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Opened 9 months ago
Closed 9 months ago
#17088 closed defect (limitation)
MemoryError saving maps in sessions
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18363
ChimeraX Version: 1.8rc202406072045 (2024-06-07 20:45:50 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/4--42-C_582-688-
> DENSITY.cxs"
Opened C4-J1199_008_volume_map_inv_2_5A.mrc as #2, grid size 384,384,384,
pixel 0.825, shown at level 0.0371, step 1, values float32
Log from Wed Mar 12 11:21:59 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350--Orient1b.cxs"
Log from Mon Mar 3 14:44:48 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350--Orient1.cxs"
Log from Thu Feb 27 11:53:00 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350-WT--Orient2.cxs"
Log from Wed Feb 26 18:37:53 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/WT.cxs"
Log from Wed Feb 26 17:44:38 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/WT.cxs"
Log from Wed Feb 26 17:33:05 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/WT-2subunit.cxs"
Log from Wed Jan 22 10:24:18 2025UCSF ChimeraX version: 1.8rc202406072045
(2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C13.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C13.pdb #1
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> hide atoms
> color #1 #dd22bbff
> color #1 #eeee88ff
> color #1 violet
> select : 560-710
4600 atoms, 4692 bonds, 4 pseudobonds, 564 residues, 2 models selected
> select ~sel & ##selected
15720 atoms, 16064 bonds, 8 pseudobonds, 1920 residues, 2 models selected
> hide sel cartoons
> select : 707710
Nothing selected
> select : 707-710
152 atoms, 160 bonds, 16 residues, 1 model selected
> hide sel cartoons
> select : 570, 689, 581, 586 677
Expected a keyword
> select : 570, 689, 581, 586, 677
172 atoms, 152 bonds, 20 residues, 1 model selected
> show sel atoms
> select : 570, 689, 581, 586, 677,680, 682
236 atoms, 208 bonds, 28 residues, 1 model selected
> show sel atoms
> color sel lime
> color sel byhetero
> select : 677
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel yellow
> select clear
> cartoon style modeHelix tube sides 20
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/1--WT-ALL.cxs"
> select : 691
32 atoms, 28 bonds, 4 residues, 1 model selected
> select : 691,417
72 atoms, 68 bonds, 8 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select : 690,417
84 atoms, 80 bonds, 8 residues, 1 model selected
> show sel cartoons
> show sel atoms
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2
---
Chain | Description
A B C D | No description available
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select : sel : 570, 689, 581, 586, 677,680, 682
472 atoms, 416 bonds, 56 residues, 2 models selected
> color #2 #8877ccff
> color #2 #eeee88ff
> color #2 violet
> select : sel : 570, 689, 581, 586, 677,680, 682
472 atoms, 416 bonds, 56 residues, 2 models selected
> hide #!1 models
> show sel & #!2 atoms
> color (#!2 & sel) lime
> color (#!2 & sel) byhetero
> show #!1 models
> hide #!2 models
> select : sel : 560-706
8896 atoms, 9056 bonds, 8 pseudobonds, 1096 residues, 4 models selected
> show #!2 models
> hide #!1 models
> select ~sel & ##selected
31744 atoms, 32456 bonds, 16 pseudobonds, 3872 residues, 4 models selected
> hide sel & #!2 cartoons
> select clear
> hide #!2 atoms
> select :570, 689, 581, 586, 677,680, 682,417, 690
640 atoms, 584 bonds, 72 residues, 2 models selected
> show sel & #!2 atoms
> ui tool show H-Bonds
> hbonds sel reveal true
252 hydrogen bonds found
> select clear
> select : 677
64 atoms, 56 bonds, 8 residues, 2 models selected
> color (#!2 & sel) yellow
> select clear
> select : 690, 417
168 atoms, 160 bonds, 8 pseudobonds, 16 residues, 3 models selected
> color (#!2 & sel) lime
> color (#!2 & sel) byhetero
> select clear
[Repeated 1 time(s)]
> select #2/B:417@ND1
1 atom, 1 residue, 1 model selected
> select add #2/B:690@NH1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> ui tool show Distances
> distance #2/B:417@ND1 #2/B:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/B HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select #2/C:417@ND1
1 atom, 1 residue, 1 model selected
> select clear
> select #2/C:417@ND1
1 atom, 1 residue, 1 model selected
> select add #2/C:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #2/C:417@ND1 #2/C:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/C HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select clear
> select add #2/D:690@NH1
1 atom, 1 bond, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #2/D:417@ND1
1 atom, 1 residue, 1 model selected
> select add #2/D:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #2/D:417@ND1 #2/D:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/D HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select add #2/A:690@NH1
1 atom, 1 bond, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #2/A:417@ND1
1 atom, 1 residue, 1 model selected
> select add #2/A:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #2/A:417@ND1 #2/A:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/A HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select #2/A:689@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:689@OE2
1 atom, 1 residue, 1 model selected
> select add #2/A:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #2/A:689@OE2 #2/A:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/A GLU
689 OE2 and GLN 570 NE2: 2.476Å
> select #2/D:689@OE2
1 atom, 1 residue, 1 model selected
> select clear
> select #2/D:689@OE2
1 atom, 1 residue, 1 model selected
> select add #2/D:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #2/D:689@OE2 #2/D:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/D GLU
689 OE2 and GLN 570 NE2: 2.562Å
> select #2/B:689@OE2
1 atom, 1 residue, 1 model selected
> select add #2/B:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #2/B:689@OE2 #2/B:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/B GLU
689 OE2 and GLN 570 NE2: 2.602Å
> select clear
> select #2/C:689@OE2
1 atom, 1 residue, 1 model selected
> select add #2/C:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #2/C:689@OE2 #2/C:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/C GLU
689 OE2 and GLN 570 NE2: 2.683Å
> select #2/D:680@OG1
1 atom, 1 residue, 1 model selected
> select add #2/A:682@OE1
2 atoms, 2 residues, 1 model selected
> distance #2/D:680@OG1 #2/A:682@OE1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/D THR
680 OG1 and /A GLU 682 OE1: 3.095Å
> select #2/D:682@OE1
1 atom, 1 residue, 1 model selected
> select add #2/C:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #2/D:682@OE1 #2/C:680@OG1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/D GLU
682 OE1 and /C THR 680 OG1: 3.095Å
> select #2/C:682@OE1
1 atom, 1 residue, 1 model selected
> select add #2/B:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #2/C:682@OE1 #2/B:680@OG1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/C GLU
682 OE1 and /B THR 680 OG1: 3.095Å
> select #2/D:581@NZ
1 atom, 1 residue, 1 model selected
> select add #2/D:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #2/D:581@NZ #2/D:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/D LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #2/C:581@NZ
1 atom, 1 residue, 1 model selected
> select add #2/C:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #2/C:581@NZ #2/C:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/C LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #2/B:581@NZ
1 atom, 1 residue, 1 model selected
> select add #2/B:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #2/B:581@NZ #2/B:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/B LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #2/A:581@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #2/A:581@NZ #2/A:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/A LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #2/A:680@OG1
