Session save: function 'set_pbgroup_py_instance' not found

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /Users/martinpacesa/Documents/JinekLab/Projects/R-loop/ChimeraX/Cas9_all_models.cxs

Log from Mon Aug 1 19:23:22 2022

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> lighting soft

> set bgColor white

> distance style color black

[Repeated 1 time(s)]

> distance style decimalPlaces 1

[Repeated 1 time(s)]

> distance style dashes 7

[Repeated 1 time(s)]

> distance style symbol false

[Repeated 1 time(s)]

> style stick

Changed 0 atom styles  
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/martinpacesa/Downloads/R-loop/SpCas9-sgRNA-binary_4zt0_x-ray.pdb

Summary of feedback from opening
/Users/martinpacesa/Downloads/R-loop/SpCas9-sgRNA-binary_4zt0_x-ray.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 67 AH4 ALA C
59 ASP C 94 1 36  
Start residue of secondary structure not found: HELIX 68 AH5 SER C 96 GLU C
103 1 8  
Start residue of secondary structure not found: HELIX 69 AH6 ASN C 121 TYR C
132 1 12  
Start residue of secondary structure not found: HELIX 70 AH7 THR C 134 SER C
145 1 12  
Start residue of secondary structure not found: HELIX 71 AH8 ASP C 150 PHE C
164 1 15  
89 messages similar to the above omitted  
Cannot find LINK/SSBOND residue GLU (89 )  
Cannot find LINK/SSBOND residue MSE (90 )  
Cannot find LINK/SSBOND residue HIS (160 )  
Cannot find LINK/SSBOND residue MSE (161 )  
Cannot find LINK/SSBOND residue SER (320 )  
35 messages similar to the above omitted  
  
SpCas9-sgRNA-binary_4zt0_x-ray.pdb title:  
Crystal structure of catalytically-active streptococcus pyogenes CAS9 In
complex with single-guide RNA At 2.9 angstrom resolution [more info...]  
  
Chain information for SpCas9-sgRNA-binary_4zt0_x-ray.pdb #1  
---  
Chain | Description  
A | crispr-associated endonuclease CAS9  
B | single-guide RNA  
  

> open
> /Users/martinpacesa/Downloads/R-loop/6c6b_P3_J819_MP3_real_space_refined_061.pdb

Chain information for 6c6b_P3_J819_MP3_real_space_refined_061.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /Users/martinpacesa/Downloads/R-loop/8c8b_ref33_2_8_real_space_refined_056_MP5_real_space_refined_068.pdb

Chain information for
8c8b_ref33_2_8_real_space_refined_056_MP5_real_space_refined_068.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /Users/martinpacesa/Downloads/R-loop/10c10b_P32_J126_MP7_real_space_refined_012.pdb

Chain information for 10c10b_P32_J126_MP7_real_space_refined_012.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /Users/martinpacesa/Downloads/R-loop/12c12b_P33_J45_MP3_real_space_refined_011.pdb

Chain information for 12c12b_P33_J45_MP3_real_space_refined_011.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /Users/martinpacesa/Downloads/R-loop/14c14b_J46_MP9_real_space_refined_021.pdb

Chain information for 14c14b_J46_MP9_real_space_refined_021.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /Users/martinpacesa/Downloads/R-loop/16c16b_P27_J73_MP2_fixedMM_prot_newduplex2_real_space_refined_021.pdb

Chain information for
16c16b_P27_J73_MP2_fixedMM_prot_newduplex2_real_space_refined_021.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open /Users/martinpacesa/Downloads/R-loop/18c18b_JP38_J288_008_MP2.pdb

Chain information for 18c18b_JP38_J288_008_MP2.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> /Users/martinpacesa/Downloads/R-loop/18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb

Chain information for 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
c | No description available  
  

