Opened 8 months ago

Closed 8 months ago

#17000 closed defect (can't reproduce)

MemoryError saving session

Reported by: chimerax-bug-report@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Tom Goddard, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open E:/huawei/HaozhuoDownloads/CRFR2a/20250302.cxs

Log from Sun Mar 2 21:26:07 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\self fig\20220923-3.cxs"
> format session

Log from Fri Sep 23 22:16:09 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\self fig\CD\13.cxs" format
> session

Log from Sun May 22 17:33:39 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/2.cxs"

Log from Tue May 17 16:56:32 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/2.cxs"

Log from Tue May 17 12:54:29 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\self fig\CD\1.cxs" format
> session

Log from Mon May 16 11:38:14 2022UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\pdb\peptide 20211015.cxs"
> format session

Log from Fri Oct 15 10:40:57 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\作图学习\peptide.cxs" format
> session

Log from Thu Oct 14 15:31:06 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\作图学习\peptide.cxs" format
> session

Log from Thu Oct 14 13:34:09 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\自己作图\new pdb\20201223-6.cxs"
> format session

Log from Wed Dec 23 14:21:14 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201223-3.cxs"

Log from Wed Dec 23 11:54:32 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:\huawei\HaozhuoDownloads\CRFR2a\paper 2\自己作图\new pdb\20201211-7.cxs"
> format session

Log from Fri Dec 11 16:50:38 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201211-1.cxs"

Log from Fri Dec 11 11:15:26 2020UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper
> 2/pdb/crf2-g11-seq3-alld31_real_space_refined20201210 ZUIHOU.pdb"

Summary of feedback from opening E:/huawei/HaozhuoDownloads/CRFR2a/paper
2/pdb/crf2-g11-seq3-alld31_real_space_refined20201210 ZUIHOU.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.003 0.046 10113  
  
Ignored bad PDB record found on line 23  
ANGLE : 0.728 9.457 13694  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.050 0.367 1521  
  
17 messages similar to the above omitted  
  
Chain information for crf2-g11-seq3-alld31_real_space_refined20201210
ZUIHOU.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
P | No description available  
U | No description available  
  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper
> 2/pdb/crf2-go-62-1c_real_space_refined20201210ZUIHOU.pdb"

Summary of feedback from opening E:/huawei/HaozhuoDownloads/CRFR2a/paper
2/pdb/crf2-go-62-1c_real_space_refined20201210ZUIHOU.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.004 0.058 10522  
  
Ignored bad PDB record found on line 23  
ANGLE : 0.832 10.039 14274  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.055 0.390 1599  
  
17 messages similar to the above omitted  
  
Chain information for crf2-go-62-1c_real_space_refined20201210ZUIHOU.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
P | No description available  
U | No description available  
  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/pdb/crf2-gs-
> april-19_real_space_refined.pdb"

Summary of feedback from opening E:/huawei/HaozhuoDownloads/CRFR2a/paper
2/pdb/crf2-gs-april-19_real_space_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 22  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 23  
BOND : 0.002 0.044 9846  
  
Ignored bad PDB record found on line 24  
ANGLE : 0.553 7.914 13360  
  
26 messages similar to the above omitted  
  
Chain information for crf2-gs-april-19_real_space_refined.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
N | No description available  
P | No description available  
U | No description available  
  

> show cartoons

> hide atoms

> ui tool show Matchmaker

> matchmaker #!2-3 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 crf2-g11-seq3-alld31_real_space_refined20201210 ZUIHOU.pdb, chain P
(#1) with crf2-go-62-1c_real_space_refined20201210ZUIHOU.pdb, chain P (#2),
sequence alignment score = 1782  
RMSD between 320 pruned atom pairs is 0.688 angstroms; (across all 341 pairs:
1.347)  
  
