Cannot save command history

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.66.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/gkherrma/coot/R853A/GC_Binary-rsr00.pdb
> /home/gkherrma/coot/R853A/GC_ternary_R__rsr57.pdb

Chain information for GC_Binary-rsr00.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
P | No description available  
T | No description available  
  
Chain information for GC_ternary_R__rsr57.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 2126, resource id:
29522293, major code: 40 (TranslateCoords), minor code: 0  

> close #2

> open /home/gkherrma/coot/R853A/R853A_sca_hm11_refine_42_dCTP.pdb

Chain information for R853A_sca_hm11_refine_42_dCTP.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

> style stick

Changed 29946 atom styles  

> show cartoons

> hide atoms

> nucleotides atoms

> style nucleic stick

Changed 1908 atom styles  

> open /home/gkherrma/coot/R853A/GC_ternary_R__rsr57.pdb

Chain information for GC_ternary_R__rsr57.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 7526, resource id:
29525287, major code: 40 (TranslateCoords), minor code: 0  

> style stick

Changed 59947 atom styles  

> hide atoms

> show cartoons

> lighting simple

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> lighting simple

> ui tool show Matchmaker

> matchmaker #2/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GC_ternary_R__rsr57.pdb, chain A (#3) with
R853A_sca_hm11_refine_42_dCTP.pdb, chain A (#2), sequence alignment score =
4571.8  
RMSD between 826 pruned atom pairs is 0.928 angstroms; (across all 953 pairs:
3.750)  
  

> matchmaker #1/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GC_ternary_R__rsr57.pdb, chain A (#3) with GC_Binary-rsr00.pdb,
chain A (#1), sequence alignment score = 4973.1  
RMSD between 852 pruned atom pairs is 0.690 angstroms; (across all 974 pairs:
2.409)  
  

> matchmaker #1/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GC_ternary_R__rsr57.pdb, chain A (#3) with GC_Binary-rsr00.pdb,
chain A (#1), sequence alignment score = 4973.1  
RMSD between 852 pruned atom pairs is 0.690 angstroms; (across all 974 pairs:
2.409)  
  

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> show #!1 models

> select #1-3/P-T

3404 atoms, 3751 bonds, 56 pseudobonds, 140 residues, 4 models selected  

> show sel atoms

> nucleotides sel fill

> style nucleic & sel stick

Changed 3404 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 3404 atom styles  

> hide #!3 target m

> close #2

> close #3

> open /home/gkherrma/coot/R853A/R853A_sca_hm11_refine_42_dCTPasChainN.pdb

Chain information for R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 46962, resource id:
29539898, major code: 40 (TranslateCoords), minor code: 0  

> style sel stick

Changed 945 atom styles  

> show sel cartoons

> hide sel atoms

> open /home/gkherrma/coot/R853A/GC_ternary_R__rsr57.pdb

Chain information for GC_ternary_R__rsr57.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 48104, resource id:
29541395, major code: 40 (TranslateCoords), minor code: 0  

> style sel stick

Changed 945 atom styles  

> show sel cartoons

> hide sel atoms

> style sel stick

Changed 945 atom styles  

> select clear

> style stick

Changed 59947 atom styles  

> show cartoons

> hide atoms

> ui tool show Matchmaker

> matchmaker #2/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GC_ternary_R__rsr57.pdb, chain A (#3) with
R853A_sca_hm11_refine_42_dCTPasChainN.pdb, chain A (#2), sequence alignment
score = 4571.8  
RMSD between 826 pruned atom pairs is 0.928 angstroms; (across all 953 pairs:
3.750)  
  

> matchmaker #1/A to #3/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 GC_ternary_R__rsr57.pdb, chain A (#3) with GC_Binary-rsr00.pdb,
chain A (#1), sequence alignment score = 4973.1  
RMSD between 852 pruned atom pairs is 0.690 angstroms; (across all 974 pairs:
2.409)  
  

