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Opened 4 years ago
Closed 4 years ago
#6192 closed defect (fixed)
Segger fit dialog tried to save a closed volume model in a session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> BothModels-Rigid-FitTOsegment.cxs" format session
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc as
#4, grid size 320,320,320, pixel 1.03, shown at level 0.448, step 1, values
float32
Opened cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #5, grid size 196,196,196, pixel 1.02, shown at level 0.596, step
1, values float32
Log from Mon Feb 14 13:43:45 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Volumes/MEMO/Grad School/Side-ACC/AccM-Manual-Fitting-Domains.cxs"
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc as
#4, grid size 320,320,320, pixel 1.03, shown at level 0.448, step 1, values
float32
Opened cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #5, grid size 196,196,196, pixel 1.02, shown at level 0.596, step
1, values float32
Log from Mon Feb 14 12:41:57 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Coparison-
> Aligned-All-Maps.cxs"
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #2, grid size 320,320,320, pixel 1.03, shown at level 0.57, step
1, values float32
Opened cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #3, grid size 196,196,196, pixel 1.02, shown at level 0.416, step
1, values float32
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc as
#6, grid size 320,320,320, pixel 1.03, shown at level 0.581, step 1, values
float32
Log from Thu Feb 3 20:10:27 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
g.caballerosilva@ubc.ca is subscribed to the ChimeraX announcements list
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
> format pdb
No such file/path: /Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
> format pdb
No such file/path: /Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
> format pdb
Chain information for output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb #1
---
Chain | Description
B C | No description available
> set bgColor linen
> lighting soft
> lighting fillIntensity .2
> solor /B,C bychain
Unknown command: solor /B,C bychain
> color /B,C bychain
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 2 time(s)]
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> interfaces protein
1 buried areas: B C 10472
> color select pink
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel hot pink
> ui mousemode right select
> select clear
> color sel blue
> select clear
> Explode All
Unknown command: Explode All
> interfaces ~solvent
1 buried areas: B C 10472
> select clear
[Repeated 2 time(s)]
> color sel blue
> select clear
[Repeated 3 time(s)]
> graphics silhouettes false
> lighting flat
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> interfaces select
Missing or invalid "atoms" argument: empty atom specifier
> interfaces select atoms
Missing or invalid "atoms" argument: invalid atoms specifier
> color /B,C bychain
> select clear
> save /Users/gcaballero/Desktop/image1.png supersample 3
> select clear
> open "/Volumes/MEMO/Grad School/Side-
> ACC/J674-Models/cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
> sharpened-flipz.mrc"
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #2, grid size 320,320,320, pixel 1.03, shown at level 0.112, step