1 atom, 1 residue, 1 model selected
> select add #2/B:682@OE1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #2/A:680@OG1 #2/B:682@OE1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C14.pdb #2/A THR
680 OG1 and /B GLU 682 OE1: 3.095Å
> select : 689
72 atoms, 64 bonds, 8 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel reveal true
36 hydrogen bonds found
> hide #!4 models
> select : 570
72 atoms, 64 bonds, 8 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel reveal true
20 hydrogen bonds found
> hide #!2 models
> show #!2 models
> show #!4 models
> distance style color black
[Repeated 2 time(s)]
> cartoon style (#!2 & sel) modeHelix tube sides 20
> select clear
> hide #4.1 models
> hide #!2 models
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C13b.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C13b.pdb #5
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!5 atoms
> select : 570
108 atoms, 96 bonds, 12 residues, 3 models selected
> show sel & #!5 atoms
> ui tool show H-Bonds
> hbonds sel reveal true
45 hydrogen bonds found
> close #5
> show #!1 models
> hide #!1 models
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-
> refined_244-C15.header.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-
refined_244-C15.header.pdb #5
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15.pdb #6
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!5 models
> close #6
> close #5
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15.pdb #5
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select : 570
108 atoms, 96 bonds, 12 residues, 3 models selected
> show sel & #!5 atoms
> ui tool show H-Bonds
> hbonds sel reveal true
54 hydrogen bonds found
> close #5
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5
---
Chain | Description
A B C D | No description available
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select : 570
108 atoms, 96 bonds, 12 residues, 3 models selected
> show sel & #!5 atoms
> ui tool show H-Bonds
> hbonds sel reveal true
54 hydrogen bonds found
> color #5 #ffaa88ff
> color #5 #222288ff
> color #5 #2282eeff
> color #5 #222288ff
> color #5 #eeee88ff
> color #5 violet
> select : 560-708
13524 atoms, 13776 bonds, 78 pseudobonds, 1668 residues, 8 models selected
> select ~sel & ##selected
47436 atoms, 48492 bonds, 28 pseudobonds, 5784 residues, 7 models selected
> hide sel & #!5 cartoons
> select : 707-708
180 atoms, 180 bonds, 24 residues, 3 models selected
> hide sel & #!5 cartoons
> hide sel & #!5 atoms
[Repeated 1 time(s)]
> select clear
> hide #!5 atoms
> select : 570, 689, 581, 586, 677,680, 682
708 atoms, 624 bonds, 30 pseudobonds, 84 residues, 5 models selected
> show sel & #!5 atoms
> color (#!5 & sel) lime
> color (#!5 & sel) byhetero
> ui tool show H-Bonds
> hbonds sel reveal true
450 hydrogen bonds found
> select clear
> select #5/D:680@OG1
1 atom, 1 residue, 1 model selected
> select add #5/A:682@OE1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #5/D:680@OG1 #5/A:682@OE1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/D THR
680 OG1 and /A GLU 682 OE1: 3.095Å
> select #5/C:680@OG1
1 atom, 1 residue, 1 model selected
> select add #5/D:682@OE1
2 atoms, 2 residues, 1 model selected
> distance #5/C:680@OG1 #5/D:682@OE1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/C THR
680 OG1 and /D GLU 682 OE1: 3.095Å
> select #5/C:682@OE1
1 atom, 1 residue, 1 model selected
> select add #5/B:680@OG1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #5/C:682@OE1 #5/B:680@OG1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/C GLU
682 OE1 and /B THR 680 OG1: 3.095Å
> select #5/B:682@OE1
1 atom, 1 residue, 1 model selected
> select add #5/A:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #5/B:682@OE1 #5/A:680@OG1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/B GLU
682 OE1 and /A THR 680 OG1: 3.095Å
> select : 570, 689, 581, 586, 677,680, 682, 471, 690
960 atoms, 876 bonds, 142 pseudobonds, 108 residues, 5 models selected
> ui tool show H-Bonds
> hbonds sel reveal true
582 hydrogen bonds found
> select clear
> select :471, 536
192 atoms, 180 bonds, 36 pseudobonds, 24 residues, 4 models selected
> hide sel & #!5 atoms
> select :417, 690
252 atoms, 240 bonds, 28 pseudobonds, 24 residues, 5 models selected
> color (#!5 & sel) lime
> color (#!5 & sel) byhetero
> select clear
[Repeated 1 time(s)]
> select #5/B:417@ND1
1 atom, 1 residue, 1 model selected
> select add #5/B:690@NH1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #5/B:417@ND1 #5/B:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/B HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select #5/C:417@ND1
1 atom, 1 residue, 1 model selected
> select add #5/C:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #5/C:417@ND1 #5/C:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/C HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select #5/D:417@ND1
1 atom, 1 residue, 1 model selected
> select add #5/D:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #5/D:417@ND1 #5/D:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/D HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select #5/A:417@ND1
1 atom, 1 residue, 1 model selected
> select add #5/A:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #5/A:417@ND1 #5/A:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/A HIS
417 ND1 and ARG 690 NH1: 3.013Å
> select #5/A:689@OE2
1 atom, 1 residue, 1 model selected
> select add #5/A:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #5/A:689@OE2 #5/A:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/A GLU
689 OE2 and GLN 570 NE2: 2.602Å
> select #5/D:581@NZ
1 atom, 1 residue, 1 model selected
> select add #5/D:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #5/D:581@NZ #5/D:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/D LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #5/A:581@NZ
1 atom, 1 residue, 1 model selected
> select add #5/A:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #5/A:581@NZ #5/A:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/A LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #5/B:581@NZ
1 atom, 1 residue, 1 model selected
> select add #5/B:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #5/B:581@NZ #5/B:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/B LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #5/C:581@NZ
1 atom, 1 residue, 1 model selected
> select add #5/C:586@OD2
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #5/C:581@NZ #5/C:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/C LYS
581 NZ and ASP 586 OD2: 2.821Å
> select #5/D:689@OE2
1 atom, 1 residue, 1 model selected
> select add #5/D:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #5/D:689@OE2 #5/D:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/D GLU
689 OE2 and GLN 570 NE2: 2.602Å
> select #5/C:689@OE2
1 atom, 1 residue, 1 model selected
> select add #5/C:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #5/C:689@OE2 #5/C:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb #5/C GLU
689 OE2 and GLN 570 NE2: 2.602Å
> cartoon style sel modeHelix tube sides 20
> hide #3 models
> distance style color gold
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/2--WT-ALL.cxs"
> close #1
> close #2
> select :477
40 atoms, 40 bonds, 4 residues, 1 model selected
> select :677
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel yellow
> select clear
> open 6PLV
Summary of feedback from opening 6PLV fetched from pdb
---
note | Fetching compressed mmCIF 6plv from http://files.rcsb.org/download/6plv.cif
6plv title:
CryoEM structure of zebra fish alpha-1 glycine receptor bound with GABA in
nanodisc, closed state [more info...]