Matchmaker crf2-g11-seq3-alld31_real_space_refined20201210 ZUIHOU.pdb, chain P
(#1) with crf2-gs-april-19_real_space_refined.pdb, chain P (#3), sequence
alignment score = 1770  
RMSD between 324 pruned atom pairs is 0.849 angstroms; (across all 341 pairs:
1.221)  
  

> ui tool show "Color Actions"

> set bgColor white

> select #1/U#2/U#3/U

990 atoms, 999 bonds, 120 residues, 3 models selected  

> ui tool show "Color Actions"

> set bgColor coral

> set bgColor coral

> ui tool show "Color Actions"

> set bgColor white

No target buttons for the coloring action are checked  

> color sel red

> ui tool show "Color Actions"

No target buttons for the coloring action are checked  

> color sel bychain

No target buttons for the coloring action are checked  

> select #1/U#2/U#3/U

990 atoms, 999 bonds, 120 residues, 3 models selected  

> color sel orange red

> ui tool show "Color Actions"

No target buttons for the coloring action are checked  
No target buttons for the coloring action are checked  

> select #1/B#2/B#3/B

7818 atoms, 7959 bonds, 1017 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel dark red target c

> color sel aquamarine target c

> color sel aquamarine

> ui tool show "Color Actions"

> color sel coral

> color sel aquamarine

> select #1/U#2/U#3/U

990 atoms, 999 bonds, 120 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel coral

> select #1/G#2/G#3/G

1308 atoms, 1326 bonds, 171 residues, 3 models selected  

> ui tool show "Color Actions"

> color sel deep pink

> select #1/H#2/H

3562 atoms, 3654 bonds, 4 pseudobonds, 464 residues, 4 models selected  

> ui tool show "Color Actions"

> color sel medium purple

> color sel medium purple

> color sel medium purple

> select #3/N

961 atoms, 983 bonds, 126 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel slate gray

> select #1/A

1852 atoms, 1884 bonds, 2 pseudobonds, 224 residues, 2 models selected  

> color (#!1 & sel) hot pink

> select #2/A

1767 atoms, 1795 bonds, 4 pseudobonds, 221 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark khaki

> select #3/A

1890 atoms, 1924 bonds, 6 pseudobonds, 227 residues, 2 models selected  

> color sel dark slate blue

> select clear

> select #1/P

2851 atoms, 2940 bonds, 2 pseudobonds, 341 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel cornflower blue

> select #2/P

3137 atoms, 3236 bonds, 381 residues, 1 model selected  

> color sel medium blue

> select #3/P

3162 atoms, 3262 bonds, 384 residues, 1 model selected  

> color sel dark gray

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201211-1.cxs"

opened ChimeraX session  

> select clear

> select #2/B

2616 atoms, 2663 bonds, 341 residues, 1 model selected  

> color sel lime

> select #3/B

2601 atoms, 2648 bonds, 338 residues, 1 model selected  

> color sel forest green

> ui tool show "Color Actions"

> color sel light sea green

> color sel chartreuse

> color sel spring green

> color sel medium aquamarine

> color sel dark cyan

> select clear

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201211-7.cxs"

opened ChimeraX session  

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201223-1.cxs"

> select #1/A#2/A#3/A

5509 atoms, 5603 bonds, 12 pseudobonds, 672 residues, 6 models selected  

> cartoon hide (#!1-3 & sel)

> select #1/G#2/G#3/G

1308 atoms, 1326 bonds, 171 residues, 3 models selected  

> cartoon hide sel

> select #1/H#2/H

3562 atoms, 3654 bonds, 4 pseudobonds, 464 residues, 4 models selected  

> cartoon hide (#!1-2 & sel)

> select #3/N

961 atoms, 983 bonds, 126 residues, 1 model selected  

> cartoon hide sel

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201223-2.cxs"

> ui tool show H-Bonds

> hbonds color #aa00ff dashes 6 showDist true saltOnly true select true reveal
> true retainCurrent true