2, values float32
> volume #2 step 1
> volume #2 level 0.2756
> select #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.38902,-0.75441,-0.5287,315.41,0.92035,0.34335,0.18726,-70.932,0.040259,-0.55944,0.82789,116.53
> view matrix models
> #2,-0.69169,0.12806,-0.71075,373.59,0.3314,-0.81814,-0.46992,331,-0.64167,-0.56058,0.52347,279.01
> view matrix models
> #2,0.49894,-0.72772,-0.47063,283.24,0.8638,0.46149,0.20218,-84.109,0.070057,-0.5074,0.85886,97.709
> view matrix models
> #2,-0.67479,0.42779,-0.60138,302,0.027068,-0.79997,-0.59943,399.3,-0.73752,-0.42077,0.52823,270.3
> view matrix models
> #2,-0.20187,0.95643,-0.21093,70.331,-0.63001,-0.2917,-0.71972,441.05,-0.74989,-0.012399,0.66144,181.19
> view matrix models
> #2,0.072616,0.99449,-0.075624,-3.5478,-0.74262,0.0032983,-0.66971,401.34,-0.66577,0.10479,0.73876,134.76
> view matrix models
> #2,0.86958,0.48234,0.10572,-77.699,-0.44692,0.85984,-0.24688,137.92,-0.20998,0.16743,0.96326,12.211
> view matrix models
> #2,-0.51229,0.74927,-0.41971,190.88,-0.33854,-0.62532,-0.70311,446.91,-0.78927,-0.2181,0.574,236.93
> view matrix models
> #2,-0.33435,-0.53421,-0.77642,437.86,0.89662,-0.43409,-0.08744,109.96,-0.29032,-0.72538,0.62413,232.58
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.33435,-0.53421,-0.77642,376.19,0.89662,-0.43409,-0.08744,29.253,-0.29032,-0.72538,0.62413,177.66
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.51609,-0.36705,-0.7739,208.5,0.51884,-0.58493,0.62342,-2.1173,-0.68151,-0.72327,-0.11144,363.99
> view matrix models
> #2,0.62593,-0.67499,-0.39063,178.56,0.38593,-0.16715,0.90726,-98.232,-0.67769,-0.71864,0.15588,317.99
> view matrix models
> #2,0.086044,-0.7884,-0.60912,322.43,0.44747,-0.51567,0.73065,-20.024,-0.89015,-0.33543,0.30841,262.62
> view matrix models
> #2,0.070564,-0.70037,-0.71028,326.98,0.40604,-0.63023,0.66177,17.572,-0.91113,-0.3351,0.23991,277.42
> view matrix models
> #2,0.058876,-0.5128,-0.85648,321.64,0.32677,-0.80081,0.50193,85.984,-0.94327,-0.30942,0.12042,298.28
> view matrix models
> #2,0.074146,-0.22833,-0.97076,290.2,0.22049,-0.94559,0.23925,171.62,-0.97257,-0.23178,-0.019768,313.36
> view matrix models
> #2,0.75848,0.02978,-0.65101,81.408,0.43072,-0.77257,0.46649,70.134,-0.48906,-0.63423,-0.59881,398.81
> view matrix models
> #2,0.76577,-0.63165,-0.12089,103.38,-0.030207,-0.2231,0.97433,-31.936,-0.64241,-0.74246,-0.18992,373.93
> view matrix models
> #2,0.6283,-0.72608,-0.27938,168.23,0.24848,-0.15301,0.95648,-86.353,-0.73722,-0.67037,0.084274,331.52
> view matrix models
> #2,0.6282,-0.71379,-0.30962,171.22,0.25776,-0.18454,0.94842,-81.207,-0.73411,-0.67561,0.068055,334.6
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.6282,-0.71379,-0.30962,63.807,0.25776,-0.18454,0.94842,-164.31,-0.73411,-0.67561,0.068055,258.48
> view matrix models
> #2,0.6282,-0.71379,-0.30962,59.136,0.25776,-0.18454,0.94842,-170.44,-0.73411,-0.67561,0.068055,250.81
> volume #2 color #b2b2b27d
> volume #2 level 0.4328
> view matrix models
> #2,0.6282,-0.71379,-0.30962,49.967,0.25776,-0.18454,0.94842,-163.96,-0.73411,-0.67561,0.068055,234.58
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.32945,-0.80545,-0.49266,143.98,0.56395,-0.25061,0.78686,-175.85,-0.75724,-0.53707,0.37167,164.98
> view matrix models
> #2,0.40551,-0.7928,-0.45502,123.35,0.50959,-0.21718,0.83255,-180.26,-0.75887,-0.56948,0.31593,179.92