Chain information for 6plv #1
---
Chain | Description | UniProt
A B C D E | Glycine receptor subunit alphaZ1 | GLRA1_DANRE -7-436
Non-standard residues in 6plv #1
---
ABU — γ-amino-butanoic acid (γ(amino)-butyric acid)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
UNL — unknown ligand
> select add #1
14655 atoms, 14965 bonds, 5 pseudobonds, 1800 residues, 2 models selected
> cartoon style (#!1 & sel) xsection oval modeHelix default
> close #1
> open 6PVL
Summary of feedback from opening 6PVL fetched from pdb
---
note | Fetching compressed mmCIF 6pvl from http://files.rcsb.org/download/6pvl.cif
6pvl title:
Cryo-EM structure of mouse TRPV3 in closed state at 42 degrees Celsius [more
info...]
Chain information for 6pvl #1
---
Chain | Description | UniProt
A B C D | Transient receptor potential cation channel subfamily V member 3 | TRPV3_MOUSE 1-791
Non-standard residues in 6pvl #1
---
NA — sodium ion
> ui tool show Matchmaker
> matchmaker #!5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6pvl, chain A (#1) with rsr25_mTRPV3WT_Coot-24_chain-D-
refined_244-C16.pdb, chain A (#5), sequence alignment score = 2850.7
RMSD between 492 pruned atom pairs is 1.249 angstroms; (across all 620 pairs:
1.938)
> select #1:677
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> hide #1 models
> show #1 models
> hide #1 models
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15b.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15b.pdb #2
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!2 to #5
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 rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb, chain A (#5)
with rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15b.pdb, chain A (#2),
sequence alignment score = 3211.5
RMSD between 620 pruned atom pairs is 0.000 angstroms; (across all 620 pairs:
0.000)
> select :677
96 atoms, 84 bonds, 12 residues, 3 models selected
> show sel & #!2,5 atoms
> hide #!2 models
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-
> refined_244-C17.header.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-
refined_244-C17.header.pdb #6
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C17.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C17.pdb #7
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!6 models
> close #7
> close #6
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.pdb #6
---
Chain | Description
A B C D | No description available
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C17.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C17.pdb #7
---
Chain | Description
A B C D | No description available
104 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #6
> close #7
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-WT/rsr25_mTRPV3WT_Coot-24_chain-D-
> refined_244-C18.hede.pdb"
Chain information for rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb
#6
---
Chain | Description
A B C D | No description available
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!6 to #5
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 rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C16.pdb, chain A (#5)
with rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb, chain A (#6),
sequence alignment score = 3207.9
RMSD between 620 pruned atom pairs is 0.046 angstroms; (across all 620 pairs:
0.046)
> close #1
> select :560-707
13440 atoms, 13680 bonds, 83 pseudobonds, 1656 residues, 8 models selected
> select ~sel & ##selected
47520 atoms, 48588 bonds, 36 pseudobonds, 5796 residues, 8 models selected
> hide sel & #!5-6 cartoons
> select clear
> hide #!5 models
> hide #!6 atoms
> color #6 #dd33ddff
> color #6 #eeee88ff
> color #6 violet
> select :570, 689, 581, 586, 677,680, 682,417, 690
960 atoms, 876 bonds, 35 pseudobonds, 108 residues, 5 models selected
> show sel & #!6 atoms
> hide sel & #!6 atoms
> select :570, 689, 581, 586, 677,680, 682, 690
840 atoms, 756 bonds, 27 pseudobonds, 96 residues, 5 models selected
> show sel & #!6 atoms
> color (#!6 & sel) lime
> ui tool show H-Bonds
> hbonds sel reveal true
557 hydrogen bonds found
> color (#!6 & sel) byhetero
> show #3 models
> select :570, 689, 581, 586, 677,680, 682, 690, 417
960 atoms, 876 bonds, 191 pseudobonds, 108 residues, 5 models selected
> color (#!6 & sel) lime
> color (#!6 & sel) byhetero
> select clear
> cartoon style #3,6#!4 modeHelix tube sides 20
> show #!5 models
> hide #!5 models
> select #6/C:417@ND1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #6/C:417@ND1
1 atom, 1 residue, 1 model selected
> select add #6/C:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #6/C:417@ND1 #6/C:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/C
HIS 417 ND1 and ARG 690 NH1: 3.013Å
> select #6/C:689@OE2
1 atom, 1 residue, 1 model selected
> select add #6/C:570@NE2
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #6/C:689@OE2 #6/C:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/C
GLU 689 OE2 and GLN 570 NE2: 2.602Å
> select #6/C:581@NZ
1 atom, 1 residue, 1 model selected
> select add #6/C:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #6/C:581@NZ #6/C:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/C
LYS 581 NZ and ASP 586 OD2: 2.821Å
> select #6/B:581@NZ
1 atom, 1 residue, 1 model selected
> select add #6/B:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #6/B:581@NZ #6/B:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/B
LYS 581 NZ and ASP 586 OD2: 2.821Å
> select #6/B:690@NH1
1 atom, 1 residue, 1 model selected
> select add #6/B:417@ND1
2 atoms, 2 residues, 1 model selected
> distance #6/B:690@NH1 #6/B:417@ND1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/B
ARG 690 NH1 and HIS 417 ND1: 3.013Å
> select #6/B:689@OE2
1 atom, 1 residue, 1 model selected
> select add #6/B:570@NE2
2 atoms, 2 residues, 1 model selected
> distance #6/B:689@OE2 #6/B:570@NE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/B
GLU 689 OE2 and GLN 570 NE2: 2.602Å
> select #6/B:680@OG1
1 atom, 1 residue, 1 model selected
> select add #6/C:682@OE2
2 atoms, 2 residues, 1 model selected
> distance #6/B:680@OG1 #6/C:682@OE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/B
THR 680 OG1 and /C GLU 682 OE2: 3.770Å
> ~distance #5/B:417@ND1 #5/B:690@NH1
> ~distance #6/C:417@ND1 #6/C:690@NH1
> select clear
> ~distance #6/B:680@OG1 #6/C:682@OE2
> select #6/C:682@OE1
1 atom, 1 residue, 1 model selected
> select add #6/B:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #6/C:682@OE1 #6/B:680@OG1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/C
GLU 682 OE1 and /B THR 680 OG1: 3.095Å
> select #6/C:680@OG1
1 atom, 1 residue, 1 model selected
> select add #6/D:682@OE1
2 atoms, 2 residues, 1 model selected
> distance #6/C:680@OG1 #6/D:682@OE1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/C
THR 680 OG1 and /D GLU 682 OE1: 3.095Å
> select #6/B:682@OE1
1 atom, 1 residue, 1 model selected
> select add #6/A:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #6/B:682@OE1 #6/A:680@OG1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/B
