Hysteresis with clip cap transparency

[micaela.boierosanders@…]

The following bug report has been submitted:
Platform:        macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Hello! I was playing around with surfaces, transparency and clipping and I realized something. For example if you clip a surface that is not transparent you see a full section and you cannot see inside. If you make it transparent you can see things inside (for example stick representation) but if you make transparency 0 again, it will make the outside of the surface representation transparent but not the inside, so if you clip through the color is not full but transparent. Is it possible to make the inside not transparent again?

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

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/SurfacesTrial2.cxs

Opened PointedEnd_cryosparc_P48_J79_003_volume_map_sharp.mrc as #12, grid size
360,360,360, pixel 0.9, shown at step 1, values float32  
Opened PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc as
#13, grid size 480,480,480, pixel 0.88, shown at step 1, values float32  
Opened cryosparc_P50_J37_003_volume_map_sharp.mrc as #14, grid size
320,320,320, pixel 0.88, shown at step 1, values float32  
Opened Moved_cryosparc_P50_J39_004_volume_map_sharp.mrc as #15, grid size
320,320,320, pixel 0.88, shown at step 1, values float32  
Log from Thu Oct 19 10:30:20 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/SurfacesTrial1.cxs

Opened PointedEnd_cryosparc_P48_J79_003_volume_map_sharp.mrc as #12, grid size
360,360,360, pixel 0.9, shown at step 1, values float32  
Opened PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc as
#13, grid size 480,480,480, pixel 0.88, shown at step 1, values float32  
Opened cryosparc_P50_J37_003_volume_map_sharp.mrc as #14, grid size
320,320,320, pixel 0.88, shown at step 1, values float32  
Opened Moved_cryosparc_P50_J39_004_volume_map_sharp.mrc as #15, grid size
320,320,320, pixel 0.88, shown at step 1, values float32  
Log from Thu Oct 19 10:19:49 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  

> windowsize 1000 1000

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb

Chain information for
DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb
#1  
---  
Chain | Description  
A B C D | No description available  
E F | No description available  
G H I J | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb

Chain information for
Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb
#2  
---  
Chain | Description  
A B C D | No description available  
E F | No description available  
G H I J | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb

Chain information for
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb

Chain information for
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#4  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/PhalloidinPointedEnd_230711_ActinPhalloidin-
> Phx4-coot-8_real_space_refined_011.pdb

Chain information for PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
H I J K | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/PhalloidinPointedEnd_230711_ActinPhalloidin-
> Phx4-coot-8_real_space_refined_011.pdb

Chain information for PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
H I J K | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/3hbt.pdb

3hbt.pdb title:  
The structure of native G-actin [more info...]  
  
Chain information for 3hbt.pdb #7  
---  
Chain | Description | UniProt  
A | α-actin-1 | ACTS_RABIT 1-375  
  
Non-standard residues in 3hbt.pdb #7  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
SO4 — sulfate ion  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #8  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #8  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #9  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #9  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #10  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #10  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #11  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #11  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Maps/PointedEnd_cryosparc_P48_J79_003_volume_map_sharp.mrc

Opened PointedEnd_cryosparc_P48_J79_003_volume_map_sharp.mrc as #12, grid size
360,360,360, pixel 0.9, shown at level 0.229, step 2, values float32  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Maps/PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc

Opened PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc as
#13, grid size 480,480,480, pixel 0.88, shown at level 0.115, step 2, values
float32  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Maps/cryosparc_P50_J37_003_volume_map_sharp.mrc

Opened cryosparc_P50_J37_003_volume_map_sharp.mrc as #14, grid size
320,320,320, pixel 0.88, shown at level 0.189, step 2, values float32  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Maps/Moved_cryosparc_P50_J39_004_volume_map_sharp.mrc

Opened Moved_cryosparc_P50_J39_004_volume_map_sharp.mrc as #15, grid size
320,320,320, pixel 0.88, shown at level 0.188, step 2, values float32  

> set bgColor white

> lighting soft

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.03

> cartoon style width 1.5 thickness 0.3

> colordef marine 0.0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> colordef paleskyblue #accbde

Color 'paleskyblue' is opaque: rgb(67.5%, 79.6%, 87.1%) hex: #accbde

  

> colordef lilacblue #b8c1de

Color 'lilacblue' is opaque: rgb(72.2%, 75.7%, 87.1%) hex: #b8c1de

  

> colordef lightpaleyellow #ded19f

Color 'lightpaleyellow' is opaque: rgb(87.1%, 82%, 62.4%) hex: #ded19f

  

> dssp

> hide atoms

> show cartoons

> style stick

Changed 102951 atom styles  

> color #1,2/D #e38a25

> color #1,2/C #ef9544

> color #1,2/B #f9a25a

> color #1,2/A #fab27b

> color #3/A #3cb3b6

> color #3/B #5dc6c7

> color #3/C #82d0d2

> color #3/D #9dd9de

> color #4 #9dd9de

> color #5/A #e38a25

> color #5/B #ef9544

> color #5/C #f9a25a

> color #5/D #fab27b

> color #6 #fab27b

> color #1,2/E,F #c7e493ff

> select #1/E,F:263,264 #2/E,F:263,264

112 atoms, 116 bonds, 8 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:18

32 atoms, 28 bonds, 4 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:172,198,251,39

132 atoms, 116 bonds, 16 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:261,262

8 atoms, 8 residues, 2 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #8,9,10,11/B,C #60c46c

> select #8,9,10,11/B:18 #8,9,10,11/C #9,10,11,12/B:172,198,201,203,205,207

279 atoms, 265 bonds, 30 residues, 4 models selected  

> select clear

> select #8,9,10,11/B:1272,1273

8 atoms, 8 residues, 4 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #7 #8,9,10,11/A light grey

> color #8/A #3cb3b6

> color #10/A #5dc6c7

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> matchmaker #1,2/D #5,6,8,9/A #7 to #3/A

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb,
chain D (#1), sequence alignment score = 1693.1  
RMSD between 237 pruned atom pairs is 0.779 angstroms; (across all 357 pairs:
2.740)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb,
chain D (#2), sequence alignment score = 1669.1  
RMSD between 240 pruned atom pairs is 0.801 angstroms; (across all 357 pairs:
2.685)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#5), sequence alignment score
= 1618.8  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1618.8  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#8), sequence alignment score = 1711.7  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#9), sequence alignment score = 1711.7  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 3hbt.pdb, chain A (#7), sequence alignment score = 1696.7  
RMSD between 349 pruned atom pairs is 0.707 angstroms; (across all 356 pairs:
0.767)  
  

> matchmaker #10,11/A to #3/B

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#10), sequence alignment score = 1749.5  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#11), sequence alignment score = 1749.5  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  

> matchmaker #4/A to #3/C

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain C (#3) with
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#4), sequence alignment score = 1703.3  
RMSD between 244 pruned atom pairs is 0.763 angstroms; (across all 357 pairs:
2.824)  
  

> matchmaker #6/A to #5/C

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 PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain C (#5) with
PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1680.7  
RMSD between 357 pruned atom pairs is 0.464 angstroms; (across all 359 pairs:
0.504)  
  

> hide #4/A,B target abcs

> hide #6/A,B target abcs

> view matrix camera
> 0.93969,1.4138e-25,0.34202,292.8,-0.34202,1.1102e-16,0.93969,516.96,-3.7971e-17,-1,1.0432e-16,166.14

