Session files get larger on each save

[drorn@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
At some point every time I'm saving a session my files get larger and larger regardless of what I have in them . The session contains no surfsce, just a few proteins that are relatively small - on the order of 200 AA.
I had the same problem two years ago: refe #5139
Then I was provided with a python script to clean up some "zombie"sequences from the session. I tried to run it on the current sessions but it doesn't work.


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

> open "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"

Log from Tue Oct 17 18:44:05 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs" format session

Log from Tue Oct 17 18:18:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs" format
> session

Log from Tue Oct 17 14:26:21 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs" format
> session

Frozen name "ChlideX2" not restored: nothing is selected by specifier  

Log from Tue Oct 17 13:50:43 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap Chl prot
> interactions.cxs"

Log from Wed Aug 16 16:38:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap
> packing.cxs" format session

Log from Wed Aug 16 15:24:32 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7pbw format mmcif fromDatabase pdb

7pbw title:  
Cryo-EM structure of light harvesting complex 2 from Rba. sphaeroides. [more
info...]  
  
Chain information for 7pbw #1  
---  
Chain | Description | UniProt  
AA AB AC AD AE AF AG AH AI | Light-harvesting protein B-800/850 alpha chain |
LHA2_RHOS4 1-50  
BA BB BC BD BE BF BG BH BI | Light-harvesting protein B-800/850 beta chain |
LHB2_RHOS4 5-51  
  
Non-standard residues in 7pbw #1  
---  
7OT — spheroidene
((6E,10E,12E,14E,16E,18E,20E,22E,24E,26E,28E)-31-methoxy-2,6,10,14,19,23,27,31-octamethyl-
dotriaconta-2,6,10,12,14,16,18,20,22,24,26,28-dodecaene)  
BCL — bacteriochlorophyll A  
CA — calcium ion  
LDA — lauryl dimethylamine-N-oxide  
  

> select protein

6525 atoms, 6696 bonds, 873 residues, 1 model selected  

> style sel stick

Changed 6525 atom styles  

> hide sel atoms

> show sel cartoons

> select helix

5310 atoms, 5427 bonds, 720 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /BA /BB /BC /BD /BE /BF /BG /BH /BI

Alignment identifier is 1  

> sequence chain /AA /AB /AC /AD /AE /AF /AG /AH /AI

Alignment identifier is 2  

********** Deleted several thousands lines to stay within Trac limits ***********

BCL 101 CED   -0.262    3.902
    LH2_Sphaeroides.pdb #1.1/J ALA 39 C    LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD   -0.270    3.760
    LH2_Sphaeroides.pdb #1.1/J ALA 39 O    LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD   -0.311    3.611
    LH2_Sphaeroides.pdb #1.1/J ALA 36 CA   LH2_Sphaeroides.pdb #1.1/A BCL 101 CGD   -0.338    3.828
    LH2_Sphaeroides.pdb #1.1/J HIS 40 N    LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD   -0.340    3.860
    LH2_Sphaeroides.pdb #1.1/J ALA 39 CB   LH2_Sphaeroides.pdb #1.1/A BCL 101 CMD   -0.346    4.106
    LH2_Sphaeroides.pdb #1.1/J PHE 32 CD1  LH2_Sphaeroides.pdb #1.1/A BCL 101 CED   -0.362    4.002
    LH2_Sphaeroides.pdb #1.1/J MET 35 CG   LH2_Sphaeroides.pdb #1.1/A BCL 101 O1D   -0.363    3.663
    LH2_Sphaeroides.pdb #1.1/J PHE 32 CZ   LH2_Sphaeroides.pdb #1.1/A BCL 101 O2D   -0.367    3.587
    LH2_Sphaeroides.pdb #1.1/J ALA 36 CA   LH2_Sphaeroides.pdb #1.1/A BCL 101 O1D   -0.373    3.673
    

  
32 contacts  

> close #2-3

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> select add #1.2

9531 atoms, 9495 bonds, 325 pseudobonds, 1191 residues, 5 models selected  

> select subtract #1.2

31 atoms, 7 residues, 1 model selected  

> hide #!1.2 models

> show #!1.2 models

> select add #1.2

9531 atoms, 9495 bonds, 325 pseudobonds, 1191 residues, 5 models selected  

> hide #!1.2 models

> show #!1.2 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> select subtract #1.2