> ui tool show Matchmaker

> hide atoms

> show cartoons

> ui tool show Matchmaker

> matchmaker #!2-9 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 SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
6c6b_P3_J819_MP3_real_space_refined_061.pdb, chain B (#2), sequence alignment
score = 6656.3  
RMSD between 651 pruned atom pairs is 0.900 angstroms; (across all 1356 pairs:
8.841)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
8c8b_ref33_2_8_real_space_refined_056_MP5_real_space_refined_068.pdb, chain B
(#3), sequence alignment score = 6617.3  
RMSD between 475 pruned atom pairs is 1.175 angstroms; (across all 1356 pairs:
12.027)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
10c10b_P32_J126_MP7_real_space_refined_012.pdb, chain B (#4), sequence
alignment score = 6602.9  
RMSD between 564 pruned atom pairs is 0.727 angstroms; (across all 1357 pairs:
11.137)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
12c12b_P33_J45_MP3_real_space_refined_011.pdb, chain B (#5), sequence
alignment score = 5611.6  
RMSD between 365 pruned atom pairs is 1.057 angstroms; (across all 1187 pairs:
12.168)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
14c14b_J46_MP9_real_space_refined_021.pdb, chain B (#6), sequence alignment
score = 6502.3  
RMSD between 532 pruned atom pairs is 0.822 angstroms; (across all 1333 pairs:
11.070)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
16c16b_P27_J73_MP2_fixedMM_prot_newduplex2_real_space_refined_021.pdb, chain B
(#7), sequence alignment score = 6525.7  
RMSD between 354 pruned atom pairs is 0.888 angstroms; (across all 1337 pairs:
13.418)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
18c18b_JP38_J288_008_MP2.pdb, chain B (#8), sequence alignment score = 6500.7  
RMSD between 348 pruned atom pairs is 0.894 angstroms; (across all 1336 pairs:
13.478)  
  
Matchmaker SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1) with
18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9), sequence
alignment score = 6480.1  
RMSD between 378 pruned atom pairs is 1.200 angstroms; (across all 1344 pairs:
17.760)  
  

> ui tool show Matchmaker

> matchmaker #1#!2-8 to #9

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 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with SpCas9-sgRNA-binary_4zt0_x-ray.pdb, chain A (#1), sequence alignment
score = 6480.1  
RMSD between 378 pruned atom pairs is 1.200 angstroms; (across all 1344 pairs:
17.760)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 6c6b_P3_J819_MP3_real_space_refined_061.pdb, chain B (#2), sequence
alignment score = 6448.4  
RMSD between 772 pruned atom pairs is 0.871 angstroms; (across all 1337 pairs:
14.119)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 8c8b_ref33_2_8_real_space_refined_056_MP5_real_space_refined_068.pdb,
chain B (#3), sequence alignment score = 6401.2  
RMSD between 795 pruned atom pairs is 0.881 angstroms; (across all 1337 pairs:
13.606)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 10c10b_P32_J126_MP7_real_space_refined_012.pdb, chain B (#4), sequence
alignment score = 6438.4  
RMSD between 790 pruned atom pairs is 0.617 angstroms; (across all 1338 pairs:
14.010)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 12c12b_P33_J45_MP3_real_space_refined_011.pdb, chain B (#5), sequence
alignment score = 5625.2  
RMSD between 780 pruned atom pairs is 0.719 angstroms; (across all 1183 pairs:
6.016)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 14c14b_J46_MP9_real_space_refined_021.pdb, chain B (#6), sequence
alignment score = 6412.1  
RMSD between 786 pruned atom pairs is 0.708 angstroms; (across all 1328 pairs:
13.811)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 16c16b_P27_J73_MP2_fixedMM_prot_newduplex2_real_space_refined_021.pdb,
chain B (#7), sequence alignment score = 6593.8  
RMSD between 800 pruned atom pairs is 0.639 angstroms; (across all 1336 pairs:
10.137)  
  
Matchmaker 18c10b_J353_MP4_real_space_refined_016_fixedMg.pdb, chain B (#9)
with 18c18b_JP38_J288_008_MP2.pdb, chain B (#8), sequence alignment score =
6650.2  
RMSD between 801 pruned atom pairs is 0.631 angstroms; (across all 1336 pairs:
10.142)  
  

> hide #1 models

> show #1 models

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs

> lighting soft

[Repeated 2 time(s)]