163 hydrogen bonds found  

> hide #!2 models

> hide #!3 models

> select clear

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!3 models

> hide #!1 models

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201223-3.cxs"

opened ChimeraX session  

> lighting simple

> show #!1 models

> lighting simple

> hide #!1 models

> show #!1 models

> hide #!3 models

> show #!2 models

> show #!3 models

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201223-5.cxs"

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #3-4 target a

> select #1/B#2/B#3/B

7818 atoms, 7959 bonds, 27 pseudobonds, 1017 residues, 4 models selected  

> cartoon hide (#!3 & sel)

> show #!1 models

> show #!2 models

> hide (#!1-3 & sel) target a

> select #1/B#2/B#3/B

7818 atoms, 7959 bonds, 27 pseudobonds, 1017 residues, 4 models selected  

> cartoon hide (#!1-3 & sel)

> hide (#!1-3 & sel) target a

> select #1/G#2/G#3/G

1308 atoms, 1326 bonds, 3 pseudobonds, 171 residues, 4 models selected  

> hide (#!1-3 & sel) target a

> select #1/H#2/H

3562 atoms, 3654 bonds, 33 pseudobonds, 464 residues, 5 models selected  

> hide (#!1-2 & sel) target a

> select #1/A#2/A#3/A

5509 atoms, 5603 bonds, 40 pseudobonds, 672 residues, 9 models selected  

> hide (#!1-3 & sel) target a

> select #1/P#2/P#3/P

9150 atoms, 9438 bonds, 17 pseudobonds, 1106 residues, 5 models selected  

> hide (#!1-3 & sel) target a

> select #1/U#2/U#3/U

990 atoms, 999 bonds, 6 pseudobonds, 120 residues, 4 models selected  

> hide (#!1-3 & sel) target a

> select clear

> hide target a

> ui tool show "Side View"

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/自己作图/new pdb/20201223-6.cxs"

opened ChimeraX session  

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/作图学习/peptide.cxs"

opened ChimeraX session  

> select #1/U

330 atoms, 333 bonds, 1 pseudobond, 40 residues, 2 models selected  

> select #2/U

330 atoms, 333 bonds, 1 pseudobond, 40 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel olive

> select #3/U

330 atoms, 333 bonds, 40 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel fire brick

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/作图学习/peptide.cxs"

> hbonds sel

159 hydrogen bonds found  

> ~hbonds

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> select #1/U

330 atoms, 333 bonds, 40 residues, 1 model selected  

> hbonds sel

176 hydrogen bonds found  

> ~hbonds

> select #1/P:340

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

> select clear

> hbonds sel

19 hydrogen bonds found  

> ~hbonds

> select clear

> show #!2 models

> show #!3 models

> ui tool show "Volume Viewer"

> ui tool show Toolbar

> ui tool show "Side View"

> hide #!2 models

> hide #!3 models

> select #1/U:3

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select #1/P:258

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

> style sel stick

Changed 9 atom styles  

> show sel atoms

> hbonds sel

4 hydrogen bonds found  

> select clear

> hide #!1 models

> show #!2 models

> select #2/P:258

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

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select #2/U:3

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

> style sel stick

Changed 7 atom styles  

> show sel atoms

> hbonds sel

3 hydrogen bonds found  

> show sel atoms

> style sel stick

Changed 16 atom styles  

> select #2/U:9

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

> select #2/U:1

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

> style sel stick

Changed 55 atom styles  

> show sel atoms

> hbonds sel

16 hydrogen bonds found  

> ~hbonds

> show #!1 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide sel atoms

> select clear

> select #2/P:258

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

> show sel atoms

> select #2/U:3

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

> style sel stick

Changed 7 atom styles  

> show sel atoms

> hbonds sel

3 hydrogen bonds found  

> hbonds sel

3 hydrogen bonds found  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> select #3/P:258

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

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select #3/U:8

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

> select clear

> select #3/U:3

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

> show #!2 models

> show #!1 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> select #4

3 pseudobonds, 1 model selected  

> hide #4 models

> show #!1 models

> show #4 models

> show #!3 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> show #!3 models