> select #1-3/P-T

3404 atoms, 3751 bonds, 56 pseudobonds, 140 residues, 4 models selected  

> show sel atoms

> select #2-3/N

68 atoms, 70 bonds, 2 residues, 2 models selected  

> show sel atoms

> select clear

> color #1 #dcc6bf transparency 0

> color #1 #dc978d transparency 0

> color #2 #abfca5 transparency 0

> color #2 #a8fca4 transparency 0

> color #3 #9bc9dc transparency 0

> color #3 #9ac5dc transparency 0

> select #1-3/A-D

56474 atoms, 57556 bonds, 33 pseudobonds, 5313 residues, 6 models selected  

> hide sel cartoons

> select #1-3/N

68 atoms, 70 bonds, 2 residues, 2 models selected  

> hide sel surfaces

> hide sel cartoons

> hide sel atoms

> select clear

> select #1-3/P:1-17

1097 atoms, 1214 bonds, 45 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #1-3/T:12-25

1013 atoms, 1109 bonds, 42 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> show sel cartoons

> show sel atoms

> select #1-3/P:1-17

1097 atoms, 1214 bonds, 45 residues, 3 models selected  

> show sel cartoons

> show sel atoms

> select clear

> select H

14696 atoms, 1834 residues, 1 model selected  

> hide sel atoms

> select clear

> select #3/T:4@N2

1 atom, 1 residue, 1 model selected  

> angle #3/T:4@N2 #3/T:4@CA #1/T:4@N2

Must specify exactly 3 atoms/centroids or two measureable objects (e.g.
axes/planes)  

> hide #!2 models

> hide #!1 models

> angle #3/T:4@N2 #3/T:4@C3' #1/T:4@N2

Angle between GC_ternary_R__rsr57.pdb #3/T DG 4 N2, GC_ternary_R__rsr57.pdb
#3/T DG 4 C3', and GC_Binary-rsr00.pdb #1/T DG 4 N2: 38.204  

> show #!2 models

> show #!1 models

> angle #3/T:4@C3' #3/T:4@N2 #1/T:4@N2

Angle between GC_ternary_R__rsr57.pdb #3/T DG 4 C3', GC_ternary_R__rsr57.pdb
#3/T DG 4 N2, and GC_Binary-rsr00.pdb #1/T DG 4 N2: 69.950  

> select clear

> select #1-3/P:1-17 #1-3/T:12-28

2183 atoms, 2402 bonds, 38 pseudobonds, 90 residues, 4 models selected  

> hide sel cartoons

> hide sel atoms

> select #1-3/P:1-22 #1-3/T:7-28

2910 atoms, 3204 bonds, 51 pseudobonds, 120 residues, 4 models selected  

> hide sel cartoons

> hide sel atoms

> select #3/T:4@N2

1 atom, 1 residue, 1 model selected  

> distance #1/T:4@N2 #2/T:4@N2

Distance between GC_Binary-rsr00.pdb #1/T DG 4 N2 and
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 N2: 2.404Å  

> distance #2/T:4@N2 #3/T:4@N2

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 N2 and
GC_ternary_R__rsr57.pdb #3/T DG 4 N2: 2.889Å  

> distance #1/T:4@N2 #3/T:4@N2

Distance between GC_Binary-rsr00.pdb #1/T DG 4 N2 and GC_ternary_R__rsr57.pdb
#3/T DG 4 N2: 4.440Å  

> select #1/T:4@O6

1 atom, 1 residue, 1 model selected  

> distance #1/T:4@O6 #3/T:4@O6

Distance between GC_Binary-rsr00.pdb #1/T DG 4 O6 and GC_ternary_R__rsr57.pdb
#3/T DG 4 O6: 4.748Å  

> distance #1/T:4@O6 #2/T:4@O6

Distance between GC_Binary-rsr00.pdb #1/T DG 4 O6 and
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6: 2.541Å  

> distance #3/T:4@O6 #2/T:4@O6

Distance between GC_ternary_R__rsr57.pdb #3/T DG 4 O6 and
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6: 2.743Å  