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> color #12 #b5e1e6

> color #13 #fcc6a0

> color #3 #fcc6a0

> color #4 #fcc6a0

> volume #12-15 step 1

> volume #12 level 0.689

> volume #13 level 0.6479

> color zone #12 near #3 distance 4

> color zone #13 near #5 distance 3.03

> surface dust #12 size 4

> surface dust #13 size 4

> volume #14 level 0.3428

> surface dust #14 size 5.28

> color zone #14 near #1 distance 5

> volume #15 level 0.3371

> surface dust #15 size 5.28

> color zone #15 near #2 distance 5

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> view matrix camera
> 0.93969,1.4138e-25,0.34202,292.8,-0.34202,1.1102e-16,0.93969,516.96,-3.7971e-17,-1,1.0432e-16,166.14

> view name pos1

> view matrix camera
> -0.93969,1.4138e-25,-0.34202,29.726,0.34202,1.1102e-16,-0.93969,-193.7,3.7971e-17,-1,-1.0433e-16,166.14

> view name pos2

> view matrix camera
> 0.93969,1.4138e-25,0.34202,245.66,-0.34202,1.1102e-16,0.93969,397.33,-3.7971e-17,-1,1.0432e-16,133.28

> view name pos1zoomed

> view matrix camera
> -0.93969,1.4138e-25,-0.34202,84.687,0.34202,1.1102e-16,-0.93969,-52.496,3.7971e-17,-1,-1.0433e-16,128.24

> view name pos2zoomed

> view pos1

> turn y -50 center #1

> view name pos150

> view matrix camera
> 0.34202,4.5416e-25,0.93969,346.14,-0.93969,1.1102e-16,0.34202,225.68,-1.0432e-16,-1,3.7967e-17,121.93

> view name pos150zoom

> view matrix camera
> 0.26193,-0.49013,0.83136,353.17,-0.96475,-0.15553,0.21226,210.08,0.025264,-0.85766,-0.51359,2.4186

> view name pos3

> view matrix camera
> -0.98467,0.072211,-0.15879,124.8,0.16305,0.057436,-0.98494,-72.458,-0.062003,-0.99573,-0.068329,110.92

> view name pos4

> view matrix camera
> 0.73528,-0.19841,0.64807,320.17,-0.6721,-0.33679,0.65943,327.74,0.087424,-0.92044,-0.38099,38.834

> view name pos5

> view matrix camera
> 0.88847,0.020898,0.45847,199.43,-0.44663,-0.19049,0.8742,216.85,0.1056,-0.98147,-0.15991,112.23

> view name pos6

> view matrix camera
> 0.91176,-0.14523,0.38418,255.12,-0.41057,-0.34634,0.84349,373.39,0.010559,-0.9268,-0.37541,38.982

> view name pos7

> view matrix camera
> -0.99452,-1.1451e-24,-0.10453,115.28,0.10453,1.1102e-16,-0.99452,-285.16,1.1605e-17,-1,-1.1042e-16,184.08

> view name pos8

> view matrix camera
> 0.85695,-0.045343,0.5134,202.48,-0.30437,-0.84839,0.43311,206.98,0.41593,-0.52742,-0.74083,78.41

> ~clip

> clip near 1

> clip near -55

> clip far -17

> view name posphd1

> ~clip

> view matrix camera
> 0.85695,-0.045343,0.5134,193.19,-0.30437,-0.84839,0.43311,194.94,0.41593,-0.52742,-0.74083,97.362

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> ~clip

> clip near 1

> clip near -55

> clip far -17

> view name posphd2

> view posphd1

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_2.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> color byhetero

> view posphd1

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_byhetero.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_2_byhetero.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide 1-15 models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> transparency #13 70

> view posphd2

> hide 1-15 models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> set bgColor white

> lighting soft

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.03

> cartoon style width 1.5 thickness 0.3

> colordef marine 0.0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> colordef paleskyblue #accbde

Color 'paleskyblue' is opaque: rgb(67.5%, 79.6%, 87.1%) hex: #accbde

  

> colordef lilacblue #b8c1de

Color 'lilacblue' is opaque: rgb(72.2%, 75.7%, 87.1%) hex: #b8c1de

  

> colordef lightpaleyellow #ded19f

Color 'lightpaleyellow' is opaque: rgb(87.1%, 82%, 62.4%) hex: #ded19f

  

> dssp

> hide atoms

> show cartoons

> style stick

Changed 102951 atom styles  

> color #1,2/D #e38a25

> color #1,2/C #ef9544

> color #1,2/B #f9a25a

> color #1,2/A #fab27b

> color #3/A #3cb3b6

> color #3/B #5dc6c7

> color #3/C #82d0d2

> color #3/D #9dd9de

> color #4 #9dd9de

> color #5/A #e38a25

> color #5/B #ef9544

> color #5/C #f9a25a

> color #5/D #fab27b

> color #6 #fab27b

> color #1,2/E,F #c7e493ff

> select #1/E,F:263,264 #2/E,F:263,264

112 atoms, 116 bonds, 8 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:18

32 atoms, 28 bonds, 4 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:172,198,251,39

132 atoms, 116 bonds, 16 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:261,262

8 atoms, 8 residues, 2 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #8,9,10,11/B,C #60c46c

> select #8,9,10,11/B:18 #8,9,10,11/C #9,10,11,12/B:172,198,201,203,205,207

279 atoms, 265 bonds, 30 residues, 4 models selected  

> select clear

> select #8,9,10,11/B:1272,1273

8 atoms, 8 residues, 4 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #7 #8,9,10,11/A light grey

> color #8/A #3cb3b6

> color #10/A #5dc6c7

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd1

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_2.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> color byhetero

> view posphd1

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_byhetero.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_2_byhetero.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> select #5/H:4@CG2

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

55 atoms, 59 bonds, 7 residues, 1 model selected  

> color sel byhetero

> select clear

> show #!3 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!9 models

> hide #!9 models

> view posphd2

> hide #!3 models

> hide #!5 atoms

> show #5/H target ab

> select up

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

> select up

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

> select up

55 atoms, 59 bonds, 7 residues, 1 model selected  

> show sel target s

> select clear

> hide #!13 models

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> show #!10 models

> hide #!10 models

> show #!8 models

> hide #!8 models

> show #!3 models

> select #5/H:6@CA

1 atom, 1 residue, 1 model selected  

> select up

8 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

55 atoms, 59 bonds, 7 residues, 2 models selected  

> hide sel surfaces

> show sel atoms

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> volume #13 level 0.6073

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> close session

> windowsize 1000 1000

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb

Chain information for
DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb
#1  
---  
Chain | Description  
A B C D | No description available  
E F | No description available  
G H I J | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb

Chain information for
Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb
#2  
---  
Chain | Description  
A B C D | No description available  
E F | No description available  
G H I J | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb

Chain information for
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb

Chain information for
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#4  
---  
Chain | Description  
A B | No description available  
C D | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/PhalloidinPointedEnd_230711_ActinPhalloidin-
> Phx4-coot-8_real_space_refined_011.pdb

Chain information for PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
H I J K | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/PhalloidinPointedEnd_230711_ActinPhalloidin-
> Phx4-coot-8_real_space_refined_011.pdb

Chain information for PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C D | No description available  
H I J K | No description available  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Models/3hbt.pdb

3hbt.pdb title:  
The structure of native G-actin [more info...]  
  
Chain information for 3hbt.pdb #7  
---  
Chain | Description | UniProt  
A | α-actin-1 | ACTS_RABIT 1-375  
  
Non-standard residues in 3hbt.pdb #7  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
SO4 — sulfate ion  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #8  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #8  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #9  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #9  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #10  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #10  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Models/2a42.pdb

2a42.pdb title:  
Actin-DNAse I complex [more info...]  
  