> hide #4 models

> ~select #4

Nothing selected  

> hide #!2 models

> hide #!1 models

> select #3/P:258@CA

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> style sel stick

Changed 1 atom style  

> show sel atoms

> select #3/P:258

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

> hide sel atoms

> show #!1 models

> show #!2 models

> select clear

> lighting simple

> lighting soft

> save peptide.tif width 2000 height 2000 supersample 3 transparentBackground
> true

> lighting full

> lighting simple

> save peptide2.tif width 2000 height 2000 supersample 3 transparentBackground
> true

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/作图学习/peptide.cxs"

opened ChimeraX session  

> show #4 models

> save peptide3.tif width 2000 height 2000 supersample 3 transparentBackground
> true

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/pdb/peptide 20211015.cxs"

opened ChimeraX session  

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/1.cxs"

opened ChimeraX session  

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self
> fig/CD/修回/crf2-g11-refm15c2i10b-newmap11-ls3_real_space_refined2.pdb"

Summary of feedback from opening E:/huawei/HaozhuoDownloads/CRFR2a/paper
2/self fig/CD/修回/crf2-g11-refm15c2i10b-newmap11-ls3_real_space_refined2.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 21  
BOND : 0.003 0.041 9866  
  
Ignored bad PDB record found on line 22  
ANGLE : 0.686 9.817 13367  
  
Ignored bad PDB record found on line 23  
CHIRALITY : 0.047 0.184 1506  
  
Ignored bad PDB record found on line 24  
PLANARITY : 0.005 0.048 1691  
  
15 messages similar to the above omitted  
  
Chain information for
crf2-g11-refm15c2i10b-newmap11-ls3_real_space_refined2.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
P | No description available  
U | No description available  
  

> hide atoms

> show cartoons

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/修回/crf2-go-
> trunct-Rall2-ls-183b-15c2i10loos3_real_space_refined.pdb"

Summary of feedback from opening E:/huawei/HaozhuoDownloads/CRFR2a/paper
2/self fig/CD/修回/crf2-go-trunct-
Rall2-ls-183b-15c2i10loos3_real_space_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.003 0.055 9812  
  
Ignored bad PDB record found on line 23  
ANGLE : 0.796 8.578 13299  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.052 0.233 1496  
  
17 messages similar to the above omitted  
  
Chain information for crf2-go-trunct-
Rall2-ls-183b-15c2i10loos3_real_space_refined.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
P | No description available  
U | No description available  
  

> hide atoms

> show cartoons

> matchmaker #6/P to #3/P

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 crf2-gs-april-19_real_space_refined.pdb, chain P (#3) with crf2-go-
trunct-Rall2-ls-183b-15c2i10loos3_real_space_refined.pdb, chain P (#6),
sequence alignment score = 1486.4  
RMSD between 269 pruned atom pairs is 0.643 angstroms; (across all 296 pairs:
1.412)  
  

> matchmaker #5/P to #3/P

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 crf2-gs-april-19_real_space_refined.pdb, chain P (#3) with
crf2-g11-refm15c2i10b-newmap11-ls3_real_space_refined2.pdb, chain P (#5),
sequence alignment score = 1659.4  
RMSD between 304 pruned atom pairs is 1.014 angstroms; (across all 330 pairs:
1.306)  
  

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/2.cxs"

> hide #!2 models

> hide #!3 models

> hide #4 models

> hide #!5 models

> hide #!6 models

> hide #5.1 models

> show #!6 models

> show #!5 models

> hide #!6 models

> select #5/B

2601 atoms, 2648 bonds, 338 residues, 1 model selected  

> color sel cornflower blue

> select #5/U

322 atoms, 325 bonds, 39 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel coral

> hide #!5 models

> hide #!1 models

> show #!5 models

> select #5/P

2630 atoms, 2708 bonds, 6 pseudobonds, 330 residues, 2 models selected  

> color (#!5 & sel) cornflower blue

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select #5/U

322 atoms, 325 bonds, 39 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel coral