31 atoms, 7 residues, 1 model selected  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> select #1.1

9500 atoms, 9495 bonds, 350 pseudobonds, 1184 residues, 5 models selected  

> select #1.2

9500 atoms, 9495 bonds, 325 pseudobonds, 1184 residues, 4 models selected  

> select #1.1

9500 atoms, 9495 bonds, 350 pseudobonds, 1184 residues, 5 models selected  

> show sel cartoons

> hide sel cartoons

> select #1.2

9500 atoms, 9495 bonds, 325 pseudobonds, 1184 residues, 4 models selected  

> show sel cartoons

> select #1.2

9500 atoms, 9495 bonds, 217 pseudobonds, 1184 residues, 3 models selected  

> hide sel cartoons

> close #1.2

> view

> help help:user

> combine #1.1 modelID 2

Expected a keyword  

> combine #1.1

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> close #1

> rename #2 LH2_Sphaeroides.pdb

> hide #!4 models

> select #2/A-B/J-K

2129 atoms, 2125 bonds, 228 pseudobonds, 266 residues, 5 models selected  

> split #2 atoms /A-B/J-K

Split LH2_Sphaeroides.pdb (#2) into 2 models  
Chain information for LH2_Sphaeroides.pdb 1 #2.1  
---  
Chain | Description  
A B | No description available  
J K | No description available  
  
Chain information for LH2_Sphaeroides.pdb 2 #2.2  
---  
Chain | Description  
C D E F G H I | No description available  
L M N O P Q R | No description available  
  

> hide #!2.2 models

> hide #!2.1 models

> show #!2.1 models

> show #!4 models

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap
> refine.cxs"

> help help:user

> select #4/A:21@CA,CB,CG,CD2,C4D,ND1,NE2

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

> select #4/A:21@CA,CB,CG,CD2,CE1,ND1,NE2

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

> align #4/A:21@CA,CB,CG,CD2,CE1,ND1,NE2 toAtoms #2.1/A:31 move atoms
> matchAtomNames

Missing "matchAtomNames" keyword's argument  

> align #4/A:21@CA,CB,CG,CD2,CE1,ND1,NE2 toAtoms #2.1/A:31 move atoms
> matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 7 atom pairs is 0.046 angstroms  

> select up

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

> select #4/D#2.1/K

613 atoms, 608 bonds, 70 pseudobonds, 94 residues, 6 models selected  

> select #4/D@CA #2.1/K@CA

76 atoms, 54 pseudobonds, 76 residues, 4 models selected  

> align #4/D@CA toAtoms #2.1/K@CA move chains matchAtomNames true

Pairing dropped 0 atoms and 20 reference atoms  
RMSD between 28 atom pairs is 4.361 angstroms  

> align #4/D@CA toAtoms #2.1/K:20-47@CA move chains matchAtomNames true

RMSD between 28 atom pairs is 0.972 angstroms  

> align #4/D:21@CA,CB,CG,CD2,CE1,ND1,NE2 toAtoms #2.1/K:40 move atoms
> matchAtomNames true

Pairing dropped 0 atoms and 3 reference atoms  
RMSD between 7 atom pairs is 0.067 angstroms  

> select #4:1@N,C,CA

15 atoms, 10 bonds, 5 residues, 1 model selected  

> show sel atoms

> select #4:1@N,C

10 atoms, 5 residues, 1 model selected  

> select #4:1@C

5 atoms, 5 residues, 1 model selected  

> hide sel atoms

> select #4:28@C,O

10 atoms, 5 bonds, 5 residues, 1 model selected  

> show sel atoms

> select #4/D:28@C#2.1/K:48@N

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance #4/D:28@C #2.1/K:48@N

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 28 C and
LH2_Sphaeroides.pdb 1 #2.1/K PRO 48 N: 3.877Å  

> select #4/E:1@N#2.1/K:49@C

2 atoms, 2 residues, 2 models selected  

> distance #4/E:1@N #2.1/K:49@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/E GLY 1 N and
LH2_Sphaeroides.pdb 1 #2.1/K TRP 49 C: 12.120Å  

> select #4/E:28@C#4/C:1@N

2 atoms, 2 residues, 1 model selected  

> select #4/E:28@D#4/C:1@N

1 atom, 1 residue, 1 model selected  

> select #4/E:28@D#4/D:1@N

1 atom, 1 residue, 1 model selected  

> select #4/E:28@C#4/D:1@N

2 atoms, 2 residues, 1 model selected  

> distance #4/D:1@N #4/E:28@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 1 N and /E GLY 28 C:
15.336Å  