> distance delete #3/T:4@O6 #2/T:4@O6

> distance delete #1/T:4@O6 #2/T:4@O6

> distance delete #1/T:4@O6 #3/T:4@O6

> select clear

> hide #!4 models

> label #1/T:5

> close #4.1

> label delete #1/T:5

> label #1/T:4

> label delete #1/T:4

> select #1-3/P:23-24

142 atoms, 154 bonds, 6 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #1-3/T:5-6

149 atoms, 161 bonds, 6 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> select #1-3/P-T

3404 atoms, 3751 bonds, 59 pseudobonds, 140 residues, 5 models selected  

> show sel cartoons

> select clear

> show #4 models

> hide #4 models

> close #4

> hide #!3 models

> distance #1/T:4@O6 #2/T:4@O6

Distance between GC_Binary-rsr00.pdb #1/T DG 4 O6 and
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6: 2.541Å  

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> distance #2/T:4@O6 #3/T:4@O6

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6 and
GC_ternary_R__rsr57.pdb #3/T DG 4 O6: 2.743Å  

> hide #!2 models

> show #!1 models

> distance #1/T:4@O6 #3/T:4@O6

Distance between GC_Binary-rsr00.pdb #1/T DG 4 O6 and GC_ternary_R__rsr57.pdb
#3/T DG 4 O6: 4.748Å  

> show #!2 models

> angle #1/T:4@O6 #2/T:4@O6 #3/T:4@O6

Angle between GC_Binary-rsr00.pdb #1/T DG 4 O6,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6, and
GC_ternary_R__rsr57.pdb #3/T DG 4 O6: 127.911  

> angle #2/T:4@O6 #1/T:4@O6 #3/T:4@O6

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6,
GC_Binary-rsr00.pdb #1/T DG 4 O6, and GC_ternary_R__rsr57.pdb #3/T DG 4 O6:
27.112  

> hide #!4 models

> hide #4.1 models

> select #3/A

15392 atoms, 15600 bonds, 6 pseudobonds, 975 residues, 2 models selected  

> select #3/A:955,957,958

38 atoms, 37 bonds, 3 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> select #1-3/A:955-960

158 atoms, 161 bonds, 18 residues, 3 models selected  

> show sel cartoons

> show sel atoms

> hide #!2 models

> hide #!1 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> select clear

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #1-3/A:955-960

158 atoms, 161 bonds, 18 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #1-3/A:940-960

643 atoms, 655 bonds, 61 residues, 3 models selected  

> show sel cartoons

> select #1-3/N

68 atoms, 70 bonds, 2 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> select #1-3/A:957-960