GLU 682 OE1 and /A THR 680 OG1: 3.095Å
> select #6/D:680@OG1
1 atom, 1 residue, 1 model selected
> select add #6/A:682@OE1
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> distance #6/D:680@OG1 #6/A:682@OE1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/D
THR 680 OG1 and /A GLU 682 OE1: 3.095Å
> select #6/A:586@OD2
1 atom, 1 residue, 1 model selected
> select add #6/A:581@NZ
2 atoms, 2 residues, 1 model selected
> distance #6/A:586@OD2 #6/A:581@NZ
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/A
ASP 586 OD2 and LYS 581 NZ: 2.821Å
> select #6/D:570@NE2
1 atom, 1 residue, 1 model selected
> select add #6/D:689@OE2
2 atoms, 2 residues, 1 model selected
> distance #6/D:570@NE2 #6/D:689@OE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/D
GLN 570 NE2 and GLU 689 OE2: 2.602Å
> select #6/D:581@NZ
1 atom, 1 residue, 1 model selected
> select add #6/D:586@OD2
2 atoms, 2 residues, 1 model selected
> distance #6/D:581@NZ #6/D:586@OD2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/D
LYS 581 NZ and ASP 586 OD2: 2.821Å
> select #6/C:690@NH1
1 atom, 1 residue, 1 model selected
> select add #6/C:417@ND1
2 atoms, 2 residues, 1 model selected
> distance #6/C:690@NH1 #6/C:417@ND1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/C
ARG 690 NH1 and HIS 417 ND1: 3.013Å
> select #6/A:570@NE2
1 atom, 1 residue, 1 model selected
> select add #6/A:689@OE2
2 atoms, 2 residues, 1 model selected
> distance #6/A:570@NE2 #6/A:689@OE2
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/A
GLN 570 NE2 and GLU 689 OE2: 2.602Å
> select #6/A:690@NH1
1 atom, 1 residue, 1 model selected
> select add #6/A:417@ND1
2 atoms, 2 residues, 1 model selected
> distance #6/A:690@NH1 #6/A:417@ND1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/A
ARG 690 NH1 and HIS 417 ND1: 3.013Å
> distance style color gold
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select :677
96 atoms, 84 bonds, 12 residues, 3 models selected
> color (#!6 & sel) yellow
> select clear
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/3--WT-ALL.cxs"
> close #5
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/3--WT-ALL.cxs"
> hide #3 models
> save C:\Users\anon/Desktop\image370.png supersample 3
> select add #6/D:689
9 atoms, 9 bonds, 1 residue, 1 model selected
> select clear
> select #6/D:417@ND1
1 atom, 1 residue, 1 model selected
> select add #6/D:690@NH1
2 atoms, 2 residues, 1 model selected
> distance #6/D:417@ND1 #6/D:690@NH1
Distance between rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb #6/D
HIS 417 ND1 and ARG 690 NH1: 3.013Å
> show #4.1 models
> hide #4.1 models
> distance style color gold
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> select clear
> save C:\Users\anon/Desktop\image371.png supersample 3
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/3--WT-ALL.cxs"
> select /d
10160 atoms, 10378 bonds, 67 pseudobonds, 1242 residues, 6 models selected
> select clear
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/4--WT-ALL.cxs"
> select /d
10160 atoms, 10378 bonds, 67 pseudobonds, 1242 residues, 6 models selected
> hide sel & #!6 cartoons
> hide sel & #!6 atoms
> select /a
10160 atoms, 10378 bonds, 65 pseudobonds, 1242 residues, 6 models selected
> hide sel & #!6 cartoons
> hide sel & #!6 atoms
> select /c: 560-607
774 atoms, 792 bonds, 21 pseudobonds, 96 residues, 4 models selected
> hide sel & #!6 cartoons
> hide sel & #!6 atoms
> select /b: 608
16 atoms, 14 bonds, 2 residues, 2 models selected
> select /b: 608-650
514 atoms, 518 bonds, 2 pseudobonds, 66 residues, 4 models selected
> hide sel & #!6 cartoons
> select /b: 608, 609, 650
56 atoms, 54 bonds, 6 residues, 2 models selected
> show sel & #!6 cartoons
> select /c: 651
14 atoms, 14 bonds, 2 residues, 2 models selected
> select /c: 649
14 atoms, 12 bonds, 2 residues, 2 models selected
> select /c: 608-649
490 atoms, 492 bonds, 2 pseudobonds, 64 residues, 4 models selected
> hide sel & #!6 cartoons
> select /c: 690, 417
42 atoms, 40 bonds, 3 pseudobonds, 4 residues, 4 models selected
> hide sel & #!6 atoms
> select clear
> select /b: 530-550
344 atoms, 352 bonds, 42 residues, 2 models selected
> show sel & #!6 cartoons
> hide sel & #!6 cartoons
> select /b: 550-560
156 atoms, 158 bonds, 22 residues, 2 models selected
> show sel & #!6 cartoons
> select /b: 545-560
242 atoms, 246 bonds, 32 residues, 2 models selected
> show sel & #!6 cartoons
> select /b: 545-547
60 atoms, 60 bonds, 6 residues, 2 models selected
> hide sel & #!6 cartoons
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/WT-2subunit.cxs"
> view
> select /c: 689
18 atoms, 16 bonds, 2 residues, 2 models selected
> hide sel & #!6 atoms
> select clear
> select /c: 680
14 atoms, 12 bonds, 2 residues, 2 models selected
> hide sel & #!6 atoms
> select /b: 682
18 atoms, 16 bonds, 2 residues, 2 models selected
> hide sel & #!6 atoms
> select clear
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/final/WT-2subunit.cxs"
——— End of log from Wed Jan 22 10:24:18 2025 ———
opened ChimeraX session
> open C:/Users/anon/Box/Cryo-EM-2025/TRPV3-WT-Refine/WT-FINAL-Feb-2025/WT-
> refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb
Chain information for WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb
#1
---
Chain | Description
A B C D | No description available
86 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!2,6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb, chain A
(#1) with rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C15b.pdb, chain A (#2),
sequence alignment score = 3177.3
RMSD between 620 pruned atom pairs is 0.100 angstroms; (across all 620 pairs:
0.100)
Matchmaker WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb, chain A
(#1) with rsr25_mTRPV3WT_Coot-24_chain-D-refined_244-C18.hede.pdb, chain A
(#6), sequence alignment score = 3173.7
RMSD between 620 pruned atom pairs is 0.091 angstroms; (across all 620 pairs:
0.091)
> view
> select : 417, 690, 680, 682
444 atoms, 408 bonds, 52 pseudobonds, 48 residues, 5 models selected
> show sel & #!1,6 atoms
> hide #!6 models
> ui tool show H-Bonds
> hbonds sel reveal true
227 hydrogen bonds found
> show #3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!1 models
> hide #!6 models
> show #!1 models
> show #!6 models
> select : 417, 690, 680, 682, 581, 58+6
Expected an objects specifier or a keyword
> select : 417, 690, 680, 682, 581, 586
648 atoms, 588 bonds, 94 pseudobonds, 72 residues, 5 models selected
> ui tool show H-Bonds
> hbonds sel reveal true
387 hydrogen bonds found
> hide #!6 models
> select clear
> select #1 : 117-438
10200 atoms, 10364 bonds, 8 pseudobonds, 1272 residues, 3 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> select #1 : 117-438, 709-758
1644 atoms, 1688 bonds, 192 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1 : 117-438, 709-758, 348-567
4140 atoms, 4284 bonds, 4 pseudobonds, 492 residues, 2 models selected
> delete atoms (#!1 & sel)
> delete bonds (#!1 & sel)
> color #1 rosybrown
> select #1 : 694-707
484 atoms, 484 bonds, 56 residues, 1 model selected