> color sel coral

> select #6/P

2456 atoms, 2534 bonds, 2 pseudobonds, 296 residues, 2 models selected  

> show #!6 models

> color (#!6 & sel) medium blue

> select #6/U

301 atoms, 304 bonds, 36 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel olive

> color sel olive

> hide #!1 models

> select clear

> show #!3 models

> show sel atoms

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> show sel atoms

> color sel byhetero

> show sel atoms

> style sel stick

Changed 27 atom styles  

> color sel byhetero

> show sel atoms

> style sel stick

Changed 34 atom styles  

> color sel byhetero

> style sel sphere

Changed 34 atom styles  

> style sel stick

Changed 34 atom styles  

> select clear

> show sel atoms

> style sel stick

Changed 7 atom styles  

> color sel byelement

> color sel byhetero

> style sel ball

Changed 7 atom styles  

> show sel atoms

> style sel stick

Changed 7 atom styles  

> select clear

> show sel atoms

> style sel stick

Changed 7 atom styles  

> color sel byhetero

> select clear

> show #4 models

> hide #4 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!3 models

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/2.cxs"

opened ChimeraX session  

> select clear

> save 202205017-CRF2R11-1.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 202205017-CRF2R11-2.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 202205017-CRF2R11-3.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 202205017-CRF2R11-4.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 202205017-CRF2R11-4.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 202205017-CRF2R11-4.tif width 2000 height 2000 supersample 3
> transparentBackground true

> show #!1 models

> show #!2 models

> show #4 models

> show sel atoms

> select clear

> hide #!1 models

> hide #!2 models

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/2.cxs"

opened ChimeraX session  

> cartoon supress false

Expected an atoms specifier or a keyword  

> cartoon suppressBackboneDisplay false

> hide sel atoms

> hide sel atoms

> select up

12 atoms, 1 bond, 3 residues, 3 models selected  

> select up

27 atoms, 16 bonds, 3 residues, 3 models selected  

> hide sel atoms

> show (sel-residues & sidechain) target ab

> select clear

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/13.cxs"

> save 20220522-CRF2R11-11.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 20220522-CRF2R11-11.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 20220522-CRF2R11-11.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 20220522-CRF2R11-11.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/CD/13.cxs"

opened ChimeraX session  

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/20220923-2.cxs"

> select clear

> open "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self
> fig/CD/revised/最后pdb/PDB file/crf2-g11-rosetta3_real_space_refined.pdb"

Summary of feedback from opening E:/huawei/HaozhuoDownloads/CRFR2a/paper
2/self fig/CD/revised/最后pdb/PDB file/crf2-g11-rosetta3_real_space_refined.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.004 0.048 9978  
  
Ignored bad PDB record found on line 23  
ANGLE : 0.801 12.218 13516  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.051 0.206 1507  
  
17 messages similar to the above omitted  
  
Chain information for crf2-g11-rosetta3_real_space_refined.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
G | No description available  
H | No description available  
P | No description available  
U | No description available  
  

> hide #!3 models

> hide #4 models

> hide #!6 models

> hide #!5 models

> hide #!7 atoms

> show #!7 cartoons

> show #!6 models

> show #!3 models

> matchmaker #7/P to #3/P

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 crf2-gs-april-19_real_space_refined.pdb, chain P (#3) with
crf2-g11-rosetta3_real_space_refined.pdb, chain P (#7), sequence alignment
score = 1664.2  
RMSD between 287 pruned atom pairs is 0.877 angstroms; (across all 330 pairs:
1.331)  
  

> hide #7.1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> select #7/P

2774 atoms, 2858 bonds, 6 pseudobonds, 330 residues, 2 models selected  

> color (#!7 & sel) cornflower blue

> color (#!7 & sel) cornflower blue

> select #7/U

322 atoms, 325 bonds, 39 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel coral