> view matrix models
> #2,-0.10797,-0.92104,-0.37421,215.51,0.1167,-0.38555,0.91528,-101.02,-0.98728,0.055156,0.14912,136.25
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.10797,-0.92104,-0.37421,220.1,0.1167,-0.38555,0.91528,-97.483,-0.98728,0.055156,0.14912,138.09
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.29091,-0.89434,-0.33988,239.53,0.33449,-0.4279,0.83965,-113.14,-0.89637,0.13057,0.42363,65.656
> view matrix models
> #2,-0.29391,-0.90923,-0.29483,235.26,0.35802,-0.39072,0.84803,-124.74,-0.88625,0.14369,0.44036,59.028
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.29391,-0.90923,-0.29483,234.68,0.35802,-0.39072,0.84803,-126.04,-0.88625,0.14369,0.44036,67.212
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.042827,-0.92103,-0.38712,211.07,0.031434,-0.38853,0.9209,-85.38,-0.99859,0.027271,0.045591,169.77
> view matrix models
> #2,0.1157,-0.88571,-0.44959,189.46,0.22756,-0.41695,0.87998,-105.58,-0.96687,-0.20412,0.15331,187.04
> ui tool show "Fit in Map"
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#2)
using 28024 atoms
average map value = 0.1593, steps = 288
shifted from previous position = 28.6
rotated from previous position = 30.1 degrees
atoms outside contour = 23649, contour level = 0.43284
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#2)
coordinates:
Matrix rotation and translation
0.56019523 -0.00238662 -0.82835711 163.40044241
-0.77331941 -0.35994169 -0.52193769 170.95604110
-0.29691461 0.93297169 -0.20348325 167.61795532
Axis 0.84089961 -0.30715988 -0.44557901
Axis point 0.00000000 56.34517284 186.73608879
Rotation angle (degrees) 120.10689732
Shift along axis 10.20548764
> view matrix models
> #2,-0.31145,-0.6761,-0.66775,257.99,-0.16967,-0.65185,0.73913,22.239,-0.93499,0.3435,0.088307,97.931
> view matrix models
> #2,-0.31246,-0.9002,-0.30333,237.51,0.39641,-0.41375,0.81955,-123.65,-0.86327,0.13584,0.48613,57.394
> view matrix models
> #2,0.56742,-0.77092,-0.28935,70.392,0.27805,-0.15137,0.94856,-170.77,-0.77506,-0.61869,0.12846,231.57
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.56742,-0.77092,-0.28935,65.396,0.27805,-0.15137,0.94856,-157.69,-0.77506,-0.61869,0.12846,227.94
> view matrix models
> #2,0.56742,-0.77092,-0.28935,157.62,0.27805,-0.15137,0.94856,-96.881,-0.77506,-0.61869,0.12846,317.61
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.38012,-0.87989,-0.28513,206.08,0.13139,-0.25377,0.9583,-57.033,-0.91556,-0.40173,0.019147,320.71
> view matrix models
> #2,0.13923,-0.96865,-0.20577,247.51,0.41845,-0.13078,0.89877,-115.07,-0.8975,-0.21124,0.38712,225.01
> view matrix models
> #2,0.067643,-0.93479,-0.34871,276.53,0.44854,-0.2837,0.84754,-85.211,-0.8912,-0.21374,0.4001,222.3
> view matrix models
> #2,-0.33934,-0.90982,-0.2389,320.27,0.11484,-0.29214,0.94945,-46.289,-0.93363,0.29475,0.20362,173.39
> view matrix models
> #2,-0.48781,-0.84423,-0.22206,330.26,-0.011251,-0.24828,0.96862,-36.556,-0.87288,0.475,0.11161,147.41
> view matrix models
> #2,-0.63361,-0.749,-0.19376,332.83,0.14375,-0.36007,0.92179,-34.744,-0.76018,0.5562,0.33581,78.647
> view matrix models
> #2,-0.46626,-0.8828,-0.0571,306.57,0.080993,-0.10687,0.99097,-79.544,-0.88093,0.45742,0.12133,150.17
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.46626,-0.8828,-0.0571,230.61,0.080993,-0.10687,0.99097,-138.22,-0.88093,0.45742,0.12133,79.203