98 atoms, 98 bonds, 12 residues, 3 models selected  

> hide sel cartoons

> select #1-3/A

31021 atoms, 31646 bonds, 20 pseudobonds, 2961 residues, 6 models selected  

> show sel surfaces

> hide sel surfaces

> show sel cartoons

> undo

> select #1-3/A:1090-1110

686 atoms, 698 bonds, 63 residues, 3 models selected  

> show sel cartoons

> select clear

> select #1-3/A

31021 atoms, 31646 bonds, 20 pseudobonds, 2961 residues, 6 models selected  

> show sel cartoons

> undo

> select #1-3/A:880-900

603 atoms, 615 bonds, 63 residues, 3 models selected  

> show sel cartoons

> select #1-3/A:890,1102

63 atoms, 57 bonds, 6 residues, 3 models selected  

> show sel atoms

> select clear

> select #1-3

59947 atoms, 61377 bonds, 92 pseudobonds, 5456 residues, 7 models selected  

> select H

14696 atoms, 1834 residues, 1 model selected  

> hide sel atoms

> select clear

> select #1-3/A:940-1000

1819 atoms, 1848 bonds, 1 pseudobond, 169 residues, 4 models selected  

> show sel cartoons

> undo

> select #1-3/A

31021 atoms, 31646 bonds, 20 pseudobonds, 2961 residues, 6 models selected  

> show sel cartoons

> select clear

> select #1-3/P-T

3404 atoms, 3751 bonds, 59 pseudobonds, 140 residues, 5 models selected  

> show sel atoms

> select clear

> select #3/A

15392 atoms, 15600 bonds, 6 pseudobonds, 975 residues, 2 models selected  

> select H

14696 atoms, 1834 residues, 1 model selected  

> select clear

> select #1-3/A

31021 atoms, 31646 bonds, 20 pseudobonds, 2961 residues, 6 models selected  

> hide sel cartoons

> select #1-3/A:910-1095

4328 atoms, 4394 bonds, 5 pseudobonds, 426 residues, 6 models selected  

> show sel cartoons

> select #1-3/A:815-910

2885 atoms, 2942 bonds, 288 residues, 3 models selected  

> show sel cartoons

> select clear

> select #3

30001 atoms, 30483 bonds, 10 pseudobonds, 1835 residues, 2 models selected  

> show sel cartoons

> show sel atoms

> hide sel atoms

> show sel atoms

> select H

14696 atoms, 1834 residues, 1 model selected  

> hide sel atoms

> select #3

30001 atoms, 30483 bonds, 10 pseudobonds, 1835 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> select #1-3/A:815-1095

7183 atoms, 7309 bonds, 5 pseudobonds, 711 residues, 6 models selected  

> show sel cartoons

> select #1-3/A:815-1239

11751 atoms, 11944 bonds, 5 pseudobonds, 1134 residues, 6 models selected  

> show sel cartoons

> undo

> select #1-3/P:1-19

1242 atoms, 1374 bonds, 51 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #1-3/T:11-28

1154 atoms, 1262 bonds, 48 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> select #1-3/P:19

68 atoms, 71 bonds, 3 residues, 3 models selected  

> show sel atoms

> show sel cartoons

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select #1-3/A:997-1049

359 atoms, 364 bonds, 3 pseudobonds, 42 residues, 6 models selected  

> hide sel cartoons

> undo

> hide sel cartoons

> select #1-3/A:997-1055

505 atoms, 510 bonds, 3 pseudobonds, 60 residues, 6 models selected  

> hide sel cartoons

> undo

> select #1-3/A:993-1055

682 atoms, 696 bonds, 3 pseudobonds, 72 residues, 6 models selected  

> hide sel cartoons

> select #1-3/A:989-1055

785 atoms, 799 bonds, 3 pseudobonds, 84 residues, 6 models selected  

> hide sel cartoons

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> select #3/T:2-10

293 atoms, 317 bonds, 9 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> select #3/P:19-24

187 atoms, 200 bonds, 6 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> select clear

> hide #!3 models

> show #!3 models

> hide #!2 models

> select #3/P-T

1496 atoms, 1613 bonds, 47 residues, 1 model selected  

> select H

14696 atoms, 1834 residues, 1 model selected  

> hide sel atoms

> select clear

> show #!2 models

> show #!1 models

> select #1-3/A

31021 atoms, 31646 bonds, 20 pseudobonds, 2961 residues, 6 models selected  

> hide sel cartoons

> select #1-3/A:943-955

469 atoms, 478 bonds, 39 residues, 3 models selected  

> show sel cartoons

> show sel atoms

> hide sel atoms

> select #1-3/A:940-955

530 atoms, 539 bonds, 46 residues, 3 models selected  

> show sel cartoons

> undo

> select #1-3/A:943,947

86 atoms, 80 bonds, 6 residues, 3 models selected  

> show sel atoms

> select H

14696 atoms, 1834 residues, 1 model selected  

> hide sel atoms

> select #1-3/N

68 atoms, 70 bonds, 2 residues, 2 models selected  

> show sel atoms

> select #1-3/890

Nothing selected  

> hide atoms

> undo

> select #1-3/A:890

28 atoms, 25 bonds, 3 residues, 3 models selected  

> hide sel atoms

> select clear

> select #1-3/A:1102

35 atoms, 32 bonds, 3 residues, 3 models selected  

> hide sel atoms

> select #1-3/P:19-22

282 atoms, 306 bonds, 12 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #1-3/T:7-10