> nucleotides tube/slab shape box

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> hide #!9 models

> color #1/A:1-56 dodger blue

> color #1/A:57-94 magenta

> color #1/A:95-174 gainsboro

> color #1/A:175-304 #aaaaff

> color #1/A:305-494 gainsboro

> color #1/A:495-717 tan

> color #1/A:718-766 dodger blue

> color #1/A:767-925 yellow

> color #1/A:926-1099 dodger blue

> color #1/A:1100-1368 salmon

> color #1/B orange

> show #1/B atoms

> color #2/B:1-56 dodger blue

> color #2/B:57-94 magenta

> color #2/B:95-174 gainsboro

> color #2/B:175-304 #aaaaff

> color #2/B:305-494 gainsboro

> color #2/B:495-717 tan

> color #2/B:718-766 dodger blue

> color #2/B:767-925 yellow

> color #2/B:926-1099 dodger blue

> color #2/B:1100-1368 salmon

> color #2/C steel blue

> color #2/D medium blue

> color #2/A orange

> show #2/A,C,D atoms

> color #3/B:1-56 dodger blue

> color #3/B:57-94 magenta

> color #3/B:95-174 gainsboro

> color #3/B:175-304 #aaaaff

> color #3/B:305-494 gainsboro

> color #3/B:495-717 tan

> color #3/B:718-766 dodger blue

> color #3/B:767-925 yellow

> color #3/B:926-1099 dodger blue

> color #3/B:1100-1368 salmon

> color #3/C steel blue

> color #3/D medium blue

> color #3/A orange

> show #3/A,C,D atoms

> color #4/B:1-56 dodger blue

> color #4/B:57-94 magenta

> color #4/B:95-174 gainsboro

> color #4/B:175-304 #aaaaff

> color #4/B:305-494 gainsboro

> color #4/B:495-717 tan

> color #4/B:718-766 dodger blue

> color #4/B:767-925 yellow

> color #4/B:926-1099 dodger blue

> color #4/B:1100-1368 salmon

> color #4/C steel blue

> color #4/D medium blue

> color #4/A orange

> show #4/A,C,D atoms

> color #5/B:1-56 dodger blue

> color #5/B:57-94 magenta

> color #5/B:95-174 gainsboro

> color #5/B:175-304 #aaaaff

> color #5/B:305-494 gainsboro

> color #5/B:495-717 tan

> color #5/B:718-766 dodger blue

> color #5/B:767-925 yellow

> color #5/B:926-1099 dodger blue

> color #5/B:1100-1368 salmon

> color #5/C steel blue

> color #5/D medium blue

> color #5/A orange

> show #5/A,C,D atoms

> color #6/B:1-56 dodger blue

> color #6/B:57-94 magenta

> color #6/B:95-174 gainsboro

> color #6/B:175-304 #aaaaff

> color #6/B:305-494 gainsboro

> color #6/B:495-717 tan

> color #6/B:718-766 dodger blue

> color #6/B:767-925 yellow

> color #6/B:926-1099 dodger blue

> color #6/B:1100-1368 salmon

> color #6/C steel blue

> color #6/D medium blue

> color #6/A orange

> show #6/A,C,D atoms

> color #7/B:1-56 dodger blue

> color #7/B:57-94 magenta

> color #7/B:95-174 gainsboro

> color #7/B:175-304 #aaaaff

> color #7/B:305-494 gainsboro

> color #7/B:495-717 tan

> color #7/B:718-766 dodger blue

> color #7/B:767-925 yellow

> color #7/B:926-1099 dodger blue

> color #7/B:1100-1368 salmon

> color #7/C steel blue

> color #7/D medium blue

> color #7/A orange

> show #7/A,C,D atoms

> color #8/B:1-56 dodger blue

> color #8/B:57-94 magenta

> color #8/B:95-174 gainsboro

> color #8/B:175-304 #aaaaff

> color #8/B:305-494 gainsboro

> color #8/B:495-717 tan

> color #8/B:718-766 dodger blue

> color #8/B:767-925 yellow

> color #8/B:926-1099 dodger blue

> color #8/B:1100-1368 salmon

> color #8/C steel blue

> color #8/D medium blue

> color #8/A orange

> show #8/A,C,D atoms

> color #9/B:1-56 dodger blue

> color #9/B:57-94 magenta

> color #9/B:95-174 gainsboro

> color #9/B:175-304 #aaaaff

> color #9/B:305-494 gainsboro

> color #9/B:495-717 tan

> color #9/B:718-766 dodger blue

> color #9/B:767-925 yellow

> color #9/B:926-1099 dodger blue

> color #9/B:1100-1368 salmon

> color #9/C steel blue

> color #9/c steel blue

> color #9/D medium blue

> color #9/A orange

> show #9/A,C,c,D atoms

> hide #1 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!6 models

> show #!7 models

> show #!4 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> hide #!6 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> show #!9 models