> ~distance #4/D:1@N #4/E:28@C

> select #4/E:28@C#4/C:1@N

2 atoms, 2 residues, 1 model selected  

> distance #4/C:1@N #4/E:28@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/C GLY 1 N and /E GLY 28 C:
8.966Å  

> select #2.1/B:41

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

> show sel atoms

> hide sel atoms

> select #4/B:1@N#2.1/B:40@C

2 atoms, 2 residues, 2 models selected  

> distance #4/B:1@N #2.1/B:40@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/B GLY 1 N and
LH2_Sphaeroides.pdb 1 #2.1/B TRP 40 C: 4.651Å  

> select #4/B:28@C#4/A:1@N

2 atoms, 2 residues, 1 model selected  

> distance #4/A:1@N #4/B:28@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/A GLY 1 N and /B GLY 28 C:
10.907Å  

> select #4/A:23-28

30 atoms, 29 bonds, 5 pseudobonds, 6 residues, 2 models selected  

> show sel atoms

> select #4/A:23-28#2.1/A:33-38

71 atoms, 69 bonds, 8 pseudobonds, 12 residues, 4 models selected  

> show sel atoms

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap refine
> and connect.cxs"

> align #4/A:23-28 toAtoms #2.1/A:33-38 matchAtomNames true move atoms

Pairing dropped 6 atoms and 17 reference atoms  
RMSD between 24 atom pairs is 0.630 angstroms  

> select #4/A:23-28@N,C,O,H

24 atoms, 17 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select #4/A:28@C,O

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

> show sel atoms

> select #4/A:28

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

> delete atoms sel

> delete bonds sel

> select #4/A:27@C,O

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

> show sel atoms

> select #4/A:27@C#2.1:38@N

5 atoms, 5 residues, 2 models selected  
Exactly two atoms must be selected!  

> select #4/A:27@C#2.1/A:38@N

2 atoms, 2 residues, 2 models selected  

> distance #4/A:27@C #2.1/A:38@N

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/A GLY 27 C and
LH2_Sphaeroides.pdb 1 #2.1/A THR 38 N: 1.023Å  

> align #4/A:27 toAtoms #2.1/A:37 matchAtomNames true move atoms

Pairing dropped 1 atoms and 3 reference atoms  
RMSD between 4 atom pairs is 0.258 angstroms  

> align #4/A:27@CA,C,O toAtoms #2.1/A:37 matchAtomNames true move atoms

Pairing dropped 0 atoms and 4 reference atoms  
RMSD between 3 atom pairs is 0.014 angstroms  

> ~distance #4/E:1@N #2.1/K:49@C

> ~distance #4/C:1@N #4/E:28@C

> select up

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

> select #4/C:28@C#4/E:1@N

2 atoms, 2 residues, 1 model selected  

> distance #4/C:28@C #4/E:1@N

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/C GLY 28 C and /E GLY 1 N:
14.583Å  

> select #4/D:1@N#4/E:28@C

2 atoms, 2 residues, 1 model selected  

> distance #4/D:1@N #4/E:28@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 1 N and /E GLY 28 C:
15.336Å  

> ~distance #4/D:28@C #2.1/K:48@N

> select #2.1/K:48

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

> hide sel atoms

> select #2.1/K:48

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

> show sel atoms

> hide sel atoms

> select #2.1/K:49

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

> select #2.1/K:50

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

> show sel atoms

> select #2.1/K:50-55

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

> show sel atoms

> select #2.1/K:50-59

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

> show sel atoms

> select #2.1/K:52

Nothing selected  

> select #2.1/K:48-49

21 atoms, 23 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #2.1/K:47-49

28 atoms, 30 bonds, 1 pseudobond, 3 residues, 2 models selected  

> ~distance #4/D:1@N #4/E:28@C

> ~distance #4/C:28@C #4/E:1@N

> select #2.1/B:38

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

> select #2.1/B:39

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

> select #2.1/B:38

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

> select #2.1/B:38@N/A:45@C

2 atoms, 2 residues, 1 model selected  

> select #2.1/B:39@N/A:45@C

2 atoms, 2 residues, 1 model selected  

> distance #2.1/A:45@C #2.1/B:39@N

Distance between LH2_Sphaeroides.pdb 1 #2.1/A TYR 45 C and /B THR 39 N: 7.111Å  

> ~distance #2.1/A:45@C #2.1/B:39@N

> hide #!1 models

> show #!1 models

> hide #!2 models

> select #4/B:1@N#4/D:28@C

2 atoms, 2 residues, 1 model selected  

> distance #4/B:1@N #4/D:28@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/B GLY 1 N and /D GLY 28 C:
13.085Å  