> select #1 : 694-709
512 atoms, 516 bonds, 60 residues, 1 model selected
> hide sel cartoons
> select #1 : 694-709,568-674
3604 atoms, 3668 bonds, 16 pseudobonds, 448 residues, 3 models selected
> select #1 : 694-709,568-673
3572 atoms, 3636 bonds, 16 pseudobonds, 444 residues, 3 models selected
> select #1 : 694-709,568-670
3476 atoms, 3540 bonds, 16 pseudobonds, 432 residues, 3 models selected
> hide sel cartoons
> select clear
> select #1 : 694-709,568-670, 577-590
3476 atoms, 3540 bonds, 16 pseudobonds, 432 residues, 3 models selected
> hide sel atoms
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/WT.cxs"
——— End of log from Wed Feb 26 17:33:05 2025 ———
opened ChimeraX session
> select #1 : 677
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel orange
> show sel atoms
> select clear
> select #1/A:680@OG1
1 atom, 1 residue, 1 model selected
> select add #1/B:682@OE2
2 atoms, 1 pseudobond, 2 residues, 2 models selected
> ui tool show Distances
> distance #1/A:680@OG1 #1/B:682@OE2
Distance between WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb #1/A
THR 680 OG1 and /B GLU 682 OE2: 2.787Å
> select #1/B:680@OG1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #1/C:682@OE2
1 atom, 1 residue, 1 model selected
> select add #1/B:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/C:682@OE2 #1/B:680@OG1
Distance between WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb #1/C
GLU 682 OE2 and /B THR 680 OG1: 2.787Å
> select #1/D:682@OE2
1 atom, 1 residue, 1 model selected
> select add #1/C:680@OG1
2 atoms, 2 residues, 1 model selected
> distance #1/D:682@OE2 #1/C:680@OG1
Distance between WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb #1/D
GLU 682 OE2 and /C THR 680 OG1: 2.787Å
> select #1/D:680@OG1
1 atom, 1 residue, 1 model selected
> select add #1/A:682@OE2
2 atoms, 2 residues, 1 model selected
> distance #1/D:680@OG1 #1/A:682@OE2
Distance between WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb #1/D
THR 680 OG1 and /A GLU 682 OE2: 2.787Å
> distance style color black
[Repeated 2 time(s)]
> select clear
> select #1 : 690
44 atoms, 40 bonds, 4 residues, 1 model selected
> hide sel atoms
> hide #3 models
> select clear
> select #1 : 680, 682
64 atoms, 56 bonds, 8 pseudobonds, 8 residues, 3 models selected
> color (#!1 & sel) byhetero
> select clear
> size #1 : 680, 682 stickRadius +.1
Changed 56 bond radii
> select #1: 680, 682
64 atoms, 56 bonds, 8 pseudobonds, 8 residues, 3 models selected
> view sel
> select clear
> save C:\Users\anon/Desktop\image78.png supersample 3
> save C:\Users\anon/Desktop\image79.png supersample 3
> save C:\Users\anon/Desktop\image80.png supersample 3
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/WT.cxs"
——— End of log from Wed Feb 26 17:44:38 2025 ———
opened ChimeraX session
> close #6
> close #2
> select /C
1056 atoms, 1075 bonds, 7 pseudobonds, 131 residues, 3 models selected
> hide sel cartoons
> select /D
1056 atoms, 1075 bonds, 7 pseudobonds, 131 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> select /C
1056 atoms, 1075 bonds, 7 pseudobonds, 131 residues, 3 models selected
> hide sel atoms
> select /a : 680, 682
16 atoms, 14 bonds, 2 residues, 1 model selected
> view sel
> select clear
> view
> select /a : 682
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select /b : 680
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> save C:\Users\anon/Desktop\image81.png supersample 3
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/WT--Orient1.cxs"
> select /A:680@OG1
1 atom, 1 residue, 1 model selected
> select add /B:682@CD
2 atoms, 2 residues, 1 model selected
> view sel
> select clear
> save C:\Users\anon/Desktop\image82.png supersample 3
> view
> save C:\Users\anon/Desktop\image83.png supersample 3
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/350/350-Most current PDB/J350-6dvw-C4_unsharp-phenix-
> refined_359-C5.pdb"
Chain information for J350-6dvw-C4_unsharp-phenix-refined_359-C5.pdb #2
---
Chain | Description
A B C D | No description available
> ui tool show Matchmaker
> matchmaker #!2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb, chain A
(#1) with J350-6dvw-C4_unsharp-phenix-refined_359-C5.pdb, chain A (#2),
sequence alignment score = 2383.8
RMSD between 114 pruned atom pairs is 0.962 angstroms; (across all 131 pairs:
1.426)
> select #2 : 117-438
10220 atoms, 10384 bonds, 4 pseudobonds, 1276 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2 : 117-438 , 709-758
1716 atoms, 1764 bonds, 200 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> delete atoms sel
> delete bonds sel
> select #2 : 117-438 , 709-758, 671-695
812 atoms, 816 bonds, 100 residues, 1 model selected
> select ~sel & ##selected
7640 atoms, 7860 bonds, 8 pseudobonds, 928 residues, 2 models selected
> hide sel cartoons
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350-WT--Orient1.cxs"
> select #2 : 681, 683, 678
96 atoms, 84 bonds, 12 residues, 1 model selected
> show sel atoms
> select clear
> hide #!1 models
> color #2 cornflowerblue
> select #2 : 681, 683, 678
96 atoms, 84 bonds, 12 residues, 1 model selected
> color sel byhetero
> select clear
> select #2 : 678
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel yellow
> select clear
> save C:\Users\anon/Desktop\image84.png supersample 3
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2/B
2113 atoms, 2169 bonds, 2 pseudobonds, 257 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/C
2113 atoms, 2169 bonds, 2 pseudobonds, 257 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> hide #!1 models
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350-WT--Orient2.cxs"
——— End of log from Wed Feb 26 18:37:53 2025 ———
opened ChimeraX session
> select #2 : 671-695
812 atoms, 816 bonds, 100 residues, 1 model selected
> show sel cartoons
> select #2 : 678, 681, 683
96 atoms, 84 bonds, 12 residues, 1 model selected
> show sel atoms
> select clear
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350--Orient1.cxs"
> size #2 : 681, 683 stickRadius +.1
Changed 56 bond radii
> select clear
> size #2 : 678
> select #2 : 678
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel orange
> select #2 : 681, 683
64 atoms, 56 bonds, 8 residues, 1 model selected
> view sel
> select clear
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350--Orient1.cxs"
——— End of log from Thu Feb 27 11:53:00 2025 ———
opened ChimeraX session
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/350/350-Most current PDB/J350-6dvw-C4_unsharp-phenix-
> refine_359-C7_034-C1_refined_036-C3-SYM-H.pdb"
Chain information for J350-6dvw-C4_unsharp-phenix-
refine_359-C7_034-C1_refined_036-C3-SYM-H.pdb #5
---
Chain | Description
A B C D | No description available
> ui tool show Matchmaker
> matchmaker #!1,5 to #2
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 J350-6dvw-C4_unsharp-phenix-refined_359-C5.pdb, chain A (#2) with
WT-refined-244-C17_refined_028-C8-SYM-H-417_691_del.pdb, chain A (#1),
sequence alignment score = 2382.6
RMSD between 114 pruned atom pairs is 0.962 angstroms; (across all 130 pairs:
1.415)
Matchmaker J350-6dvw-C4_unsharp-phenix-refined_359-C5.pdb, chain A (#2) with
J350-6dvw-C4_unsharp-phenix-refine_359-C7_034-C1_refined_036-C3-SYM-H.pdb,
chain A (#5), sequence alignment score = 2661.3
RMSD between 256 pruned atom pairs is 0.308 angstroms; (across all 257 pairs:
0.353)
> select #5: 683
36 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #5: 683, 678
68 atoms, 60 bonds, 8 residues, 1 model selected
> show sel atoms
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> select clear
> hide #!2 models
> hide #!5 models
> show #!2 models
> select #5: 671-695
812 atoms, 816 bonds, 100 residues, 1 model selected
> show #!5 models
> select ~sel & ##selected
19576 atoms, 20016 bonds, 12 pseudobonds, 2404 residues, 2 models selected
> hide sel cartoons
> select #5: 681
28 atoms, 24 bonds, 4 residues, 1 model selected
> show sel atoms
> color #5 cornflowerblue
> select #5: 681, 683, 678
96 atoms, 84 bonds, 12 residues, 1 model selected
> color sel byhetero
> select #5: 678
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel orange
> select clear
> hide #!2 models
> size #5 : 681, 683 stickRadius +.1
Changed 56 bond radii
> save C:\Users\anon/Desktop\image110.png supersample 3
> save C:\Users\anon/Desktop\image111.png supersample 3
> save C:\Users\anon/Desktop\image112.png supersample 3
> show #!1 models
> hide #!1 models
> save C:\Users\anon/Desktop\image113.png supersample 3
> save "C:/Users/anon/Box/Cryo-EM paper/Draft-2-figures/FIGURES-
> Dec_2024/Domain-domain interactions/Feb-2025/350--Orient1b.cxs"
——— End of log from Mon Mar 3 14:44:48 2025 ———
opened ChimeraX session
> select #5/a : 565-607
352 atoms, 361 bonds, 43 residues, 1 model selected
> show sel cartoons
> view
> select #5/a : 582, 587,680
26 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #5/a : 582, 587,680, 690
35 atoms, 31 bonds, 4 residues, 1 model selected
> select #5/a : 582, 587,680, 590
35 atoms, 31 bonds, 4 residues, 1 model selected
> show sel atoms
> select #5/a : 590
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select #5/a : 590, 582, 587
26 atoms, 23 bonds, 3 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel showDist true angleSlop 0.0 saltOnly true reveal true
3 hydrogen bonds found
> show #!3 models
> ui tool show H-Bonds
> hbonds sel showDist true angleSlop 0.0 reveal true
9 hydrogen bonds found
> hide #!3 models
> select #5/A:582@NZ
1 atom, 1 residue, 1 model selected
> select add #5/A:587@OD2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #5/A:582@NZ #5/A:587@OD2
Distance between J350-6dvw-C4_unsharp-phenix-
refine_359-C7_034-C1_refined_036-C3-SYM-H.pdb #5/A LYS 582 NZ and ASP 587 OD2:
3.382Å
> select #5/a :587
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/a :590
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #5/a :574
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/a :568
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/a :582
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/a :587
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel showDist true angleSlop 0.0 saltOnly true reveal true
2 hydrogen bonds found
> show #!3 models
> ui tool show H-Bonds
> hbonds sel showDist true angleSlop 0.0 reveal true
5 hydrogen bonds found
> close
> open C:/Users/anon/Box/Cryo-EM-2025/V3-42C-refine/FINAL-
> refine_099-pdb/J1199-412s-phenix-Chain-A-067-C6-SYM-Beta-C3_080-C16-SYM-
> refined_099-C2.pdb
Chain information for J1199-412s-phenix-Chain-A-067-C6-SYM-
Beta-C3_080-C16-SYM-refined_099-C2.pdb #1
---
Chain | Description
A B C D | No description available
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/V3-412S-42C-HEAT/C4-J1199_008_volume_map_inv_2_5A.mrc"
Opened C4-J1199_008_volume_map_inv_2_5A.mrc as #2, grid size 384,384,384,
pixel 0.825, shown at level 0.0425, step 2, values float32
> volume #2 level 0.09739
> select #5/a :587
Nothing selected
> select #5/a :587
Nothing selected
> select #5/a :587
Nothing selected
> select #1/a : 582
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> surface zone #2 nearAtoms #1/a : 582
> volume #2 level 0.009178
> volume #2 step 1
> volume #2 style mesh
> volume #2 level 0.02803
> surface zone #2 nearAtoms #1/a : 582, 688
> volume #2 level 0.01432
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/42-C_582-688-
> DENSITY.cxs"
> select clear
> select H
21068 atoms, 2552 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> sEL #1: 582, 688
Unknown command: sEL #1: 582, 688
> select #1: 582, 688
72 atoms, 64 bonds, 8 residues, 1 model selected
> select #1/a: 582, 688
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> select ~sel & ##selected
20758 atoms, 21212 bonds, 4 pseudobonds, 2550 residues, 2 models selected
> hide sel cartoons
> volume #2 level 0.02974
> volume #2 level 0.0006103
> surface dust #2 size 8.25
[Repeated 1 time(s)]
> volume #2 level 0.0246
> volume #2 level 0.2251
> select #1/a: 582, 688
18 atoms, 16 bonds, 2 residues, 1 model selected
> view sel
> volume #2 level 0.1925
> volume #2 level 0.1566
> volume #2 level 0.05202
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/2--42-C_582-688-
> DENSITY.cxs"
> select #2
2 models selected
> select clear
> volume #2 level 0.02289
> select #1/a: 582, 688
18 atoms, 16 bonds, 2 residues, 1 model selected
> view sel
> select #2
2 models selected
> select clear
> color #1 burlywood
> select #1/a: 582, 688
18 atoms, 16 bonds, 2 residues, 1 model selected
> color sel byhetero
> select clear
> select #1/a: 680-698
163 atoms, 164 bonds, 19 residues, 1 model selected
> show sel cartoons
> select #2
2 models selected
> select clear
> volume #2 level 0.01432
> volume #2 level 0.03831
> volume #2 level 0.03488
> save C:\Users\anon/Desktop\image122.png supersample 3
> select #1/a: 575-585
90 atoms, 90 bonds, 11 residues, 1 model selected
> show sel cartoons
> select #2
2 models selected
> select clear
> select #1/a: 575-595
181 atoms, 185 bonds, 21 residues, 1 model selected
> show sel cartoons
> select clear
> save C:\Users\anon/Desktop\image123.png supersample 3
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/3--42-C_582-688-
> DENSITY.cxs"
> volume #2 level 0.05545
> volume #2 level 0.0654
> volume #2 level 0.0454
> volume #2 level 0.0354
> save C:\Users\anon/Desktop\image124.png supersample 3
> volume #2 step 2
> volume #2 step 1
> volume #2 color blue
> volume #2 color #00007f
> volume #2 color #550000
> volume #2 color blue
> volume #2 color #00007f
> volume #2 color blue
> save C:\Users\anon/Desktop\image125.png supersample 3
> select #1/a: 587
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #2
2 models selected
> select clear
> volume #2 level 0.02683
> select #1/a: 680
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> volume #2 level 0.009696
> volume #2 level 0.04911
> volume #2 level 0.03711
> open C:/Users/anon/Box/Cryo-EM-2025/V3-42C-refine/FINAL-
> refine_099-pdb/J1199-412s-phenix-Chain-A-067-C6-SYM-Beta-C3_080-C16-SYM-
> refined_099-C3.pdb
Chain information for J1199-412s-phenix-Chain-A-067-C6-SYM-