> show surfaces

> color #1/A:1-56 dodger blue

> color #1/A:57-94 magenta

> color #1/A:95-174 gainsboro

> color #1/A:175-304 #aaaaff

> color #1/A:305-494 gainsboro

> color #1/A:495-717 tan

> color #1/A:718-766 dodger blue

> color #1/A:767-925 yellow

> color #1/A:926-1099 dodger blue

> color #1/A:1100-1368 salmon

> color #1/B orange

> show #1/B atoms

> color #2/B:1-56 dodger blue

> color #2/B:57-94 magenta

> color #2/B:95-174 gainsboro

> color #2/B:175-304 #aaaaff

> color #2/B:305-494 gainsboro

> color #2/B:495-717 tan

> color #2/B:718-766 dodger blue

> color #2/B:767-925 yellow

> color #2/B:926-1099 dodger blue

> color #2/B:1100-1368 salmon

> color #2/C steel blue

> color #2/D medium blue

> color #2/A orange

> show #2/A,C,D atoms

> color #3/B:1-56 dodger blue

> color #3/B:57-94 magenta

> color #3/B:95-174 gainsboro

> color #3/B:175-304 #aaaaff

> color #3/B:305-494 gainsboro

> color #3/B:495-717 tan

> color #3/B:718-766 dodger blue

> color #3/B:767-925 yellow

> color #3/B:926-1099 dodger blue

> color #3/B:1100-1368 salmon

> color #3/C steel blue

> color #3/D medium blue

> color #3/A orange

> show #3/A,C,D atoms

> color #4/B:1-56 dodger blue

> color #4/B:57-94 magenta

> color #4/B:95-174 gainsboro

> color #4/B:175-304 #aaaaff

> color #4/B:305-494 gainsboro

> color #4/B:495-717 tan

> color #4/B:718-766 dodger blue

> color #4/B:767-925 yellow

> color #4/B:926-1099 dodger blue

> color #4/B:1100-1368 salmon

> color #4/C steel blue

> color #4/D medium blue

> color #4/A orange

> show #4/A,C,D atoms

> color #5/B:1-56 dodger blue

> color #5/B:57-94 magenta

> color #5/B:95-174 gainsboro

> color #5/B:175-304 #aaaaff

> color #5/B:305-494 gainsboro

> color #5/B:495-717 tan

> color #5/B:718-766 dodger blue

> color #5/B:767-925 yellow

> color #5/B:926-1099 dodger blue

> color #5/B:1100-1368 salmon

> color #5/C steel blue

> color #5/D medium blue

> color #5/A orange

> show #5/A,C,D atoms

> color #6/B:1-56 dodger blue

> color #6/B:57-94 magenta

> color #6/B:95-174 gainsboro

> color #6/B:175-304 #aaaaff

> color #6/B:305-494 gainsboro

> color #6/B:495-717 tan

> color #6/B:718-766 dodger blue

> color #6/B:767-925 yellow

> color #6/B:926-1099 dodger blue

> color #6/B:1100-1368 salmon

> color #6/C steel blue

> color #6/D medium blue

> color #6/A orange

> show #6/A,C,D atoms

> color #7/B:1-56 dodger blue

> color #7/B:57-94 magenta

> color #7/B:95-174 gainsboro

> color #7/B:175-304 #aaaaff

> color #7/B:305-494 gainsboro

> color #7/B:495-717 tan

> color #7/B:718-766 dodger blue

> color #7/B:767-925 yellow

> color #7/B:926-1099 dodger blue

> color #7/B:1100-1368 salmon

> color #7/C steel blue

> color #7/D medium blue

> color #7/A orange

> show #7/A,C,D atoms

> color #8/B:1-56 dodger blue

> color #8/B:57-94 magenta

> color #8/B:95-174 gainsboro

> color #8/B:175-304 #aaaaff

> color #8/B:305-494 gainsboro

> color #8/B:495-717 tan

> color #8/B:718-766 dodger blue

> color #8/B:767-925 yellow

> color #8/B:926-1099 dodger blue

> color #8/B:1100-1368 salmon

> color #8/C steel blue

> color #8/D medium blue

> color #8/A orange

> show #8/A,C,D atoms