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#2)
using 28024 atoms
average map value = 0.1517, steps = 188
shifted from previous position = 9.65
rotated from previous position = 20.9 degrees
atoms outside contour = 23973, contour level = 0.43284
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#2)
coordinates:
Matrix rotation and translation
0.29870588 0.09982458 -0.94910997 171.28174207
-0.95079706 0.11680604 -0.28695153 179.51172342
0.08221696 0.98812514 0.12980357 150.55142781
Axis 0.65468125 -0.52952926 -0.53943603
Axis point 0.00000000 88.76007302 234.04021728
Rotation angle (degrees) 103.14065025
Shift along axis -64.13462994
> ui mousemode right select
> select clear
> open "/Volumes/MEMO/Grad School/Side-
> ACC/J668-models/cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-
> sharpened.mrc"
Opened cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened.mrc as
#3, grid size 196,196,196, pixel 1.02, shown at level 0.174, step 1, values
float32
> close #3
> open "/Volumes/MEMO/Grad School/Side-
> ACC/J668-models/cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-
> sharpened-flipz.mrc"
Opened cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #3, grid size 196,196,196, pixel 1.02, shown at level 0.174, step
1, values float32
> volume #3 level 0.3149
> ui mousemode right "rotate selected models"
Drag select of 3 cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-
sharpened-flipz.mrc
> view matrix models
> #3,0.74651,0.26264,-0.61134,60.375,0.40503,0.54958,0.73069,-68.659,0.52789,-0.79308,0.30388,96.763
> view matrix models
> #3,-0.41655,0.60952,-0.67451,146.61,-0.6582,0.30959,0.68624,64.052,0.6271,0.72982,0.27223,-60.724
> view matrix models
> #3,-0.45545,0.75223,-0.47615,116.34,-0.62421,0.11152,0.77326,71.587,0.63477,0.64939,0.41876,-68.247
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.45545,0.75223,-0.47615,-7.8703,-0.62421,0.11152,0.77326,-15.978,0.63477,0.64939,0.41876,-130.06
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.45545,0.75223,-0.47615,16.367,-0.62421,0.11152,0.77326,-36.732,0.63477,0.64939,0.41876,-146.57
> view matrix models
> #3,-0.45545,0.75223,-0.47615,16.507,-0.62421,0.11152,0.77326,-37.153,0.63477,0.64939,0.41876,-145.43
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.28874,-0.6599,-0.69365,105.22,0.61187,-0.43006,0.66383,-93.908,-0.73637,-0.6161,0.2796,128.69
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
using 28024 atoms
average map value = 0.07632, steps = 204
shifted from previous position = 6.47
rotated from previous position = 9.13 degrees
atoms outside contour = 25637, contour level = 0.31487
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.85375153 0.50203901 -0.13807664 101.19888441
-0.03196357 -0.21415102 -0.97627746 105.12895600
-0.51969862 0.83791179 -0.16678480 121.14861670
Axis 0.94035086 0.19780658 -0.27679019
Axis point 0.00000000 -16.51616515 111.52350714
Rotation angle (degrees) 105.28331475
Shift along axis 82.42490860
> volume #3 color #b2ffff7d
[Repeated 1 time(s)]
> volume #3 level 0.2973
> volume #3 level 0.2446
> hide #!3 models
> color sel blue
> show #!3 models
> open "/Volumes/MEMO/Grad School/Side-ACC/Comparative Models/6g2d.pdb"
6g2d.pdb title:
Citrate-induced acetyl-coa carboxylase (acc-cit) filament At 5.4 A resolution
[more info...]