Beta-C3_080-C16-SYM-refined_099-C3.pdb #3
---
Chain | Description
A B C D | No description available
> select #3/a: 680, 582, 688
52 atoms, 49 bonds, 3 residues, 1 model selected
> show sel atoms
> select #2
2 models selected
> select clear
> select H
21068 atoms, 2552 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!1 models
> volume #2 level 0.0234
> volume #2 level 0.02855
> volume #2 level 0.03711
> save C:\Users\anon/Desktop\image126.png supersample 3
> color #3 burlywood
> select #3/a: 680, 582, 688
27 atoms, 24 bonds, 3 residues, 1 model selected
> color sel byhetero
> select clear
> save C:\Users\anon/Desktop\image127.png supersample 3
> select #3/a: 680
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #3/D:672
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> color #2 #b2b2b2ff models
> save C:\Users\anon/Desktop\image128.png supersample 3
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> close #1
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/4--42-C_582-688-
> DENSITY.cxs"
——— End of log from Wed Mar 12 11:21:59 2025 ———
opened ChimeraX session
> volume #2 level 0.0486
> hide #!2 models
> hide #!3 models
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/350/350-Most current PDB/J350-6dvw-C4_unsharp-phenix-
> refine_359-C7_034-C1_refined_036-C3-SYM-H.pdb"
Chain information for J350-6dvw-C4_unsharp-phenix-
refine_359-C7_034-C1_refined_036-C3-SYM-H.pdb #1
---
Chain | Description
A B C D | No description available
> view
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/350/J350_009_C4-unsharp_volume_map_inverted.mrc"
Opened J350_009_C4-unsharp_volume_map_inverted.mrc as #4, grid size
432,432,432, pixel 0.825, shown at level 0.0473, step 2, values float32
> volume #2 level 0.112
> volume #4 level 0.1748
> volume #4 style mesh
> volume #4 step 1
> select #1/a: 582, 587
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> view sel
> volume #4 level 0.07191
> volume #4 level 0.05476
> surface dust #4 size 8.25
> select clear
> surface dust #4 size 8.25
> volume #4 level 0.06411
> select #1/a: 582, 587, 680
26 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> select #1/a: 582, 587, 681
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/a: 582, 587, 681, 679
28 atoms, 24 bonds, 4 residues, 1 model selected
> show sel atoms
> select #1/a: 679
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1/a: 678
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> volume #4 level 0.08282
> volume #4 level 0.06879
> volume #4 level 0.0588
> select #1/a: 678-683
44 atoms, 43 bonds, 6 residues, 1 model selected
> show sel atoms
> select clear
> volume #4 level 0.09778
> volume #4 level 0.07439
> volume #4 level 0.104
> volume #4 level 0.06192
> select #1/a: 587, 582
17 atoms, 15 bonds, 2 residues, 1 model selected
> view sel
> select clear
> select #1/a: 587, 582, 688
26 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> volume #4 level 0.02605
> volume #4 level -0.005133
> volume #4 level -0.0513
> volume #4 level 0.0407
> select #4
2 models selected
> select clear
> volume #4 level 0.06877
> volume #4 level 0.0588
> select #1/a: 678-6888
692 atoms, 707 bonds, 81 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select clear
> select #1/a: 670-688
144 atoms, 143 bonds, 19 residues, 1 model selected
> select #1/a: 670-698
236 atoms, 237 bonds, 29 residues, 1 model selected
> select #1/a: 670-698, 575-589
359 atoms, 361 bonds, 44 residues, 1 model selected
> select #1/a: 670-698, 570-592
425 atoms, 429 bonds, 52 residues, 1 model selected
> select ~sel & ##selected
19963 atoms, 20403 bonds, 12 pseudobonds, 2452 residues, 2 models selected
> hide sel cartoons
> color #1 cornflowerblue
> select #1/a: 670-698, 570-592
425 atoms, 429 bonds, 52 residues, 1 model selected
> color sel byhetero
> select #4
2 models selected
> select clear
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/350-C_582-587-
> DENSITY.cxs"
> surface zone #4 nearAtoms #1/a: 670-698, 570-592
> volume #4 level 0.051
> select #1/a: 670-698, 570-592
425 atoms, 429 bonds, 52 residues, 1 model selected
> select clear
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/2--350-C_582-587-
> DENSITY.cxs"
> volume #4 level 0.051
> select #1/a: 670-698, 570-592
425 atoms, 429 bonds, 52 residues, 1 model selected
> show sel atoms
> select clear
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/2--350-C_582-587-
> DENSITY.cxs"
> save C:\Users\anon/Desktop\image129.png supersample 3
> close #2
> close #3
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/2--350-C_582-587-
> DENSITY.cxs"
> select #1/a: 680
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> hide #!1 models
> hide #!4 models
> open C:/Users/anon/Box/Cryo-
> EM-2025/412S-refine/RealSpaceRefine_73/412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
> H-edit696-A.pdb
Chain information for
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A.pdb #2
---
Chain | Description
A B C D | No description available
> view
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-412S/Inverted-MV3-412s-cryosparc-map2-fit-1.mrc"
Opened Inverted-MV3-412s-cryosparc-map2-fit-1.mrc as #3, grid size
384,384,384, pixel 0.874, shown at level 0.148, step 2, values float32
> surface dust #3 size 8.74
> volume #3 style mesh
> volume #3 step 1
> volume #3 level 0.843
> select #2/a: 696
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> volume #3 level 0.5629
> ui tool show H-Bonds
> hbonds sel showDist true angleSlop 0.0 reveal true
3 hydrogen bonds found
> close #5
> show sel atoms
> hide sel atoms
> select add #2
20060 atoms, 20492 bonds, 16 pseudobonds, 2468 residues, 2 models selected
> hide sel atoms
> select clear
> select #2/a: 670-698, 570-592
425 atoms, 429 bonds, 52 residues, 1 model selected
> select ~sel & ##selected
19635 atoms, 20063 bonds, 16 pseudobonds, 2416 residues, 2 models selected
> hide sel cartoons
> select #2/a: 670-698, 570-592
425 atoms, 429 bonds, 52 residues, 1 model selected
> surface zone #3 nearAtoms #2/a: 670-698, 570-592
> volume #3 level 0.3139
> show sel atoms
> volume #3 level 0.3036
> select clear
> sel#2/a: 582
Unknown command: sel#2/a: 582
> select #2/a: 582
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel showDist true angleSlop 0.0 reveal true
1 hydrogen bonds found
> select clear
> select #2/A:582@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:680@OE2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #2/A:582@NZ #2/A:680@OE2
Distance between
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A.pdb #2/A LYS 582 NZ and GLU 680 OE2: 3.549Å
> select #2/A:582@NZ
1 atom, 1 residue, 1 model selected
> select #2/A:582@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:587@OD2
2 atoms, 2 residues, 1 model selected
> distance #2/A:582@NZ #2/A:587@OD2
Distance between
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A.pdb #2/A LYS 582 NZ and ASP 587 OD2: 4.678Å
> select subtract #2/A:582@NZ
1 atom, 1 residue, 1 model selected
> select clear
> select #2/A:582@NZ
1 atom, 1 residue, 1 model selected
> select add #2/A:587@OD1