Chain information for 2a42.pdb #11  
---  
Chain | Description | UniProt  
A | α-actin 1 | ACTS_RABIT 1-375  
B | deoxyribonuclease-1 | DNAS1_BOVIN 1-260  
  
Non-standard residues in 2a42.pdb #11  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Maps/PointedEnd_cryosparc_P48_J79_003_volume_map_sharp.mrc

Opened PointedEnd_cryosparc_P48_J79_003_volume_map_sharp.mrc as #12, grid size
360,360,360, pixel 0.9, shown at level 0.229, step 2, values float32  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/Maps/PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc

Opened PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc as
#13, grid size 480,480,480, pixel 0.88, shown at level 0.115, step 2, values
float32  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Maps/cryosparc_P50_J37_003_volume_map_sharp.mrc

Opened cryosparc_P50_J37_003_volume_map_sharp.mrc as #14, grid size
320,320,320, pixel 0.88, shown at level 0.189, step 2, values float32  

> open
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/DNaseI_Movement/Maps/Moved_cryosparc_P50_J39_004_volume_map_sharp.mrc

Opened Moved_cryosparc_P50_J39_004_volume_map_sharp.mrc as #15, grid size
320,320,320, pixel 0.88, shown at level 0.188, step 2, values float32  

> set bgColor white

> lighting soft

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.03

> cartoon style width 1.5 thickness 0.3

> colordef marine 0.0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> colordef paleskyblue #accbde

Color 'paleskyblue' is opaque: rgb(67.5%, 79.6%, 87.1%) hex: #accbde

  

> colordef lilacblue #b8c1de

Color 'lilacblue' is opaque: rgb(72.2%, 75.7%, 87.1%) hex: #b8c1de

  

> colordef lightpaleyellow #ded19f

Color 'lightpaleyellow' is opaque: rgb(87.1%, 82%, 62.4%) hex: #ded19f

  

> dssp

> hide atoms

> show cartoons

> style stick

Changed 102951 atom styles  

> color #1,2/D #e38a25

> color #1,2/C #ef9544

> color #1,2/B #f9a25a

> color #1,2/A #fab27b

> color #3/A #3cb3b6

> color #3/B #5dc6c7

> color #3/C #82d0d2

> color #3/D #9dd9de

> color #4 #9dd9de

> color #5/A #e38a25

> color #5/B #ef9544

> color #5/C #f9a25a

> color #5/D #fab27b

> color #6 #fab27b

> color #1,2/E,F #c7e493ff

> select #1/E,F:263,264 #2/E,F:263,264

112 atoms, 116 bonds, 8 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:18

32 atoms, 28 bonds, 4 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:172,198,251,39

132 atoms, 116 bonds, 16 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:261,262

8 atoms, 8 residues, 2 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #8,9,10,11/B,C #60c46c

> select #8,9,10,11/B:18 #8,9,10,11/C #9,10,11,12/B:172,198,201,203,205,207

279 atoms, 265 bonds, 30 residues, 4 models selected  

> select clear

> select #8,9,10,11/B:1272,1273

8 atoms, 8 residues, 4 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #7 #8,9,10,11/A light grey

> color #8/A #3cb3b6

> color #10/A #5dc6c7

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> matchmaker #1,2/D #5,6,8,9/A #7 to #3/A

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb,
chain D (#1), sequence alignment score = 1699.4  
RMSD between 237 pruned atom pairs is 0.779 angstroms; (across all 357 pairs:
2.740)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb,
chain D (#2), sequence alignment score = 1675.4  
RMSD between 240 pruned atom pairs is 0.801 angstroms; (across all 357 pairs:
2.685)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#5), sequence alignment score
= 1625.1  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1625.1  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#8), sequence alignment score = 1718  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#9), sequence alignment score = 1718  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 3hbt.pdb, chain A (#7), sequence alignment score = 1703  
RMSD between 349 pruned atom pairs is 0.707 angstroms; (across all 356 pairs:
0.767)  
  

> matchmaker #10,11/A to #3/B

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#10), sequence alignment score = 1755.8  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#11), sequence alignment score = 1755.8  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  

> matchmaker #4/A to #3/C

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain C (#3) with
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#4), sequence alignment score = 1709.6  
RMSD between 244 pruned atom pairs is 0.763 angstroms; (across all 357 pairs:
2.824)  
  

> matchmaker #6/A to #5/C

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 PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain C (#5) with
PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1687  
RMSD between 357 pruned atom pairs is 0.464 angstroms; (across all 359 pairs:
0.504)  
  

> hide #4/A,B target abcs

> hide #6/A,B target abcs

> view matrix camera
> 0.93969,1.4138e-25,0.34202,292.8,-0.34202,1.1102e-16,0.93969,516.96,-3.7971e-17,-1,1.0432e-16,166.14

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> color #12 #b5e1e6

> color #13 #fcc6a0

> color #3 #fcc6a0

> color #4 #fcc6a0

> volume #12-15 step 1

> volume #12 level 0.689

> volume #13 level 0.6479

> color zone #12 near #3 distance 4

> color zone #13 near #5 distance 3.03

> surface dust #12 size 4

> surface dust #13 size 4

> volume #14 level 0.3428

> surface dust #14 size 5.28

> color zone #14 near #1 distance 5

> volume #15 level 0.3371

> surface dust #15 size 5.28

> color zone #15 near #2 distance 5

> set bgColor white

> lighting soft

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.03

> cartoon style width 1.5 thickness 0.3

> colordef marine 0.0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> colordef paleskyblue #accbde

Color 'paleskyblue' is opaque: rgb(67.5%, 79.6%, 87.1%) hex: #accbde

  

> colordef lilacblue #b8c1de

Color 'lilacblue' is opaque: rgb(72.2%, 75.7%, 87.1%) hex: #b8c1de

  

> colordef lightpaleyellow #ded19f

Color 'lightpaleyellow' is opaque: rgb(87.1%, 82%, 62.4%) hex: #ded19f

  

> dssp

> hide atoms

> show cartoons

> style stick

Changed 102951 atom styles  

> color #1,2/D #e38a25

> color #1,2/C #ef9544

> color #1,2/B #f9a25a

> color #1,2/A #fab27b

> color #3/A #3cb3b6

> color #3/B #5dc6c7

> color #3/C #82d0d2

> color #3/D #9dd9de

> color #4 #9dd9de

> color #5/A #e38a25

> color #5/B #ef9544

> color #5/C #f9a25a

> color #5/D #fab27b

> color #6 #fab27b

> color #1,2/E,F #c7e493ff

> select #1/E,F:263,264 #2/E,F:263,264

112 atoms, 116 bonds, 8 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:18

32 atoms, 28 bonds, 4 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:172,198,251,39

132 atoms, 116 bonds, 16 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:261,262

8 atoms, 8 residues, 2 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #8,9,10,11/B,C #60c46c

> select #8,9,10,11/B:18 #8,9,10,11/C #9,10,11,12/B:172,198,201,203,205,207

279 atoms, 265 bonds, 30 residues, 4 models selected  

> select clear

> select #8,9,10,11/B:1272,1273

8 atoms, 8 residues, 4 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #7 #8,9,10,11/A light grey

> color #8/A #3cb3b6

> color #10/A #5dc6c7

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> matchmaker #1,2/D #5,6,8,9/A #7 to #3/A