Chain information for 6g2d.pdb #4
---
Chain | Description | UniProt
B | acetyl-coa carboxylase 1 | ACACA_HUMAN
C D | acetyl-coa carboxylase 1 | ACACA_HUMAN
F | acetyl-coa carboxylase 1 | ACACA_HUMAN
> hide #!3 models
> color #4 #d2ff9d transparency 0
> color #4 #f4ffa9 transparency 0
> color #4 #ffef9e transparency 0
> color #4 #fffc94 transparency 0
> color #4 #fffa86 transparency 0
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb, chain C (#1) with 6g2d.pdb, chain D
(#4), sequence alignment score = 2381.8
RMSD between 309 pruned atom pairs is 1.251 angstroms; (across all 1726 pairs:
14.841)
> color /B,C bychain
> select #4
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> ~select #4
Nothing selected
> select #4
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> ~select #4
Nothing selected
> hide #1 models
> select #4
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> select up
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> select up
116193 atoms, 117624 bonds, 25 pseudobonds, 9157 residues, 7 models selected
> select up
116193 atoms, 117624 bonds, 25 pseudobonds, 9157 residues, 7 models selected
> interfaces protein
10 buried areas: #4/D #1/C 40858, #4/C #1/B 38615, #4/D #4/C 10536, #1/B #1/C
10472, #4/D #1/B 9973, #4/C #1/C 9312, #4/C #4/F 1518, #4/D #4/B 1512, #1/B
#4/F 488, #1/C #4/B 473
> color (#!4 & sel) blue
> select #4
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> ~select #4
Nothing selected
> color bychain
> select #4
88169 atoms, 89088 bonds, 25 pseudobonds, 5501 residues, 2 models selected
> ~select #4
Nothing selected
> show #1 models
Drag select of 108 residues
> select clear
> select #1
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> color bychain
> ui tool show "Color Actions"
> color sel bychain
> color sel blue
> color sel bychain
[Repeated 1 time(s)]
> select #1/B
14012 atoms, 14268 bonds, 1828 residues, 1 model selected
> color sel medium spring green
> select #1/C
14012 atoms, 14268 bonds, 1828 residues, 1 model selected
> color sel dark red
> select #1
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> ~select #1
Nothing selected
> select #1/B
14012 atoms, 14268 bonds, 1828 residues, 1 model selected
> color sel blue
> select #1
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> ~select #1
Nothing selected
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Building/placed_model_real_space_refined-
> coot-0-Ref106-Loops-1339Lys-iffy.pdb"
Chain information for placed_model_real_space_refined-
coot-0-Ref106-Loops-1339Lys-iffy.pdb #5
---
Chain | Description
A | No description available
B | No description available
> select #5/A
5243 atoms, 5293 bonds, 9 pseudobonds, 366 residues, 2 models selected
> ui tool show "Color Actions"
> color sel gold
> select #5/B
4929 atoms, 4973 bonds, 9 pseudobonds, 323 residues, 2 models selected
> color sel dodger blue
> select #5
10172 atoms, 10266 bonds, 18 pseudobonds, 689 residues, 2 models selected
> ~select #5
Nothing selected
> ui tool show Matchmaker
> matchmaker #!4-5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb, chain C (#1) with 6g2d.pdb, chain D
(#4), sequence alignment score = 2381.8
RMSD between 309 pruned atom pairs is 1.251 angstroms; (across all 1726 pairs:
14.841)
Matchmaker output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb, chain B (#1) with
placed_model_real_space_refined-coot-0-Ref106-Loops-1339Lys-iffy.pdb, chain A
(#5), sequence alignment score = 1204.8
RMSD between 247 pruned atom pairs is 1.086 angstroms; (across all 366 pairs:
12.006)
> show #!3 models
> ui tool show "Fit in Map"
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
using 28024 atoms
average map value = 0.07632, steps = 104
shifted from previous position = 0.00767
rotated from previous position = 0.0101 degrees
atoms outside contour = 25134, contour level = 0.24457
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.85367000 0.50216933 -0.13810680 101.20430535
-0.03200840 -0.21408654 -0.97629013 105.13286336
-0.51982977 0.83785018 -0.16668562 121.14514515