2 atoms, 2 residues, 1 model selected
> distance #2/A:582@NZ #2/A:587@OD1
Distance between
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A.pdb #2/A LYS 582 NZ and ASP 587 OD1: 4.158Å
> hide #6.1 models
> ~distance #2/A:582@NZ #2/A:587@OD2
> ~distance #2/A:582@NZ #2/A:587@OD1
> distance style color black
[Repeated 2 time(s)]
> select clear
> hide #!5 models
> volume #4 color #ff5500
> volume #4 color #ff557f
> volume #4 color #b2b2b2
> color #3 #b2b2b2ff models
> color #2 darkseagreen
> select add #2
20060 atoms, 20492 bonds, 18 pseudobonds, 2468 residues, 4 models selected
> color (#!2 & sel) byhetero
> select clear
> distance style color gold
[Repeated 2 time(s)]
> distance style color black
[Repeated 2 time(s)]
> volume #4 level 0.04135
> volume #4 level 0.03814
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/412S-_582-680-
> DENSITY.cxs"
> volume #3 level 0.3678
> volume #3 level 0.3143
> volume #3 level 0.2073
> save C:\Users\anon/Desktop\image130.png supersample 3
> save C:\Users\anon/Desktop\image131.png supersample 3
> close #1
> close #4
> open "C:/Users/anon/Box/Cryo-EM paper/PDB and MRC
> files_Dec-2024/TRPV3-412S/MAPS/INTERPORATED-Inverted-MV3-412s-cryosparc-
> map2-fit-1.mrc"
Opened INTERPORATED-Inverted-MV3-412s-cryosparc-map2-fit-1.mrc as #1, grid
size 768,768,768, pixel 0.437, shown at step 1, values float32
> volume #1 region 0,0,0,767,767,767 step 4
[Repeated 1 time(s)]
> volume #1 change image level -0.06106,0 level 0.3564,0.8 level 2.626,1
> volume #1 level 0.6445
> volume #1 step 1
> volume #1 level 0.1053
> volume #1 level 0.5811
> volume #1 level 0.8666
> volume #1 level 1.184
> surface dust #1 size 4.37
> color #1 #b2b2b2ff models
> surface zone #1 nearAtoms #2/a: 570-592, 670-698
> volume #1 level 0.2744
> volume #1 level 0.294
> volume #1 level 0.304
> volume #1 level 0.39
> volume #1 level 0.395
> volume #1 level 0.385
> volume #1 level 0.375
> volume #1 level 0.355
> volume #1 level 0.335
> volume #1 level 0.315
> volume #1 level 0.3
> volume #1 level 0.29
> volume #1 level 0.28
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/2--412S-_582-680-
> DENSITY.cxs"
> save C:\Users\anon/Desktop\image132.png supersample 3
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!3 models
> volume #1 step 2
> volume #1 level 0.2489
> save C:\Users\anon/Desktop\image133.png supersample 3
> volume #1 level 0.23
> volume #1 step 1
> volume #1 level 0.28
> volume #1 level 0.2
> volume #1 level 0.29
> volume #1 level 0.31
> volume #1 level 0.3
> volume #1 level 0.29
> volume #1 level 0.28
> save C:\Users\anon/Desktop\image134.png supersample 3
> volume #1 level 0.1848
> volume #1 level 0.5
> volume #1 level 0.4
> volume #1 level 0.3
> volume #1 level 0.29
> volume #1 level 0.31
> volume #1 level 0.3
> open C:/Users/anon/Box/Cryo-EM-2025/412S-refine/FINAL-
> Model/412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
> H-edit696-A-C1.pdb
Chain information for
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A-C1.pdb #4
---
Chain | Description
A B C D | No description available
> ui tool show Matchmaker
> matchmaker #!4 to #2
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
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A.pdb, chain A (#2) with
412S-refined_289-coot6-C5-Loop-1_001-C2_029-C5_030-C2_032_035-C2_037-C6_047-C9-24_refined_073-C5-SYM-
H-edit696-A-C1.pdb, chain A (#4), sequence alignment score = 3187.5
RMSD between 617 pruned atom pairs is 0.007 angstroms; (across all 617 pairs:
0.007)
> select #4/a: 570-592, 670-698
425 atoms, 429 bonds, 52 residues, 1 model selected
> select ~sel & ##selected
19635 atoms, 20063 bonds, 16 pseudobonds, 2416 residues, 2 models selected
> hide sel cartoons
> select #4/a: 570-592, 670-698
425 atoms, 429 bonds, 52 residues, 1 model selected
> show sel atoms
> color #4 darkseagreen
> color sel byhetero
> hide #!2 models
> select clear
> save C:\Users\anon/Desktop\image135.png supersample 3
> select #4/a: 570
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #4/a: 569
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/a: 571
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/a: 571, 690
18 atoms, 16 bonds, 2 residues, 1 model selected
> select clear
> close #2
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/412S-_582-680-
> DENSITY.cxs"
> save C:\Users\anon/Desktop\image136.png supersample 3
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/412S-_582-680-
> DENSITY.cxs"
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> select add #3
2 models selected
> select add #1
5 models selected
> save "C:/Users/anon/Box/Cryo-EM
> paper/Draft-2-figures/MARCH-2025-SUPPLEMENTARY FIGURES-/TEST-412S-_582-680-
> DENSITY.cxs" includeMaps true
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 651, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 147, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\\__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 56, in run_provider
what(session)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\toolbar\providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display
run(session, cmd)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\save_command\cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 922, in save
session.save(output, version=version, include_maps=include_maps)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\session.py", line 651, in save
fserialize(stream, data)
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\safesave.py", line 147, in write
self._f.write(buf)
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 740, in write
compressed = self._compressor.compress(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
MemoryError
MemoryError
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress
result = compress_chunk(
^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 456.71
OpenGL renderer: GeForce GT 710/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: Micro-Star International Co., Ltd
Model: MS-7C02
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 17,101,848,576
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5600 6-Core Processor
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406072045
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.46
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 9 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Reporter: | changed from to |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving maps in sessions |
comment:2 by , 9 months ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
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This ChimeraX error says your computer ran out of memory while saving a session. You used the "includeMaps true" option and I see you have at least one large 3 GB map. Your previous saves without the includeMaps option worked. I can't tell exactly why it ran out of memory. You are using an older ChimeraX that had a memory leak problem on Windows that may have contributed, and possibly a current ChimeraX would help.