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb,
chain D (#1), sequence alignment score = 1699.4  
RMSD between 237 pruned atom pairs is 0.779 angstroms; (across all 357 pairs:
2.740)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb,
chain D (#2), sequence alignment score = 1675.4  
RMSD between 240 pruned atom pairs is 0.801 angstroms; (across all 357 pairs:
2.685)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#5), sequence alignment score
= 1625.1  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1625.1  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#8), sequence alignment score = 1718  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#9), sequence alignment score = 1718  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 3hbt.pdb, chain A (#7), sequence alignment score = 1703  
RMSD between 349 pruned atom pairs is 0.707 angstroms; (across all 356 pairs:
0.767)  
  

> matchmaker #10,11/A to #3/B

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#10), sequence alignment score = 1755.8  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#11), sequence alignment score = 1755.8  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  

> matchmaker #4/A to #3/C

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain C (#3) with
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#4), sequence alignment score = 1709.6  
RMSD between 244 pruned atom pairs is 0.763 angstroms; (across all 357 pairs:
2.824)  
  

> matchmaker #6/A to #5/C

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 PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain C (#5) with
PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1687  
RMSD between 357 pruned atom pairs is 0.464 angstroms; (across all 359 pairs:
0.504)  
  

> hide #4/A,B target abcs

> hide #6/A,B target abcs

> view matrix camera
> 0.93969,1.4138e-25,0.34202,292.8,-0.34202,1.1102e-16,0.93969,516.96,-3.7971e-17,-1,1.0432e-16,166.14

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> color #12 #b5e1e6

> color #13 #fcc6a0

> color #3 #fcc6a0

> color #4 #fcc6a0

> volume #12-15 step 1

> volume #12 level 0.689

> volume #13 level 0.6479

> color zone #12 near #3 distance 4

> color zone #13 near #5 distance 3.03

> surface dust #12 size 4

> surface dust #13 size 4

> volume #14 level 0.3428

> surface dust #14 size 5.28

> color zone #14 near #1 distance 5

> volume #15 level 0.3371

> surface dust #15 size 5.28

> color zone #15 near #2 distance 5

> set bgColor white

> lighting soft

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.03

> cartoon style width 1.5 thickness 0.3

> colordef marine 0.0,50,100

Color 'marine' is opaque: rgb(0%, 50%, 100%) hex: #0080ff

  

> colordef paleskyblue #accbde

Color 'paleskyblue' is opaque: rgb(67.5%, 79.6%, 87.1%) hex: #accbde

  

> colordef lilacblue #b8c1de

Color 'lilacblue' is opaque: rgb(72.2%, 75.7%, 87.1%) hex: #b8c1de

  

> colordef lightpaleyellow #ded19f

Color 'lightpaleyellow' is opaque: rgb(87.1%, 82%, 62.4%) hex: #ded19f

  

> dssp

> hide atoms

> show cartoons

> style stick

Changed 102951 atom styles  

> color #1,2/D #e38a25

> color #1,2/C #ef9544

> color #1,2/B #f9a25a

> color #1,2/A #fab27b

> color #3/A #3cb3b6

> color #3/B #5dc6c7

> color #3/C #82d0d2

> color #3/D #9dd9de

> color #4 #9dd9de

> color #5/A #e38a25

> color #5/B #ef9544

> color #5/C #f9a25a

> color #5/D #fab27b

> color #6 #fab27b

> color #1,2/E,F #c7e493ff

> select #1/E,F:263,264 #2/E,F:263,264

112 atoms, 116 bonds, 8 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:18

32 atoms, 28 bonds, 4 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:172,198,251,39

132 atoms, 116 bonds, 16 residues, 2 models selected  

> show sel atoms target ab

> select #1,2/E,F:261,262

8 atoms, 8 residues, 2 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #8,9,10,11/B,C #60c46c

> select #8,9,10,11/B:18 #8,9,10,11/C #9,10,11,12/B:172,198,201,203,205,207

279 atoms, 265 bonds, 30 residues, 4 models selected  

> select clear

> select #8,9,10,11/B:1272,1273

8 atoms, 8 residues, 4 models selected  

> show sel target s

> color sel #69ff29ff

> select clear

> color #7 #8,9,10,11/A light grey

> color #8/A #3cb3b6

> color #10/A #5dc6c7

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> matchmaker #1,2/D #5,6,8,9/A #7 to #3/A

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
DNaseIx2_Actinx4_fitP50J37-coot-19_real_space_refined_024_real_space_refined_028.pdb,
chain D (#1), sequence alignment score = 1699.4  
RMSD between 237 pruned atom pairs is 0.779 angstroms; (across all 357 pairs:
2.740)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with
Moved_DNaseIx2_Actinx4_fitP50J39-coot19RSR024-fromcoot0-coot-1-2_real_space_refined_015.pdb,
chain D (#2), sequence alignment score = 1675.4  
RMSD between 240 pruned atom pairs is 0.801 angstroms; (across all 357 pairs:
2.685)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#5), sequence alignment score
= 1625.1  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1625.1  
RMSD between 247 pruned atom pairs is 0.840 angstroms; (across all 357 pairs:
2.672)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#8), sequence alignment score = 1718  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 2a42.pdb, chain A (#9), sequence alignment score = 1718  
RMSD between 339 pruned atom pairs is 0.699 angstroms; (across all 350 pairs:
0.798)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#3) with 3hbt.pdb, chain A (#7), sequence alignment score = 1703  
RMSD between 349 pruned atom pairs is 0.707 angstroms; (across all 356 pairs:
0.767)  
  

> matchmaker #10,11/A to #3/B

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#10), sequence alignment score = 1755.8  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  
Matchmaker
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain B (#3) with 2a42.pdb, chain A (#11), sequence alignment score = 1755.8  
RMSD between 345 pruned atom pairs is 0.659 angstroms; (across all 350 pairs:
0.709)  
  

> matchmaker #4/A to #3/C

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
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain C (#3) with
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb,
chain A (#4), sequence alignment score = 1709.6  
RMSD between 244 pruned atom pairs is 0.763 angstroms; (across all 357 pairs:
2.824)  
  

> matchmaker #6/A to #5/C

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 PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain C (#5) with
PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb, chain A (#6), sequence alignment score
= 1687  
RMSD between 357 pruned atom pairs is 0.464 angstroms; (across all 359 pairs:
0.504)  
  

> hide #4/A,B target abcs

> hide #6/A,B target abcs

> view matrix camera
> 0.93969,1.4138e-25,0.34202,292.8,-0.34202,1.1102e-16,0.93969,516.96,-3.7971e-17,-1,1.0432e-16,166.14

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> color #12 #b5e1e6

> color #13 #fcc6a0

> color #14 #fcc6a0

> color #15 #fcc6a0

> volume #12-15 step 1

> volume #12 level 0.689

> volume #13 level 0.6479

> color zone #12 near #3 distance 4

> color zone #13 near #5 distance 3.03

> surface dust #12 size 4

> surface dust #13 size 4

> volume #14 level 0.3428

> surface dust #14 size 5.28

> color zone #14 near #1 distance 5

> volume #15 level 0.3371

> surface dust #15 size 5.28

> color zone #15 near #2 distance 5

> view matrix camera
> 0.93969,1.4138e-25,0.34202,292.8,-0.34202,1.1102e-16,0.93969,516.96,-3.7971e-17,-1,1.0432e-16,166.14

> view name pos1

> view matrix camera
> -0.93969,1.4138e-25,-0.34202,29.726,0.34202,1.1102e-16,-0.93969,-193.7,3.7971e-17,-1,-1.0433e-16,166.14