> select #4/D:1@N#4/C:28@C

2 atoms, 2 residues, 1 model selected  

> select #4/D:1@N#4/E:28@C

2 atoms, 2 residues, 1 model selected  

> distance #4/D:1@N #4/E:28@C

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 1 N and /E GLY 28 C:
15.336Å  

> select #4/E:1@N#4/C:28@C

2 atoms, 2 residues, 1 model selected  

> distance #4/C:28@C #4/E:1@N

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/C GLY 28 C and /E GLY 1 N:
14.583Å  

> show #!2 models

> select #2.1/K@OXT#4/B:1@N

2 atoms, 2 residues, 2 models selected  

> distance #4/B:1@N #2.1/K:51@OXT

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/B GLY 1 N and
LH2_Sphaeroides.pdb 1 #2.1/K GLY 51 OXT: 13.347Å  

> ~distance #4/B:1@N #4/D:28@C

> select #2.1/K:48@N#4/D:28@C

2 atoms, 2 residues, 2 models selected  

> distance #4/D:28@C #2.1/K:48@N

Distance between CCCP LH2 5HB p_ap_p_p_ap.pdb #4/D GLY 28 C and
LH2_Sphaeroides.pdb 1 #2.1/K PRO 48 N: 3.877Å  

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB design p_ap_p_p_ap refine
> and connect.cxs"

> combine #2.1#4 Name combine 5HB

Expected a keyword  

> combine #2.1#4

Remapping chain ID 'A' in CCCP LH2 5HB p_ap_p_p_ap.pdb #4 to 'F'  
Remapping chain ID 'B' in CCCP LH2 5HB p_ap_p_p_ap.pdb #4 to 'G'  

> hide #!4 models

> hide #!2 models

> select #3/B

590 atoms, 593 bonds, 47 pseudobonds, 67 residues, 4 models selected  

> show #!4 models

> hide sel atoms

> hide #!4 models

> select #3/B/A:11-32

744 atoms, 750 bonds, 45 pseudobonds, 89 residues, 4 models selected  

> hide sel atoms

> select #3/B/A:11-32/J

1207 atoms, 1212 bonds, 64 pseudobonds, 151 residues, 4 models selected  

> select #3/A:11-45

260 atoms, 268 bonds, 11 pseudobonds, 35 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 260 atom styles  

> select #3/A:11-45/K:20-51

500 atoms, 514 bonds, 42 pseudobonds, 67 residues, 3 models selected  

> show sel atoms

> style sel stick

Changed 500 atom styles  

> select #3/A:11-45/K:20-51/J:20-47

706 atoms, 723 bonds, 38 pseudobonds, 95 residues, 3 models selected  

> show sel atoms

> style sel stick

Changed 706 atom styles  

> select #3/C/D/F/

Expected an objects specifier or a keyword  

> select #3/C/D/F

429 atoms, 428 bonds, 80 pseudobonds, 83 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> delete atoms sel

> delete bonds sel

> show #!4 models

> ui tool show "Change Chain IDs"

> select #3/C/D/F

Nothing selected  

> select #3/A

609 atoms, 608 bonds, 24 pseudobonds, 71 residues, 3 models selected  

> select #3/A/B

1199 atoms, 1201 bonds, 46 pseudobonds, 138 residues, 3 models selected  

> select #3/A

609 atoms, 608 bonds, 24 pseudobonds, 71 residues, 3 models selected  

> ui tool show "Change Chain IDs"