> color #9/B:1-56 dodger blue

> color #9/B:57-94 magenta

> color #9/B:95-174 gainsboro

> color #9/B:175-304 #aaaaff

> color #9/B:305-494 gainsboro

> color #9/B:495-717 tan

> color #9/B:718-766 dodger blue

> color #9/B:767-925 yellow

> color #9/B:926-1099 dodger blue

> color #9/B:1100-1368 salmon

> color #9/C steel blue

> color #9/c steel blue

> color #9/D medium blue

> color #9/A orange

> show #9/A,C,c,D atoms

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> show #!6 models

> show #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!7 models

> hide #1/B surfaces

> show #!2 models

> hide #!1 models

> hide #2/A,C,c,D surfaces

> hide #3/A,C,c,D surfaces

> hide #4/A,C,c,D surfaces

> hide #5/A,C,c,D surfaces

> hide #6/A,C,c,D surfaces

> hide #7/A,C,c,D surfaces

> hide #8/A,C,c,D surfaces

> hide #9/A,C,c,D surfaces

> show #!9 models

> hide #!9 models

> hide #!2 models

> show #!2 models

> show #!9 models

> hide #!2 models

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

> show #!2 models

> show #!3 models

> show #!4 models

> show #!6 models

> show #!8 models

> hide #!9 models

> hide #!8 models

> show #!5 models

> hide #!6 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!5 models

> hide #1.2 models

> hide #1.1 models

> show #!1 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> hide #!1 models

> hide #2.1 models

> show #!2 models

> show #2.1 models

> hide #2.1 models

> hide #!2 models

> hide #3.1 models

> hide #4.1 models

> hide #5.1 models

> hide #6.1 models

> hide #7.1 models

> hide #8.1 models

> hide #9.1 models

> show #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!3 models

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

> hide #!2 models

> show #!2 models

> show #!9 models

> hide #!2 models

> hide #!1 models

> ui tool show "Side View"

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

> show #!1 models

> hide #!9 models

> transparency #1/A 50 surfaces

> hide #1/A cartoons

> hide #2/B cartoons

> hide #3/B cartoons

> hide #4/B cartoons

> hide #5/B cartoons

> hide #6/B cartoons

> hide #7/B cartoons

> hide #8/B cartoons

> hide #9/B cartoons

> transparency #1/A 30 surfaces

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

> save /Users/martinpacesa/Downloads/binary.png pixelSize 0.05
> transparentBackground true supersample 5

> graphics silhouettes true width 2.0 color black

> graphics silhouettes true width 3.0 color black

> save /Users/martinpacesa/Downloads/binary.png pixelSize 0.05
> transparentBackground true supersample 5

> graphics silhouettes true width 4.0 color black

> save /Users/martinpacesa/Downloads/binary.png pixelSize 0.05
> transparentBackground true supersample 5

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

> show #!3 models

> hide #!1 models

> show #!2 models

> hide #!3 models

> transparency #2/B:1-174,305-1368 30 surfaces

> save /Users/martinpacesa/Downloads/6nt-REC2.png pixelSize 0.05
> transparentBackground true supersample 5

> lighting gentle

> save /Users/martinpacesa/Downloads/6nt-REC22.png pixelSize 0.05
> transparentBackground true supersample 5