> hide #!5 models

> hide #!3 models

> hide #!6 models

> select #7/P:258

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

> show (sel-residues & sidechain) target ab

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> select #7/U:3

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

> show sel atoms

> style sel stick

Changed 7 atom styles  

> cartoon suppressBackboneDisplay false

> color sel byhetero

> select clear

> show #!6 models

> show #!3 models

> save 20220923-CRF2R1-3.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save 20220923-CRF2R1-3.tif width 2000 height 2000 supersample 3
> transparentBackground true

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/20220923-2.cxs"

> save "E:/huawei/HaozhuoDownloads/CRFR2a/paper 2/self fig/20220923-3.cxs"

——— End of log from Fri Sep 23 22:16:09 2022 ———

opened ChimeraX session  

> hide #!3 models

> hide #!6 models

> show #!2 models

> hide #!7 models

> ui tool show "Side View"

> select #2/H

1780 atoms, 1826 bonds, 2 pseudobonds, 232 residues, 2 models selected  

> delete atoms (#!2 & sel)

> delete bonds (#!2 & sel)

> show #!3 models

> hide #!2 models

> select #3/N

961 atoms, 983 bonds, 126 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> show #!1 models

> select #1/H

1782 atoms, 1828 bonds, 2 pseudobonds, 232 residues, 2 models selected  

> delete atoms (#!1 & sel)

> delete bonds (#!1 & sel)

> save E:/huawei/HaozhuoDownloads/CRFR2a/20250302.cxs

——— End of log from Sun Mar 2 21:26:07 2025 ———

opened ChimeraX session  

> show #!2 models

> surface #1-3

> lighting shadows true

> lighting shadows false

> lighting flat

> graphics silhouettes false

> hide #!2 models

> hide #!3 models

> transparency 0 ribbons

> transparency #1 0

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> show #!2 models

> hide #!2 models

> select #1/B

2601 atoms, 2648 bonds, 338 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel light sea green

> color sel teal

> hide #!1 models

> show #!2 models

> select #2/B

2616 atoms, 2663 bonds, 341 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel teal

> hide #!2 models

> show #!3 models

> select #3/B

2601 atoms, 2648 bonds, 338 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel teal

> select clear

> save E:/huawei/HaozhuoDownloads/CRFR2a/20250302.cxs

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!1 models

> select #1/U

330 atoms, 333 bonds, 40 residues, 1 model selected  

> color (#!1 & sel) orange red

> hide #!1 models

> show #!2 models

> select #2/U

330 atoms, 333 bonds, 40 residues, 1 model selected  

> color (#!2 & sel) orange red

> hide #!2 models

> show #!3 models

> select #3/B

2601 atoms, 2648 bonds, 338 residues, 1 model selected  

> select #3/U

330 atoms, 333 bonds, 40 residues, 1 model selected  

> color (#!3 & sel) orange red

> select clear

> save E:/huawei/HaozhuoDownloads/CRFR2a/20250302.cxs

Traceback (most recent call last):  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write  
compressed = self._compressor.compress(data)  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "D:\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 "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save  
fserialize(stream, data)  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "D:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\safesave.py", line 136, in write  
self._f.write(buf)  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 740, in write  
compressed = self._compressor.compress(data)  
File "D:\Program Files\ChimeraX\bin\lib\site-packages\lz4\frame\\__init__.py",
line 258, in compress  
result = compress_chunk(  
MemoryError  
  
MemoryError  
  
File "D:\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 538.78
OpenGL renderer: NVIDIA GeForce MX150/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 20L6A09YCD
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 17,027,555,328
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 8 months ago

Cc: Tom Goddard Eric Pettersen added
Component: Unassigned → Sessions
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MemoryError saving session

comment:2 by Eric Pettersen, 8 months ago

Resolution: → can't reproduce
Status: assigned → closed

Weird that the user was able to save a session just a few commands previously, with no activity in between that would seem to add much of anything to a session file.

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