> changechains sel C

Chain IDs of 71 residues changed  

> select #3/J

463 atoms, 462 bonds, 17 pseudobonds, 62 residues, 3 models selected  

> changechains sel A

Chain IDs of 62 residues changed  

> select #3/D

Nothing selected  

> select #3/B

590 atoms, 593 bonds, 20 pseudobonds, 67 residues, 3 models selected  

> show sel cartoons

> hide sel cartoons

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> select #3/B

590 atoms, 593 bonds, 20 pseudobonds, 67 residues, 3 models selected  

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> select #3/B

Nothing selected  

> show #!4 models

> hide #!4 models

> select #3/E

140 atoms, 139 bonds, 27 pseudobonds, 28 residues, 2 models selected  

> changechains sel B

Chain IDs of 28 residues changed  

> show #!4 models

> select #3/F

Nothing selected  

> select #3/E

Nothing selected  

> select #3/C

609 atoms, 608 bonds, 24 pseudobonds, 71 residues, 3 models selected  

> changechains sel E

Chain IDs of 71 residues changed  

> select #3/K

467 atoms, 462 bonds, 16 pseudobonds, 66 residues, 3 models selected  

> changechains sel C

Chain IDs of 66 residues changed  

> hide #!4 models

> select #3/G

142 atoms, 141 bonds, 27 pseudobonds, 28 residues, 2 models selected  

> select #3/D

Nothing selected  

> select #3/G

142 atoms, 141 bonds, 27 pseudobonds, 28 residues, 2 models selected  

> changechains sel D

Chain IDs of 28 residues changed  

> select #3/A-E

1821 atoms, 1812 bonds, 151 pseudobonds, 255 residues, 5 models selected  

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"

> select #3 &~/A-E

Nothing selected  

> select #3/A-E

1821 atoms, 1812 bonds, 151 pseudobonds, 255 residues, 5 models selected  

> select #3/A/C/D

1072 atoms, 1065 bonds, 60 pseudobonds, 156 residues, 4 models selected  

> select #3/A:20-47/C:20-51/E:11-45

706 atoms, 723 bonds, 18 pseudobonds, 95 residues, 2 models selected  

> hide sel atoms

> select #3/A:20-47/C:20-51,101/E:11-45,101

838 atoms, 863 bonds, 60 pseudobonds, 97 residues, 4 models selected  

> hide sel atoms

> show sel atoms

> ~distance #4/A:27@C #2.1/A:38@N

> ~distance #4/B:1@N #2.1/B:40@C

> ~distance #4/A:1@N #4/B:28@C

> ~distance #4/B:1@N #2.1/K:51@OXT

> ~distance #4/D:28@C #2.1/K:48@N

> ~distance #4/D:1@N #4/E:28@C

> ~distance #4/C:28@C #4/E:1@N

> select #3/A:20-47/C:20-51,101/E:11-45,101/B/D

1120 atoms, 1143 bonds, 114 pseudobonds, 153 residues, 5 models selected  

> show sel atoms

> select #3 &~:BCL&~protein

197 atoms, 146 bonds, 51 residues, 1 model selected  

> show sel atoms

> delete atoms sel

> delete bonds sel

> select #3:BCL

264 atoms, 280 bonds, 16 pseudobonds, 4 residues, 2 models selected  

> show sel atoms

> select #3/A:BCL

66 atoms, 70 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> hide sel atoms

> show sel atoms

> select #3/A:BCL/E:BCL

198 atoms, 210 bonds, 12 pseudobonds, 3 residues, 2 models selected  

> select #3/A:101/E:102

132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> hide sel atoms

> show sel atoms

> delete atoms (#!3 & sel)

> delete bonds (#!3 & sel)

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"

——— End of log from Tue Oct 17 13:50:43 2023 ———

opened ChimeraX session  

> select #3/E:1-19/A:1-19

263 atoms, 269 bonds, 34 residues, 1 model selected  

> select #3/C:1-19/A:1-19

226 atoms, 230 bonds, 30 residues, 1 model selected  

> show sel atoms

> select #3/A:1

Nothing selected  

> select #3/A

353 atoms, 362 bonds, 4 pseudobonds, 47 residues, 2 models selected  

> select #3/A:47@C/B:1@N

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance #3/A:47@C #3/B:1@N

Distance between combination #3/A THR 47 C and /B GLY 1 N: 16.032Å  

> select #3/B:28@C/C:16@N

2 atoms, 2 residues, 1 model selected  

> distance #3/C:16@N #3/B:28@C

Distance between combination #3/C ALA 16 N and /B GLY 28 C: 10.723Å  

> select #3/C:1-15

85 atoms, 87 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select #3/C:51@C/D:1@N