300 atoms, 330 bonds, 12 residues, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> show #!3 models

> select #1-3/N

68 atoms, 70 bonds, 2 residues, 2 models selected  

> color sel hot pink

> color sel dark gray

> undo

[Repeated 1 time(s)]

> select clear

> hide #!1 models

> select #2/N:4003@O2G

1 atom, 1 residue, 1 model selected  

> select #2/A:943@NH1

1 atom, 1 residue, 1 model selected  

> distance #2/N:4003@O2G #2/A:943@NH1

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/N DCP 4003 O2G
and /A ARG 943 NH1: 2.995Å  

> distance #3/N:4003@O2G #3/A:943@NH1

Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
1  

> select #3/N:4000@O3G

1 atom, 1 residue, 1 model selected  

> select #3/N:4000@O1G

1 atom, 1 residue, 1 model selected  

> select #3/N:4000@O2G

1 atom, 1 residue, 1 model selected  

> distance #3/N:4000@O2G #3/A:943@NH1

Distance between GC_ternary_R__rsr57.pdb #3/N DCP 4000 O2G and /A ARG 943 NH1:
4.959Å  

> distance #3/N:4000@O3G #3/A:943@NH1

Distance between GC_ternary_R__rsr57.pdb #3/N DCP 4000 O3G and /A ARG 943 NH1:
2.497Å  

> select clear

> select #3/N

40 atoms, 41 bonds, 1 residue, 1 model selected  

> select H

14696 atoms, 1834 residues, 1 model selected  

> hide sel atoms

> select clear

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> select #2/N:4003@PG

1 atom, 1 residue, 1 model selected  

> select #3/N:4000@PG

1 atom, 1 residue, 1 model selected  

> distance #2/N:4003@PG #3/N:4000@PG

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/N DCP 4003 PG
and GC_ternary_R__rsr57.pdb #3/N DCP 4000 PG: 9.090Å  

> show #!4 models

> hide #!4 models

> select clear

[Repeated 1 time(s)]

> select #2/A:947@NZ

1 atom, 1 residue, 1 model selected  

> distance #2/A:947@NZ #3/A:947@NZ

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A LYS 947 NZ and
GC_ternary_R__rsr57.pdb #3/A LYS 947 NZ: 9.722Å  

> distance #2/A:947@CA #3/A:947@CA

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A LYS 947 CA and
GC_ternary_R__rsr57.pdb #3/A LYS 947 CA: 5.986Å  

> distance #2/A:943@CA #3/A:943@CA

Distance between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA and
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA: 9.713Å  

> define plane #2/A:943-955

Plane plane' placed at [ 42.22769492 -19.8350339 1.47379661] with normal
[-0.33947996 -0.48882656 -0.80361804]  

> define plane #3/A:943-955

Plane plane' placed at [150.04294421 135.9546867 109.59520601] with normal
[-0.54063224 0.62479026 0.56334173]  

> angle plane plane

Missing or invalid "objects" argument: invalid objects specifier  

> define plane plane1 #3/A:943-955

Missing or invalid "atoms" argument: invalid atoms specifier  

> plane1 #2/A:943-955

Unknown command: define plane1 #2/A:943-955  

> select clear

> angle #2.3 #3.3

Angle between plane #2.3 and plane #3.3: 54.929  

> hide #2.3 models

> hide #3.3 models

> select #2-3/A

23247 atoms, 23663 bonds, 17 pseudobonds, 1987 residues, 5 models selected  

> show sel cartoons

> undo

> select #2/T:4@O6

1 atom, 1 residue, 1 model selected  

> angle #2/T:4@O6 #2/A:943@CA #3/A:943@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA, and
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA: 55.315  

> angle #2/A:943@CA #2/T:4@O6 #3/A:943@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6, and
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA: 36.689  