> lighting soft

> show #!3 models

> hide #!2 models

> transparency #2/3:1-174,305-494,718-1368 30 surfaces

> show #!2 models

> hide #!3 models

> transparency #2/B:1-174,305-1368 30 surfaces

> show #!3 models

> hide #!2 models

> transparency #3/B:1-174,305-494,718-1368 30 surfaces

> save /Users/martinpacesa/Downloads/8nt-REC2-REC3.png pixelSize 0.05
> transparentBackground true supersample 5

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

> show #!4 models

> hide #!3 models

> transparency #4/B:1-174,305-494,718-1368 30 surfaces

> transparency #4/B:1-174,305-494,718-1368 50 surfaces

> save /Users/martinpacesa/Downloads/10nt-REC2-REC3.png pixelSize 0.05
> transparentBackground true supersample 5

> transparency #4/B:1-174,305-494,718-1368 30 surfaces

> transparency #4/B:767-925 70 surfaces

> save /Users/martinpacesa/Downloads/10nt-REC2-REC3.png pixelSize 0.05
> transparentBackground true supersample 5

> hide #!4 models

> show #!7 models

> transparency #7/B:1-767,925-1368 30 surfaces

> save /Users/martinpacesa/Downloads/16nt-HNH.png pixelSize 0.05
> transparentBackground true supersample 5

> show #!8 models

> hide #!7 models

> show #!9 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> hide #!8 models

> transparency #9/B:1-174, 305-494, 718-766, 925-1368 30 surfaces

> save /Users/martinpacesa/Downloads/18nt-REC2-REC3-HNH.png pixelSize 0.05
> transparentBackground true supersample 5

> save /Users/martinpacesa/Downloads/R-loop/Cas9_all_models.cxs includeMaps
> true

——— End of log from Mon Aug 1 19:23:22 2022 ———

opened ChimeraX session  

> show #!1-8 target m

> select nucleic-acid

25171 atoms, 28186 bonds, 4 pseudobonds, 1202 residues, 13 models selected  

> hide sel cartoons

> hide sel atoms

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> ui mousemode right select

> select clear

> hide #!2 models

> color #1 silver transparency 0

> color #1 #929292 transparency 0

> color #1 darkgrey transparency 0

> show #!2 models

> show #!4 models

> show #!5 models

> hide #!5 models

> show #!6 models

> show #!5 models

> show #!3 models

> show #!7 models

> show #!8 models

> show #!9 models

> color #1-9 darkgrey

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting flat

> hide #!2-9 target m

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true width 1.0

> graphics silhouettes true width 1.5

> graphics silhouettes true width 2.5

> show #!2-9 target m

> graphics silhouettes true width 2.5

> save /Users/martinpacesa/Documents/PacesaLab/Presentations/221108_EMBL-
> Heidelberg_Prof_interview/Figures/multi-state_grey_States.cxs includeMaps
> true

Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 543, in include_state  
return bool(self.group_map)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x214ed59a0, set_pbgroup_py_instance): symbol not found  
  

Populating font family aliases took 293 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

AttributeError: dlsym(0x214ed59a0, set_pbgroup_py_instance): symbol not found  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 896, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 249, in discovery  
if hasattr(sm, 'include_state') and not sm.include_state(value):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 543, in include_state  
return bool(self.group_map)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 536, in group_map  
f = c_function('set_pbgroup_py_instance',  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 31, in c_function  
f = getattr(self._c_lib, func_name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 387, in __getattr__  
func = self.__getitem__(name)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
AttributeError: dlsym(0x214ed59a0, set_pbgroup_py_instance): symbol not found  
  
AttributeError: dlsym(0x214ed59a0, set_pbgroup_py_instance): symbol not found  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ctypes/__init__.py",
line 392, in __getitem__  
func = self._FuncPtr((name_or_ordinal, self))  
  
See log for complete Python traceback.  
  




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

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.6 (21G115)
      Kernel Version: Darwin 21.6.0
      Time since boot: 5 days 22:48

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PHL 258B6QU:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
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