> select add #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> save C:\Users\hp/Desktop\image1.png supersample 3

> save C:\Users\hp/Desktop\image2.png supersample 3

> save C:\Users\hp/Desktop\image3.png supersample 3

> close session

> open "C:/Users/hp/Downloads/Unconfirmed 74153.crdownload"

Unrecognized file suffix '.crdownload'  

> open "C:/Users/hp/Downloads/Unconfirmed 74153.crdownload"

Unrecognized file suffix '.crdownload'  

> open C:/Users/hp/Downloads/3CPA_ligand_fitdock-out_5.-6.2.complex.pdb

Summary of feedback from opening C:/Users/hp/Downloads/3CPA_ligand_fitdock-
out_5.-6.2.complex.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM AT Thu May 7 10:15:33 2026  
  
Chain information for 3CPA_ligand_fitdock-out_5.-6.2.complex.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Computing secondary structure  

> combine #1.1 #1.2 modelId 2

Remapping chain ID 'A' in 3CPA_ligand_fitdock-out_5.-6.2.complex.pdb #1.2 to
'B'  
Computing secondary structure  
[Repeated 1 time(s)]

> select add #1.2/A:1@@serial_number=12

1 atom, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=16

2 atoms, 1 bond, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=16

1 atom, 1 residue, 1 model selected  

> select add #1.1/A:177

10 atoms, 10 bonds, 2 residues, 2 models selected  

> select add #1.1/A:176

17 atoms, 16 bonds, 3 residues, 2 models selected  

> select subtract #1.1/A:177

8 atoms, 8 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:176

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=10

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

> select add #1.2/A:1@@serial_number=8

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

> select add #1.2/A:1@@serial_number=6

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

> select add #1.1/A:144

12 atoms, 15 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:144

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

> select add #1.2/A:1@@serial_number=5

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

> select add #1.2/A:1@@serial_number=2

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

> select add #1.2/A:1@@serial_number=13

7 atoms, 13 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=4

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

> select add #1.2/A:1@@serial_number=14

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

> select add #1.2/A:1@@serial_number=15

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

> select add #1.2/A:1@N

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

> select add #1.2/A:1@@serial_number=7

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

> select add #1.2/A:1@@serial_number=17

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

> select subtract #1.2/A:1@@serial_number=13

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

> select add #1.2/A:1@@serial_number=13

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

> select add #1.2/A:1@@serial_number=3

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

> select add #1.2/A:1@@serial_number=16

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

> name frozen Ligand sel

> ui tool show "Add Hydrogens"

> addh #2#1.1-2

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for combination (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #2/A ASN 307  
309 hydrogen bonds  
combination #2/A ASN 307 is not terminus, removing H atom from 'C'  
No usable SEQRES records for 3CPA_ligand_fitdock-out_5.-6.2.complex.pdb (#1.1)
chain A; guessing termini instead  
Chain-initial residues that are actual N termini: 3CPA_ligand_fitdock-
out_5.-6.2.complex.pdb #1.1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: 3CPA_ligand_fitdock-
out_5.-6.2.complex.pdb #1.1/A ASN 307  
303 hydrogen bonds  
3CPA_ligand_fitdock-out_5.-6.2.complex.pdb #1.1/A ASN 307 is not terminus,
removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4722 hydrogens added  
  

> select add #1.1/A:74

34 atoms, 35 bonds, 2 residues, 2 models selected  

> select add #1.2/A:1@HC3

35 atoms, 35 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:74

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

> select add #1.2/A:1@HC4

17 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@HC1

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

> select add #1.2/A:1@HC

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

> select add #1.2/A:1@HN1

20 atoms, 23 bonds, 1 residue, 1 model selected  

> name frozen Ligand sel

> color sel red

> select add #1.2/A:1@@serial_number=11

21 atoms, 23 bonds, 1 residue, 1 model selected  

> select subtract #1.2/A:1@@serial_number=11

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

> select add #1.2/A:1@@serial_number=11

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

> color sel red

> select add #1.2/A:1@@serial_number=9

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

> select subtract #1.2/A:1@@serial_number=9

21 atoms, 18 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@@serial_number=9

22 atoms, 18 bonds, 1 residue, 1 model selected  

> color sel red

> select add #1.2/A:1@HC2

23 atoms, 18 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> select Ligand

20 atoms, 23 bonds, 1 residue, 1 model selected  

> select sel @< 5

328 atoms, 272 bonds, 48 residues, 3 models selected  

> select clear

> select Ligand

20 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel target ab

> ui tool show H-Bonds

> hbonds sel saveFile "C:/Users/hp/Downloads/again 3" color #aa557f showDist
> true select true reveal true