> view name pos2

> view matrix camera
> 0.93969,1.4138e-25,0.34202,245.66,-0.34202,1.1102e-16,0.93969,397.33,-3.7971e-17,-1,1.0432e-16,133.28

> view name pos1zoomed

> view matrix camera
> -0.93969,1.4138e-25,-0.34202,84.687,0.34202,1.1102e-16,-0.93969,-52.496,3.7971e-17,-1,-1.0433e-16,128.24

> view name pos2zoomed

> view pos1

> turn y -50 center #1

> view name pos150

> view matrix camera
> 0.34202,4.5416e-25,0.93969,346.14,-0.93969,1.1102e-16,0.34202,225.68,-1.0432e-16,-1,3.7967e-17,121.93

> view name pos150zoom

> view matrix camera
> 0.26193,-0.49013,0.83136,353.17,-0.96475,-0.15553,0.21226,210.08,0.025264,-0.85766,-0.51359,2.4186

> view name pos3

> view matrix camera
> -0.98467,0.072211,-0.15879,124.8,0.16305,0.057436,-0.98494,-72.458,-0.062003,-0.99573,-0.068329,110.92

> view name pos4

> view matrix camera
> 0.73528,-0.19841,0.64807,320.17,-0.6721,-0.33679,0.65943,327.74,0.087424,-0.92044,-0.38099,38.834

> view name pos5

> view matrix camera
> 0.88847,0.020898,0.45847,199.43,-0.44663,-0.19049,0.8742,216.85,0.1056,-0.98147,-0.15991,112.23

> view name pos6

> view matrix camera
> 0.91176,-0.14523,0.38418,255.12,-0.41057,-0.34634,0.84349,373.39,0.010559,-0.9268,-0.37541,38.982

> view name pos7

> view matrix camera
> -0.99452,-1.1451e-24,-0.10453,115.28,0.10453,1.1102e-16,-0.99452,-285.16,1.1605e-17,-1,-1.1042e-16,184.08

> view name pos8

> view matrix camera
> 0.85695,-0.045343,0.5134,202.48,-0.30437,-0.84839,0.43311,206.98,0.41593,-0.52742,-0.74083,78.41

> ~clip

> clip near 1

> clip near -55

> clip far -17

> view name posphd1

> ~clip

> view matrix camera
> 0.85695,-0.045343,0.5134,193.19,-0.30437,-0.84839,0.43311,194.94,0.41593,-0.52742,-0.74083,97.362

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> ~clip

> clip near 1

> clip near -55

> clip far -17

> hide #!15 models

> hide #!13 models

> hide #!14 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!8 models

> hide #!7 models

> hide #!1 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!6 models

> view matrix

view matrix camera
0.85695,-0.045343,0.5134,185.43,-0.30437,-0.84839,0.43311,190.39,0.41593,-0.52742,-0.74083,104.81  
view matrix models
#1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> ~clip

> clip near 1

> clip near -55

> clip far -20

> ~clip

> clip near 1

> clip near -55

> clip far -22

> ~clip

> clip near 1

> clip near -55

> clip far -20

> ~clip

> clip near 1

> clip near -55

> clip far -18

> ~clip

> clip near 1

> clip near -55

> clip far -17

> ~clip

> clip near 1

> clip near -55

> clip far -19

> view matrix camera
> 0.85695,-0.045343,0.5134,185.43,-0.30437,-0.84839,0.43311,190.39,0.41593,-0.52742,-0.74083,104.81

> view matrix models
> #1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0

> ~clip

> clip near 1

> clip near -55

> clip far -19

> view name posphd2

> view posphd1

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_2.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_2.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> color byhetero

> view posphd1

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_byhetero.png
> supersample 4 transparentBackground false

> view posphd1

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_byhetero.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/UndecoratedPointedEnd_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_2_byhetero.png
> supersample 4 transparentBackground false

> view posphd2

> hide #1-15 models

> show #3,5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PointedEnd_PDHModeled_2_byhetero.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> show #5 target c

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> select #13

2 models selected  

> select clear

> volume #13 level 0.647

> volume #13 level 0.649

> volume #13 level 0.646

> volume #13 level 0.64

> volume #13 level 0.65

> volume #13 level 0.658

> volume #13 level 0.6682

> show #!3 models

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> hide #!13 models

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> ui tool show "Fit in Map"

> fitmap #5 inMap #13

Fit molecule PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) to map
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13) using
11772 atoms  
average map value = 0.919, steps = 56  
shifted from previous position = 1.15  
rotated from previous position = 2 degrees  
atoms outside contour = 4277, contour level = 0.66816  
  
Position of PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) relative to
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13)
coordinates:  
Matrix rotation and translation  
0.99999571 -0.00012400 0.00013359 -0.01437061  
0.00012376 0.99999827 0.00001706 -0.04090364  
-0.00013347 -0.00001657 1.00000209 0.03251603  
Axis -0.09193680 0.72998731 0.67724896  
Axis point 276.56002646 0.00000000 112.14591463  
Rotation angle (degrees) 0.01048031  
Shift along axis -0.00651650  
  

> windowsize 1000 1000

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> fitmap #5 inMap #13

Fit molecule PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) to map
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13) using
11772 atoms  
average map value = 0.9191, steps = 28  
shifted from previous position = 0.0239  
rotated from previous position = 0.019 degrees  
atoms outside contour = 4284, contour level = 0.66816  
  
Position of PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) relative to
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13)
coordinates:  
Matrix rotation and translation  
0.99999571 -0.00009738 -0.00012737 0.05613733  
0.00009712 0.99999826 -0.00018499 0.02621836  
0.00012751 0.00018546 1.00000208 -0.06209929  
Axis 0.75614295 -0.52023389 0.39699439  
Axis point 0.00000000 344.20321750 153.17363521  
Rotation angle (degrees) 0.01403515  
Shift along axis 0.00415510  
  

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_2_byhetero_density.png
> supersample 4 transparentBackground false

> volume #13 level 0.606

> view posphd2

> fitmap #5 inMap #13

Fit molecule PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) to map
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13) using
11772 atoms  
average map value = 0.919, steps = 56  
shifted from previous position = 1.15  
rotated from previous position = 2 degrees  
atoms outside contour = 3761, contour level = 0.60596  
  
Position of PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) relative to
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13)
coordinates:  
Matrix rotation and translation  
0.99999571 -0.00012400 0.00013359 -0.01437061  
0.00012376 0.99999827 0.00001706 -0.04090364  
-0.00013347 -0.00001657 1.00000209 0.03251603  
Axis -0.09193680 0.72998731 0.67724896  
Axis point 276.56002646 0.00000000 112.14591463  
Rotation angle (degrees) 0.01048031  
Shift along axis -0.00651650  
  

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> volume #13 level 0.6299

> volume #13 level 0.6442

> volume #13 level 0.716

> ui tool show "Surface Zone"

> surface zone #13 nearAtoms #5 distance 2.66

> surface zone #13 nearAtoms #5 distance 2.32

> select #5/H:6@OD1

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.29

> surface zone #13 nearAtoms sel distance 2.22

> view posphd2

> volume #13 level 0.6657

> surface zone #13 nearAtoms sel distance 2.28

> surface zone #13 nearAtoms sel distance 2.22

> volume #13 level 0.6245

> surface zone #13 nearAtoms sel distance 2.19

> surface zone #13 nearAtoms sel distance 2.55

> view posphd2

> surface zone #13 nearAtoms sel distance 2.57

> surface zone #13 nearAtoms sel distance 2.47

> volume #13 level 0.6748

> select clear

> view matrix

view matrix camera
-0.84482,0.38861,0.36778,175.63,-0.010264,0.67547,-0.73731,147.65,-0.53496,-0.62667,-0.56666,118.05  
view matrix models
#1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#13.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#13.1.2,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> ~clip