2 atoms, 2 residues, 1 model selected  

> distance #3/C:51@C #3/D:1@N

Distance between combination #3/C GLY 51 C and /D GLY 1 N: 13.421Å  

> select #3/E:1-10

83 atoms, 84 bonds, 10 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #3/A:1-15

85 atoms, 87 bonds, 11 residues, 1 model selected  

> hide sel atoms

> select #3/E:1-12

99 atoms, 101 bonds, 12 residues, 1 model selected  

> hide sel atoms

> select #3/D:28@C/E:12@N

2 atoms, 2 residues, 1 model selected  

> distance #3/E:12@N #3/D:28@C

Distance between combination #3/E PRO 12 N and /D GLY 28 C: 11.557Å  

> ~distance #3/E:12@N #3/D:28@C

> select #3/D:28@C/E:13@N

2 atoms, 2 residues, 1 model selected  

> distance #3/E:13@N #3/D:28@C

Distance between combination #3/E THR 13 N and /D GLY 28 C: 9.080Å  

> select #3/A:1-19

113 atoms, 115 bonds, 15 residues, 1 model selected  

> hide sel atoms

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"

> select #3/A:1-19

113 atoms, 115 bonds, 15 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> color #!3 bychain

> color #!3 byhetero

> select #3/A

240 atoms, 246 bonds, 4 pseudobonds, 32 residues, 2 models selected  

> select #3/C:1-15

85 atoms, 87 bonds, 11 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/E:47-59

20 atoms, 19 bonds, 4 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #3/E:1-12

99 atoms, 101 bonds, 12 residues, 1 model selected  

> show sel atoms

> delete atoms sel

> delete bonds sel

> select #3/E:46-59

29 atoms, 28 bonds, 5 residues, 1 model selected  

> show sel atoms

> delete atoms sel

> delete bonds sel

> select :BCL

1914 atoms, 2030 bonds, 116 pseudobonds, 29 residues, 6 models selected  

> select #3:BCL

132 atoms, 140 bonds, 8 pseudobonds, 2 residues, 2 models selected  

> select #3:BCL@C[123456789],C[12][0123456789]

40 atoms, 38 bonds, 2 residues, 1 model selected  

> hide sel atoms

> delete atoms sel

> delete bonds sel

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"

> select #3

1126 atoms, 1151 bonds, 65 pseudobonds, 159 residues, 5 models selected  

> show sel atoms

> select #3/A:48-51

34 atoms, 36 bonds, 4 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB combined.cxs"

——— End of log from Tue Oct 17 14:26:21 2023 ———

opened ChimeraX session  

> hide #!3 models

> show #!3 models

> hide #!1 models

> show #!1 models

> close #2

> close #4

> combine #1 close true modelID 4

Expected a keyword  

> help help:user

> combine #1 close true modelId 4

No structures specified  

> combine #1

No structures specified  

> combine #3

> select #2/B

140 atoms, 139 bonds, 28 residues, 1 model selected  

> select #2/B:1@N/A:47@C

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> ui tool show "Build Structure"

> build join peptide sel length 16 omega 180 phi -120 move N

Atoms must be in different models  

> split #2

Split copy of combination (#2) into 5 models  
Chain information for copy of combination A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for copy of combination B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for copy of combination C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for copy of combination D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for copy of combination E #2.5  
---  
Chain | Description  
E | No description available  
  

> select #2/B:1@N/A:47@C

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 16 omega 180 phi -120 move N

C-terminal carbon not bonded to exactly one carbon  

> select #2/A:47@TMP

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/B:1@N/A:47@C

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 16 omega 180 phi -120 move N

> align #2.1:48-75 toAtoms #3/B matchAtomNames true move atoms

RMSD between 140 atom pairs is 0.000 angstroms  

> hide #!3 models

> select #2/C:16@N/A:75@C

2 atoms, 2 residues, 2 models selected  

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"

——— End of log from Tue Oct 17 18:18:24 2023 ———

opened ChimeraX session  

> select #2.3:BCL

46 atoms, 50 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> ui tool show "Renumber Residues"

> renumber #2.3/C:101 start 201 relative false

1 residues renumbered  

> select #2.5:BCL

46 atoms, 50 bonds, 4 pseudobonds, 1 residue, 2 models selected  

> renumber #2.5/E:101 start 202 relative false

1 residues renumbered  

> select #2/C:16@N/A:75@C

2 atoms, 2 residues, 2 models selected  

> ui tool show "Build Structure"