6 hydrogen bonds found  

> select clear

> select

9628 atoms, 9760 bonds, 6 pseudobonds, 616 residues, 6 models selected  

> color (#2#1.1-2 & sel) byhetero

> show (#2#1.1-2 & sel) target ab

> undo

> select clear

> select Ligand

20 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> hide cartoons

> select add #2/A:270@OE1

1 atom, 1 residue, 1 model selected  

> select add #2/A:248@OH

2 atoms, 2 residues, 1 model selected  

> select add #1.2/A:1@@serial_number=4

3 atoms, 3 residues, 2 models selected  

> select add #1.2/A:1@@serial_number=12

4 atoms, 3 residues, 2 models selected  

> select add #1.2/A:1@@serial_number=13

5 atoms, 3 residues, 2 models selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select clear

> undo

[Repeated 1 time(s)]

> select clear

> save "C:/Users/hp/Downloads/Tyrosine ligand bound to hydrogen bonds.cxs"

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor gray

> set bgColor #80808000

> save C:\Users\hp/Desktop\image4.png supersample 3

> set bgColor gray

> set bgColor black

> set bgColor transparent

> save C:\Users\hp/Desktop\image5.png supersample 3

> show cartoons

> ui tool show H-Bonds

> hbonds sel saveFile "C:/Users/hp/Downloads/step 5" color #00aa00 showDist
> true select true reveal true

Atom specifier selects no atoms  

> sequence chain #1.1/A#2/A

Alignment identifier is 1  

> show target m

> select #1.1/A:1 #2/A:1

24 atoms, 22 bonds, 2 residues, 2 models selected  

> select #1.1/A:1 #2/A:1

24 atoms, 22 bonds, 2 residues, 2 models selected  

> select #1.1/A:1-285 #2/A:1-285

8888 atoms, 9012 bonds, 570 residues, 2 models selected  
1 [ID: 1] region 2 chains [1-285] RMSD: 0.000  
  

> select #1.1/A:286-300 #2/A:286-300

480 atoms, 484 bonds, 30 residues, 2 models selected  

> select #1.1/A:271-285 #2/A:271-285

476 atoms, 480 bonds, 30 residues, 2 models selected  

> select #1.1/A:241-285 #2/A:241-285

1384 atoms, 1402 bonds, 90 residues, 2 models selected  
1 [ID: 1] region 2 chains [241-285] RMSD: 0.000  
  

> select #1.1/A:1 #2/A:1

24 atoms, 22 bonds, 2 residues, 2 models selected  

> select #1.1/A:1 #2/A:1

24 atoms, 22 bonds, 2 residues, 2 models selected  

> select #1.1/A #2/A

9582 atoms, 9714 bonds, 614 residues, 2 models selected  
1 [ID: 1] region 2 chains [1-307] RMSD: 0.000  
  

> save "C:/Users/hp/Downloads/Fasta sequence" format fasta alignment 1

> select clear

> hide cartoons

> select #1.1/A #2/A

9582 atoms, 9714 bonds, 1 pseudobond, 614 residues, 3 models selected  

> select clear

> show cartoons

> color cornflower blue

> select Ligand

20 atoms, 23 bonds, 1 residue, 1 model selected  

> color sel orange red

> select #1.2/A:1@@serial_number=11

1 atom, 1 residue, 1 model selected  

> color sel orange red

> select add #1.2/A:1@@serial_number=9

2 atoms, 1 residue, 1 model selected  

> color sel orange red

> select add #1.2/A:1@HC2

3 atoms, 1 residue, 1 model selected  

> color sel orange red

> select clear

> select add #2/A:248@HB2

1 atom, 2 bonds, 1 residue, 1 model selected  

> undo

[Repeated 4 time(s)]

> color byelement

> set bgColor gray

> set bgColor #80808000

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> save C:\Users\hp/Desktop\image6.png supersample 3

> save C:\Users\hp/Desktop\image7.png supersample 3

> set bgColor gray

> set bgColor #80808000

> save C:\Users\hp/Desktop\image8.png supersample 3

> close session

> open
> C:/Users/hp/Downloads/MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb

Summary of feedback from opening
C:/Users/hp/Downloads/MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb  
---  
warning | Ignored bad PDB record found on line 1  
REMARK The PDB FILE IS CREATED BY CY's PROGRAM AT Fri May 8 04:29:16 2026  
  
Chain information for
MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb  
---  
Chain | Description  
1.1/A | No description available  
  
Computing secondary structure  

> combine #1.1 #1.2 modelId 2

Remapping chain ID 'A' in
MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb
#1.2 to 'B'  
Computing secondary structure  
[Repeated 1 time(s)]