> view matrix

view matrix camera
-0.84482,0.38861,0.36778,175.63,-0.010264,0.67547,-0.73731,147.65,-0.53496,-0.62667,-0.56666,118.05  
view matrix models
#1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> ~clip

> clip near 1

> clip near -55

> clip far -19

> ~clip

> clip near 1

> clip near -1

[Repeated 30 time(s)]

> clip far -1

> clip far 1

[Repeated 2 time(s)]

> ~clip

> clip near 1

> clip near -30

> clip far 1

> ~clip

> clip near 1

> clip near -30

> clip far 10

> ~clip

> clip near 1

> clip near -30

> clip far 30

> ~clip

> clip near 1

> clip near -30

> clip far 1

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_PDHdensity_zoomed.png
> supersample 4 transparentBackground false

> ~clip

> view matrix camera
> -0.84482,0.38861,0.36778,175.63,-0.010264,0.67547,-0.73731,147.65,-0.53496,-0.62667,-0.56666,118.05

> volume #13 level 0.6748

> surface zone #13 nearAtoms sel distance 2.47

No atoms specified  

> ~clip

> clip near 1

> clip near -30

> clip far 1

> windowsize 1000 1000

> ~clip

> view matrix camera
> -0.84482,0.38861,0.36778,175.63,-0.010264,0.67547,-0.73731,147.65,-0.53496,-0.62667,-0.56666,118.05

> volume #13 level 0.6748

> surface zone #13 nearAtoms sel distance 2.47

No atoms specified  

> ~clip

> clip near 1

> clip near -30

> clip far 1

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PHDPointedEnd_PDHdensity_zoomed.png
> supersample 4 transparentBackground false

> view posphd2

> show #!3 models

> hide #!13 models

> view posphd1

> ~clip

> clip near 1

> clip near -30

> clip far 1

> view posphd1

> show #!13 models

> view posphd1

> hide #!13 models

> ~clip

> view matrix

view matrix camera
0.85695,-0.045343,0.5134,201.26,-0.30437,-0.84839,0.43311,203.57,0.41593,-0.52742,-0.74083,83.774  
view matrix models
#1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> clip near 1

> view matrix camera
> 0.85695,-0.045343,0.5134,201.26,-0.30437,-0.84839,0.43311,203.57,0.41593,-0.52742,-0.74083,83.774

> ~clip

> clip near 1

> clip near -1

[Repeated 52 time(s)]

> clip far -1

[Repeated 20 time(s)]

> clip far 1

[Repeated 1 time(s)]

> ~clip

> clip near 51

> clip far -18

clip far plane is in front of near plane  

> ~clip

> clip near 51

> ~clip

> ~clip

> clip near -51

> clip far -18

> ~clip

> clip near -51

> clip far -17

> ~clip

> clip near -51

> clip far -17

> ~clip

> clip near -51

> clip far -19

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/A:72,73,75,77,110,111,112 #5/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select clear

> select #3/A:73@CZ

1 atom, 1 residue, 1 model selected  

> select add #5/H:6@CB

2 atoms, 2 residues, 2 models selected  

> ui tool show Distances

> distance #3/A:73@CZ #5/H:6@CB

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A HIC 73 CZ and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H HYP 6 CB: 3.895Å  

> select add #3/B:199@OG

3 atoms, 3 residues, 2 models selected  

> select add #5/H:5@N

4 atoms, 4 residues, 2 models selected  

> select clear

> select add #3/B:199@OG

1 atom, 1 residue, 1 model selected  

> select add #5/H:5@N

2 atoms, 2 residues, 2 models selected  

> distance #3/B:199@OG #5/H:5@N

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B SER 199 OG and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H CYS 5 N: 2.190Å  

> select #3/B:198

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select #3/B:198@CA

1 atom, 1 residue, 1 model selected  
Drag select of 2 residues, 2 atoms, 2 bonds  

> select #3/B:198

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #3/B:198

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select add #5/H:3@O

13 atoms, 12 bonds, 2 residues, 2 models selected  
Exactly two atoms must be selected!  

> select clear

> select #3/B:198@CA

1 atom, 1 residue, 1 model selected  

> select #3/A:79

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

> select #3/B:198@CB

1 atom, 1 residue, 1 model selected  

> select add #5/H:3@O

2 atoms, 2 residues, 2 models selected  

> distance #3/B:198@CB #5/H:3@O

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B TYR 198 CB and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H ALA 3 O: 2.778Å  

> select #3/B:198

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select #3/B:198@CA

1 atom, 1 residue, 1 model selected  

> select add #5/H:3@O

2 atoms, 2 residues, 2 models selected  

> ~distance #3/B:199@OG #5/H:5@N

> ~distance #3/A:73@CZ #5/H:6@CB

> ~distance #3/B:198@CB #5/H:3@O

> undo

> ~distance #3/B:199@OG #5/H:5@N

> distance #3/B:199@OG #5/H:5@N

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B SER 199 OG and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H CYS 5 N: 2.190Å  

> distance #3/A:73@CZ #5/H:6@CB

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A HIC 73 CZ and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H HYP 6 CB: 3.895Å  

> select clear

> select #3/B:198@CA

1 atom, 1 residue, 1 model selected  

> select add #5/H:3@O

2 atoms, 2 residues, 2 models selected  

> distance #3/B:198@CA #5/H:3@O

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B TYR 198 CA and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H ALA 3 O: 2.470Å  

> ~clip

> view posphd3

Expected an objects specifier or a view name or a keyword  

> view matrix camera
> 0.85695,-0.045343,0.5134,201.26,-0.30437,-0.84839,0.43311,203.57,0.41593,-0.52742,-0.74083,83.774

> ~clip

> clip near -51

> clip far -19

> view name posphd3

> select #5/H:3@CB

1 atom, 1 residue, 1 model selected  

> select add #3/B:198@CD1

2 atoms, 2 residues, 2 models selected  

> distance #5/H:3@CB #3/B:198@CD1

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H ALA 3 CB and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B TYR 198 CD1: 2.570Å  

> select #3/B:199

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

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select clear

> select #3/B:199@N

1 atom, 1 residue, 1 model selected  

> select add #5/H:3@O

2 atoms, 2 residues, 2 models selected  

> distance #3/B:199@N #5/H:3@O

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B SER 199 N and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H ALA 3 O: 2.135Å  

> select add #3/A:72@OE2

3 atoms, 3 residues, 2 models selected  

> select clear

> select add #3/A:72@OE2

1 atom, 1 residue, 1 model selected  

> select add #5/H:7@CB

2 atoms, 2 residues, 2 models selected  

> distance #3/A:72@OE2 #5/H:7@CB

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A GLU 72 OE2 and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H ALA 7 CB: 1.683Å  

> select clear

> select #3/B:197

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> select clear

> select #5/H:1@CE3

1 atom, 1 residue, 1 model selected  

> select add #3/B:197@CA

2 atoms, 2 residues, 2 models selected  

> distance #5/H:1@CE3 #3/B:197@CA

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H TRP 1 CE3 and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B GLY 197 CA: 2.800Å  

> select #5/H:1@CZ3

1 atom, 1 residue, 1 model selected  

> select add #3/B:194@CG2

2 atoms, 2 residues, 2 models selected  

> distance #5/H:1@CZ3 #3/B:194@CG2

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H TRP 1 CZ3 and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B THR 194 CG2: 2.941Å  