> angle #2/A:943@CA #3/A:943@CA #2/T:4@O6

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA,
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA, and
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/T GD 4 O6: 87.996  

> angle #2/A:943@CA #3/A:943@CA #2/A:955@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA,
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA, and
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A TYR 955 CA: 87.377  

> select clear

> angle #2/A:943@CA #2/A:955@CA #3/A:943@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A TYR 955 CA, and
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA: 30.714  

> angle #2/A:955@CA #2/A:943@CA #3/A:943@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A TYR 955 CA,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA, and
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA: 61.909  

> angle #2/A:943@CA #2/A:955@CA #3/A:943@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A ARG 943 CA,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A TYR 955 CA, and
GC_ternary_R__rsr57.pdb #3/A ARG 943 CA: 30.714  

> angle #2/A:947@CA #2/A:955@CA #3/A:947@CA

Angle between R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A LYS 947 CA,
R853A_sca_hm11_refine_42_dCTPasChainN.pdb #2/A TYR 955 CA, and
GC_ternary_R__rsr57.pdb #3/A LYS 947 CA: 26.966  

> define plane #2/A:943-947

Plane plane' placed at [ 42.56888636 -14.80561364 -1.76688636] with normal
[-0.68723063 -0.19977323 -0.69843018]  

> define plane #3/A:943-947

Plane plane' placed at [150.11153409 131.44398864 114.10515909] with normal
[-0.85106877 0.51079731 0.12152391]  

> angle #2.4 #3.4

Angle between plane #2.4 and plane #3.4: 66.549  

> angle #2.3 #3.3

Angle between plane #2.3 and plane #3.3: 54.929  

> hide #3.4 models

Traceback (most recent call last):  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 325, in
_command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 423, in
add  
self._history.enqueue((item, typed))  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 171, in
enqueue  
self.save()  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 201, in
save  
self._history.save(self._queue)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 108, in
save  
with SaveTextFile(self._filename) as f:  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 174, in
__init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 74, in
__init__  
self._f = open(self._tmp_filename)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

xcb_shm_create_segment() failed for size 720000  

> hide #2.4 models

Traceback (most recent call last):  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 325, in
_command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 423, in
add  
self._history.enqueue((item, typed))  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 171, in
enqueue  
self.save()  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 201, in
save  
self._history.save(self._queue)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 108, in
save  
with SaveTextFile(self._filename) as f:  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 174, in
__init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 74, in
__init__  
self._f = open(self._tmp_filename)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> show #!1 models

Traceback (most recent call last):  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 325, in
_command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 423, in
add  
self._history.enqueue((item, typed))  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 171, in
enqueue  
self.save()  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 201, in
save  
self._history.save(self._queue)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 108, in
save  
with SaveTextFile(self._filename) as f:  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 174, in
__init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 74, in
__init__  
self._f = open(self._tmp_filename)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  

> select #1-3:A/943,947

Traceback (most recent call last):  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134,
in invoke  
return self._func(self._name, data)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 325, in
_command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 423, in
add  
self._history.enqueue((item, typed))  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 171, in
enqueue  
self.save()  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 201, in
save  
self._history.save(self._queue)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/history.py", line 108, in
save  
with SaveTextFile(self._filename) as f:  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 174, in
__init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 74, in
__init__  
self._f = open(self._tmp_filename)  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 30] Read-only file system:
'/home/gkherrma/.local/share/ChimeraX/commands.94854.tmp'  
  
File "/opt/apps/UCSF/ChimeraX/el7/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/safesave.py", line 173, in
open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
Nothing selected  

xcb_shm_create_segment() failed for size 1256976  




OpenGL version: 3.3.0 NVIDIA 515.48.07
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: TYAN
Model: B7105F48TV4HR-2T-N
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           188G         35G        3.2G        189M        149G        146G
	Swap:           63G        3.8M         63G

Graphics:
	04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]	
	Kernel driver in use: ast
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

User's home directory became a read-only file system in mid session!