> select add #1.2/A:1@N

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #1.1/A:268

8 atoms, 8 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:268

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@H1

2 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@H2

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@C

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

> select add #1.2/A:1@OXT

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

> select add #1.2/A:1@O

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

> select add #1.2/A:1@CB

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

> select add #1.2/A:1@CD2

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

> select add #1.2/A:1@OH

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

> select add #1.2/A:1@CE2

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

> name frozen Ligand sel

> ui tool show "Add Hydrogens"

> addh #2#1.1-2

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | No usable SEQRES records for combination (#2) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: combination #2/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #2/A ASN 307  
302 hydrogen bonds  
combination #2/A ASN 307 is not terminus, removing H atom from 'C'  
No usable SEQRES records for
MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb
(#1.1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini:
MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb
#1.1/A ALA 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:
MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb
#1.1/A ASN 307  
297 hydrogen bonds  
MutatedSequence_81cfc_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000_TYR_ideal_out_1.-6.7.complex.pdb
#1.1/A ASN 307 is not terminus, removing H atom from 'C'  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
4720 hydrogens added  
  

> select add #1.1/A:226

20 atoms, 26 bonds, 2 residues, 2 models selected  

> select

9616 atoms, 9746 bonds, 616 residues, 4 models selected  

> color sel hot pink

> select clear

> color byelement

> select Ligand

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

> select add #1.1/A:255

29 atoms, 35 bonds, 2 residues, 2 models selected  

> select subtract #1.1/A:255

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

> select add #1.2/A:1@HD2

11 atoms, 18 bonds, 1 residue, 1 model selected  

> select subtract #1.2/A:1@CD2

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

> select add #1.2/A:1@CD2

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

> select add #1.2/A:1@HE2

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

> select add #1.2/A:1@HB2

13 atoms, 19 bonds, 1 residue, 1 model selected  

> select add #1.2/A:1@HD1

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

Device loss detected in Present()  

Error after making OpenGL context current: OpenGL error out of memory  
This is a Qt window toolkit bug discussed at
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19881#comment:5Traceback (most
recent call last):  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 110, in _expose_event  
self.status(self._last_message, self._last_color)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 177, in status  
self._draw_text(msg, color, secondary)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 187, in _draw_text  
draw_overlays(dlist, self._renderer)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1613, in draw_overlays  
_draw_multiple(drawings, r, Drawing.TRANSPARENT_DRAW_PASS)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 1572, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 784, in draw  
self.draw_self(renderer, draw_pass)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 795, in draw_self  
self._draw_geometry(renderer, transparent_only = any_opaque)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\drawing.py", line 831, in _draw_geometry  
t.bind_texture()  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3191, in bind_texture  
self.fill_opengl_texture()  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3234, in fill_opengl_texture  
self.initialize_texture(size, format, iformat, tdtype, ncomp, data)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3111, in initialize_texture  
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,  
File "src/latebind.pyx", line 40, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src/wrapper.pyx", line 319, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/wrapper.pyx", line 312, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
327,  
23,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
327,  
23,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
327,  
23,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
327,  
23,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
327,  
23,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_RGBA8,  
327,  
23,  
0,  
GL_RGBA,  
GL_UNSIGNED_BYTE,  
array([[[0, 0, 0, 0],  
[0, 0, 0, 0],  
[0, 0, 0, 0],  
...,  
[0, 0, 0, 0],  
[0, 0, 0...,  
)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

Device loss detected in Present()  

[Repeated 25 time(s)]Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 110, in _expose_event  
self.status(self._last_message, self._last_color)  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\ui\statusbar.py", line 176, in status  
r.draw_background()  
File "C:\Program Files\ChimeraX 1.13.dev202605050228\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1264, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  

Device loss detected in Present()  

[Repeated 8 time(s)]




OpenGL version: 3.3.0 - Build 31.0.101.2135
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_ZA.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: windows

Manufacturer: HP
Model: HP ProBook 430 G6
OS: Microsoft Windows 11 Pro (Build 26200.8328)
Memory: 8,454,438,912
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8265U CPU @ 1.60GHz
OSLanguage: en-US

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.1.2
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.4.22
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.13.dev202605050228
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.1
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.0.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.6
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.3
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.13.5
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.13
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.20.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 2.4.4
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.5.2
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.3
    pydantic-settings: 2.14.0
    pydantic_core: 2.46.3
    pydata-sphinx-theme: 0.17.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.9.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.27
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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
    sse-starlette: 3.4.1
    stack-data: 0.6.3
    starlette: 1.0.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.14.0
    tornado: 6.5.5
    tqdm: 4.67.3
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2026.2
    Unidecode: 1.4.0
    urllib3: 2.6.3
    uvicorn: 0.46.0
    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    WMI: 1.5.1
    yarl: 1.23.0

[Tom Goddard]

Windows sometimes loses the OpenGL context and logs "Device loss detected in Present()".