> select #5/A:73@CZ

1 atom, 1 residue, 1 model selected  

> select add #5/H:6@CB

2 atoms, 2 residues, 1 model selected  

> distance #5/A:73@CZ #5/H:6@CB

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/A HIC 73 CZ and /H HYP 6 CB: 4.970Å  

> select clear

> select #5/H:1@CB

1 atom, 1 residue, 1 model selected  

> select add #3/B:197@O

2 atoms, 2 residues, 2 models selected  

> distance #5/H:1@CB #3/B:197@O

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H TRP 1 CB and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B GLY 197 O: 1.875Å  

> view name posphd3

[Repeated 1 time(s)]

> view matrix camera
> 0.85695,-0.045343,0.5134,201.26,-0.30437,-0.84839,0.43311,203.57,0.41593,-0.52742,-0.74083,83.774

> ~clip

> clip near -51

> clip far -19

> view name posphd3

> view posphd3

> select #5/A:112@CG

1 atom, 1 residue, 1 model selected  

> select add #3/A:112@CG

2 atoms, 2 residues, 2 models selected  

> distance #5/A:112@CG #3/A:112@CG

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/A PRO 112 CG and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A PRO 112 CG: 5.538Å  

> select #3/B:199@OG

1 atom, 1 residue, 1 model selected  

> select add #5/B:199@OG

2 atoms, 2 residues, 2 models selected  

> distance #3/B:199@OG #5/B:199@OG

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/B SER 199 OG and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/B SER 199 OG: 3.656Å  

> select #5/A:77

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

> select #5/A:144

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

> select #5/A:77@CA

1 atom, 1 residue, 1 model selected  

> select #5/A:77@CA

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/A:77@CA

1 atom, 1 residue, 1 model selected  

> select #5/A:77@CA

1 atom, 1 residue, 1 model selected  

> select add #3/A:77@CA

2 atoms, 2 residues, 2 models selected  

> distance #5/A:77@CA #3/A:77@CA

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/A THR 77 CA and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A THR 77 CA: 5.606Å  

> view posphd3

[Repeated 2 time(s)]

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/SessionDistances.cxs

> select #3/A:72@OE2

1 atom, 1 residue, 1 model selected  

> select #3/B:199@CB

1 atom, 1 residue, 1 model selected  

> view posphd3

[Repeated 1 time(s)]

> select clear

> select add #3/A:73@CD2

1 atom, 1 residue, 1 model selected  

> select add #5/H:7@CB

2 atoms, 2 residues, 2 models selected  

> distance #3/A:73@CD2 #5/H:7@CB

Distance between
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A HIC 73 CD2 and PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/H ALA 7 CB: 2.781Å  

> select #5/A:72@CB

1 atom, 1 residue, 1 model selected  

> select add #3/A:72@CG

2 atoms, 2 residues, 2 models selected  

> distance #5/A:72@CB #3/A:72@CG

Distance between PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb #5/A GLU 72 CB and
230621_AlphaActin_PointedEnd_coot-4-AllChains_RSR001-coot5_RSR005-coot-6_real_space_refined_006.pdb
#3/A GLU 72 CG: 2.415Å  

> ~distances

Unknown command: ~distances  

> ~distance

> windowsize 1000 1000

[Repeated 1 time(s)]

> view posphd3

> hide #1-15 models

> show #3,5 models

> select #3/A:72,73,75,77,110,111,112 #3/B:194,197,198,199,200,205,242

115 atoms, 111 bonds, 14 residues, 1 model selected  

> show sel target ab

> select #5/B:199

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

> select #3/A:72 #3/B:199

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

> show sel target ab

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_FewResidues.png
> supersample 4 transparentBackground false

> windowsize 1000 1000

> view posphd3

> hide #1-15 models

> show #3,5 models

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/B:199

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

> show sel target ab

> select #3/A:72 #3/B:199

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

> show sel target ab

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_FewResidues.png
> supersample 4 transparentBackground false

> view posphd3

> hide #1-15 models

> show #3,5 models

> show cartoons

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/B:199

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

> show sel target ab

> select #3/A:72 #3/B:199

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

> show sel target ab

> select clear

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_FewResidues.png
> supersample 4 transparentBackground false

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> fitmap #5 inMap #13

Fit molecule PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) to map
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13) using
11772 atoms  
average map value = 0.919, steps = 56  
shifted from previous position = 1.15  
rotated from previous position = 2 degrees  
atoms outside contour = 4340, contour level = 0.6748  
  
Position of PhalloidinPointedEnd_230711_ActinPhalloidin-
Phx4-coot-8_real_space_refined_011.pdb (#5) relative to
PhalloidinPointedEnd_cryosparc_P40_J237_005_volume_map_sharp.mrc (#13)
coordinates:  
Matrix rotation and translation  
0.99999571 -0.00012400 0.00013359 -0.01437061  
0.00012376 0.99999827 0.00001706 -0.04090364  
-0.00013347 -0.00001657 1.00000209 0.03251603  
Axis -0.09193680 0.72998731 0.67724896  
Axis point 276.56002646 0.00000000 112.14591463  
Rotation angle (degrees) 0.01048031  
Shift along axis -0.00651650  
  

> view posphd2

> hide #1-15 models

> show #5,13 models

> select #5/H

55 atoms, 59 bonds, 7 residues, 1 model selected  

> surface zone #13 nearAtoms sel distance 2.67

> select clear

> volume #13 color #edcbde4d

> transparency #13 70

> ~clip

> view matrix camera
> -0.84482,0.38861,0.36778,175.63,-0.010264,0.67547,-0.73731,147.65,-0.53496,-0.62667,-0.56666,118.05

> volume #13 level 0.6748

> surface zone #13 nearAtoms sel distance 2.47

No atoms specified  

> ~clip

> clip near 1

> clip near -30

> clip far 1

> view posphd3

> show #!3 models

> show #3 target s

> transparency #3 40

> hide #!13 models

> select #3/B:197@C

1 atom, 1 residue, 1 model selected  

> select clear

> show #5/H target s

> view posphd3

> hide #!5 models

> show #!5 models

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 4 models selected  

> hide sel target abc

> transparency #5/H 50

> transparency #3 0

> ~clip

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/SessionPhalloidinClashes.cxs

> view

> view matrix

view matrix camera
-0.6739,0.64418,0.36179,179.82,0.15824,0.60416,-0.78099,141.09,-0.72168,-0.46906,-0.50908,115.68  
view matrix models
#1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#3.3,1,0,0,0,0,1,0,0,0,0,1,0,#3.4,1,0,0,0,0,1,0,0,0,0,1,0,#3.5,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#5.3,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> ~clip

> show #3 target s

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> show #5/H target s

> transparency #5/H 50

> view matrix camera
> -0.6739,0.64418,0.36179,179.82,0.15824,0.60416,-0.78099,141.09,-0.72168,-0.46906,-0.50908,115.68

> view matrix camera
> -0.6739,0.64418,0.36179,179.82,0.15824,0.60416,-0.78099,141.09,-0.72168,-0.46906,-0.50908,115.68