> build join peptide sel length 4 omega 180 phi -120 move N

> show #!3 models

> hide #!3 models

> show #!3 models

> align #2.1:91-126,201 toAtoms #3/C matchAtomNames true move atoms

RMSD between 314 atom pairs is 0.000 angstroms  

> hide #!3 models

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"

> select #2@OXT

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #2/D:1@N/A:126@C

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 4 omega 180 phi -120 move N

> show #!3 models

> align #2.1:127-154 toAtoms #3/D matchAtomNames true move atoms

RMSD between 142 atom pairs is 0.000 angstroms  

> hide #!3 models

> select #2/E:13@N/A:154@C

2 atoms, 2 residues, 2 models selected  

> build join peptide sel length 4 omega 180 phi -120 move N

> select #2/A:167-202

336 atoms, 351 bonds, 20 pseudobonds, 35 residues, 3 models selected  

> select #2/A:167-199,202

290 atoms, 301 bonds, 16 pseudobonds, 34 residues, 3 models selected  

> select #2/A:167-200,202

290 atoms, 301 bonds, 16 pseudobonds, 34 residues, 3 models selected  

> select #2/A:167-201,202

336 atoms, 351 bonds, 20 pseudobonds, 35 residues, 3 models selected  

> select #2/A:167-199,202

290 atoms, 301 bonds, 16 pseudobonds, 34 residues, 3 models selected  

> align #2.1:167-199,202 toAtoms #3/E matchAtomNames true move atoms

RMSD between 290 atom pairs is 0.000 angstroms  

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"

> align #2.1:47@C:48@N

Missing required "to_atoms" argument  

> select #2.1:47@C:48@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> ~bond sel

> select #2.1:75@C:91@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> ~bond sel

> select #2.1:126@C:127@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> ~bond sel

> select #2.1:154@C:167@N

2 atoms, 1 bond, 2 residues, 1 model selected  

> ~bond sel

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"

——— End of log from Tue Oct 17 18:44:05 2023 ———

opened ChimeraX session  

> open "/Users/drornoy/Desktop/ChimeraX cleaner/clean.py"

executed clean.py  

> save "/Users/drornoy/Desktop/LH2 helices/LH2 5hB joined.cxs"




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 16 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 20 days 5:27

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    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: 2021.10.8
    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
    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: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    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
    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
    setuptools-scm: 7.0.5
    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
    zipp: 3.15.0
File attachment: LH2 5HB for design.cxs

LH2 5HB for design.cxs​

[drorn@…]

Added by email2trac

[Tom Goddard]

The session file you attached is very small, only 48946 bytes. Are you talking about the file increasing in size by small amounts (e.g. 1 kbyte?). The session contains the log of all the commands you used to produce the session from all previous saves that led to this session, so the file size should grow by small amounts each time you save because at least a few commands were added. I see also that you used the "contacts" command with "log true" which put hundreds of lines of output into the log. The log reported in this bug report is over 256 Kbytes -- the session file is smaller because it is compressed.

Probably if you use the command "log clear" and then save the session it will remove all those logged commands and make the file smaller. But usually it is worth keeping the log information since it documents how the session was created.

[Eric Pettersen]

Yes, as Tom explained, we would expect session files to get slightly larger for various reasons as they get resaved. If I take your session file and resave it, it gets about 700 bytes larger. If I then clear the log and resave, it's about the same size as the original session file.

I guess we need some clarification on why small increases like these are a problem.

[drorn@…]

Hi
I think you’re completely missing the point here. This is not about a few KBs added but many MBs. It is something that happened to a specific session.
Please look at the attached 27MB session file. That’s the one that stated all of it. It contains two models, one a relatively large pdb file of a complex and another a small protein. When I close the large model (#1) and save the session the file grows to 400 MB
Thanks
Dror


>
>
>
>
>
>

LH2 5hB design p_ap_p_p_ap refine.cxs​

[drorn@…]

Added by email2trac

[Eric Pettersen]

Hi Dror,

Though that second session doesn't get anywhere near 400 MB when resaved, it nonetheless has "dead" models in it that it should not have. If you get tomorrow's daily build and resave that session, it drops in size from 27.1 MB to 663 KB.

--Eric

Fix: ​https://github.com/RBVI/ChimeraX/commit/bd0299b3e68784fe711e765dcce5c847a4693bab