> view matrix

view matrix camera
-0.6739,0.64418,0.36179,176.96,0.15824,0.60416,-0.78099,146.15,-0.72168,-0.46906,-0.50908,118.36  
view matrix models
#1,0.99686,0.042647,-0.066792,26.054,-0.045615,0.99801,-0.043572,36.092,0.064801,0.046482,0.99682,4.7607,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.9958,0.064298,-0.065224,23.104,-0.06671,0.99714,-0.0355,37.779,0.062755,0.039702,0.99724,5.8204,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#3.2,1,0,0,0,0,1,0,0,0,0,1,0,#3.3,1,0,0,0,0,1,0,0,0,0,1,0,#3.4,1,0,0,0,0,1,0,0,0,0,1,0,#3.5,1,0,0,0,0,1,0,0,0,0,1,0,#4,0.89481,-0.44638,0.0074684,88.101,0.44619,0.89474,0.018558,-57.206,-0.014966,-0.013273,0.9998,60.094,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,0.99933,0.033418,-0.014899,-54.861,-0.034017,0.99854,-0.041934,-32.568,0.013476,0.042413,0.99901,-60.688,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,1,0,0,0,0,1,0,0,0,0,1,0,#5.3,1,0,0,0,0,1,0,0,0,0,1,0,#6,0.91595,-0.40113,-0.011406,52.53,0.40035,0.91538,-0.042387,-108.53,0.027443,0.034258,0.99904,-6.8028,#6.1,1,0,0,0,0,1,0,0,0,0,1,0,#6.2,1,0,0,0,0,1,0,0,0,0,1,0,#7,0.41167,-0.68113,-0.60547,158.94,0.89578,0.18019,0.40634,109.18,-0.16767,-0.70964,0.68432,119.75,#7.1,1,0,0,0,0,1,0,0,0,0,1,0,#7.2,1,0,0,0,0,1,0,0,0,0,1,0,#8,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#8.1,1,0,0,0,0,1,0,0,0,0,1,0,#8.2,1,0,0,0,0,1,0,0,0,0,1,0,#8.3,1,0,0,0,0,1,0,0,0,0,1,0,#9,0.080031,0.93226,-0.35282,154.68,0.70268,0.19828,0.68332,115.72,0.70699,-0.30261,-0.63922,100.46,#9.1,1,0,0,0,0,1,0,0,0,0,1,0,#9.2,1,0,0,0,0,1,0,0,0,0,1,0,#9.3,1,0,0,0,0,1,0,0,0,0,1,0,#10,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#10.1,1,0,0,0,0,1,0,0,0,0,1,0,#10.2,1,0,0,0,0,1,0,0,0,0,1,0,#10.3,1,0,0,0,0,1,0,0,0,0,1,0,#11,0.081731,-0.86012,0.50351,159.96,-0.68149,-0.41687,-0.60149,207.23,0.72725,-0.29397,-0.62023,127.08,#11.1,1,0,0,0,0,1,0,0,0,0,1,0,#11.2,1,0,0,0,0,1,0,0,0,0,1,0,#11.3,1,0,0,0,0,1,0,0,0,0,1,0,#12,1,0,0,0,0,1,0,0,0,0,1,0,#12.1,1,0,0,0,0,1,0,0,0,0,1,0,#13,0.99973,0.023354,-0.0015103,-55.282,-0.02337,0.99966,-0.011616,-40.885,0.0012385,0.011648,0.99993,-51.551,#13.1,1,0,0,0,0,1,0,0,0,0,1,0,#14,0.99828,0.042988,-0.039871,22.514,-0.044223,0.99855,-0.03062,34.221,0.038497,0.03233,0.99874,9.8935,#14.1,1,0,0,0,0,1,0,0,0,0,1,0,#15,0.99741,0.059365,-0.040585,20.507,-0.060488,0.9978,-0.027024,35.858,0.038891,0.029409,0.99881,10.1,#15.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> ~clip

> show #3 target s

> select #5

11772 atoms, 12037 bonds, 3 pseudobonds, 1503 residues, 3 models selected  

> ~select #5/H

11717 atoms, 11978 bonds, 3 pseudobonds, 1496 residues, 3 models selected  

> hide sel target abc

> show #5/H target s

> transparency #5/H 50

> view matrix camera
> -0.6739,0.64418,0.36179,176.96,0.15824,0.60416,-0.78099,146.15,-0.72168,-0.46906,-0.50908,118.36

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEnd_Surfaces.png
> supersample 4 transparentBackground false

> windowsize 1000 1000

> view posphd3

> hide #1-15 models

> show #3,5 models

> show cartoons

> hide atoms

> show #5 target c

> select #1,2/G,H,I,J #5,6/H,I,J,K

880 atoms, 944 bonds, 112 residues, 4 models selected  

> color sel pink

> hide sel target c

> show sel atoms target ab

> select clear

> select #1,2,5,6:376 #3,4:401

648 atoms, 696 bonds, 24 residues, 6 models selected  

> color sel lightpaleyellow

> show sel atoms target ab

> select clear

> select #5/B:199

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

> show sel target ab

> select #3/A:72 #3/B:199

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

> show sel target ab

> select clear

> hide surfaces

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/PHD1_PointedEndComparisons_FewResidues.png
> supersample 4 transparentBackground false

> show #!3,5 surfaces

> ui tool show "Side View"

> hide #!3,5 cartoons

> hide #!5 models

> show #!5 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!3 models

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/SurfacesTrial1.cxs

——— End of log from Thu Oct 19 10:19:49 2023 ———

opened ChimeraX session  

> transparency #5/H 40

> view postest1

Expected an objects specifier or a view name or a keyword  

> view name postest1

> show #!4 models

> hide #!4 models

> show #!2 models

> hide #!2 models

> show #!3 models

> view name postest2

> save
> /Users/m.boierosanders/Documents/Projects/2023_PointedEnd/Figures/PointedEnd_vs_PhalloidinPontedEnd/ChimeraX_Phalloidin/SurfacesTrial2.cxs

——— End of log from Thu Oct 19 10:30:20 2023 ———

opened ChimeraX session  

> show #!4 models

> hide #!4 models

> show #5/H target s

> transparency #5/H 0

> hide #!3,5 surfaces

> show #!3,5 surfaces

> hide #5/H target ab

> transparency #5/H 0

> show #5/H target s

> hide #!3,5 surfaces

> show #!3,5 surfaces

> transparency #5/H 0 target s

> transparency #5/H 100 target s

> transparency #5/H 0 target s

> transparency #5/H 0 target abcsp




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Max
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: Mac Studio
      Model Identifier: Mac13,1
      Model Number: Z14J0002MD/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (22F82)
      Kernel Version: Darwin 22.5.0
      Time since boot: 28 days, 6 hours, 55 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        EV2795:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        EV2456:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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-Clipper: 0.21.0
    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-ISOLDE: 1.6.0
    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: 2022.2.22
    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

[Eric Pettersen]

Reported by Micaela Boiero Sanders.

[Tom Goddard]

The flat surface cap where you clip a surface can be made transparent or opaque but not with the command you are using

transparency #5/H 0 target s

It is a bit weird that that does not work. A command that will work is

transparency #5 0

Or if you really just want the surface cap for chain H then you can look in the Models panel to see what the model ID number of that surface cap is by clicking the ">" to the left of model #5 to see the surface models beneath it e.g. #5.1, #5.2, ..., and then clicking the chain H surface ">" to see the cap beneath it, e.g. #5.7.1 then use a command

transparency #5.7.1 0

I think the trouble with your original command

transparency #5/H 0 target s

is that "#5/H" names the atoms chain H. And those atoms are associated with the surface of chain H -- each atom contributes a patch of the surface. But the clip cap of the surface is not associated with the atoms. Parts of that flat clip cap are not associated with any specific atoms. So "#5/H" does not refer to the cap and you need to name the cap in the command in a different way. The reason "#5" works is because that refers to the atoms and all child models (the surfaces and caps shown in the Models panel under the ">" disclosure arrows).