Axis 0.94031456 0.19785661 -0.27687776
Axis point 0.00000000 -16.52399549 111.53092792
Rotation angle (degrees) 105.28087547
Shift along axis 82.42271806
> hide #!5 models
> hide #!4 models
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
using 28024 atoms
average map value = 0.07632, steps = 80
shifted from previous position = 0.00605
rotated from previous position = 0.0112 degrees
atoms outside contour = 25134, contour level = 0.24457
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.85374351 0.50205140 -0.13808118 101.20226613
-0.03193593 -0.21419939 -0.97626775 105.12751700
-0.51971349 0.83789201 -0.16683786 121.14635212
Axis 0.94035016 0.19781500 -0.27678658
Axis point 0.00000000 -16.51380501 111.51934707
Rotation angle (degrees) 105.28656529
Shift along axis 82.42968188
> select #1
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> ~select #1
Nothing selected
> select #1
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> select #3
2 models selected
> view matrix models
> #3,0.43514,-0.67577,-0.59497,82.804,0.67167,-0.19643,0.71433,-127.81,-0.59959,-0.71046,0.36842,115.94
> view matrix models
> #3,0.51007,-0.80542,-0.30187,59.741,0.60534,0.086817,0.79122,-156.79,-0.61105,-0.58631,0.53184,88.879
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
using 28024 atoms
average map value = 0.07588, steps = 348
shifted from previous position = 8.52
rotated from previous position = 15.8 degrees
atoms outside contour = 25133, contour level = 0.24457
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.89211248 0.40368635 0.20291046 92.37648596
0.15831239 0.14133723 -0.97722105 109.17648147
-0.42316960 0.90391433 0.06218015 117.43202502
Axis 0.94164473 0.31339849 -0.12282747
Axis point 0.00000000 -33.50053114 106.91354985
Rotation angle (degrees) 87.25936146
Shift along axis 106.77769741
> view matrix models
> #3,0.52846,-0.78247,-0.32935,58.338,0.58335,0.052835,0.8105,-153.14,-0.61679,-0.62044,0.48438,97.437
> view matrix models
> #3,-0.17064,-0.90191,-0.39679,145.41,0.45118,-0.42952,0.78227,-89.698,-0.87597,-0.045532,0.48022,66.444
> view matrix models
> #3,0.46266,-0.82016,-0.33659,69.236,0.58768,-0.00053264,0.80909,-148.15,-0.66376,-0.57214,0.48174,97.532
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
using 28024 atoms
average map value = 0.07765, steps = 120
shifted from previous position = 3.54
rotated from previous position = 4.49 degrees
atoms outside contour = 25077, contour level = 0.24457
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.93778113 0.32800814 0.11391759 93.80876961
0.11472134 0.01696744 -0.99325280 107.62237816
-0.32772789 0.94452251 -0.02171779 121.16211153
Axis 0.96943128 0.22094664 -0.10670323
Axis point 0.00000000 -22.72913584 108.20543773
Rotation angle (degrees) 91.91888572
Shift along axis 101.79156891
> view matrix models
> #3,0.21008,-0.72895,-0.65153,115.68,0.837,-0.21031,0.50518,-122.33,-0.50528,-0.65146,0.56595,81.609
Fit molecule output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
using 28024 atoms
average map value = 0.0777, steps = 120
shifted from previous position = 3.94
rotated from previous position = 6.42 degrees
atoms outside contour = 25090, contour level = 0.24457
Position of output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.78152225 0.62366437 0.01630095 100.70601266
0.24147091 -0.27829190 -0.92964801 99.90127227
-0.57525192 0.73047681 -0.36808811 121.22090056
Axis 0.92058537 0.32803251 -0.21193690
Axis point 0.00000000 -16.66567562 95.16624269
Rotation angle (degrees) 115.62180211
Shift along axis 99.78816497
> view matrix models
> #3,0.21032,-0.85753,-0.46947,110.66,0.84039,-0.086776,0.535,-137.78,-0.49952,-0.50706,0.70241,53.48
> view matrix models
> #3,0.39322,-0.90563,-0.1588,67.212,0.53046,0.082383,0.8437,-154.1,-0.75099,-0.41599,0.51279,87.637
Drag select of 39 residues, 3
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
> view matrix models
> #1,0.32927,-0.019221,0.94404,-14.429,0.24738,0.96663,-0.0666,2.8307,-0.91126,0.25547,0.32303,34.517,#3,0.39173,-0.91959,-0.030115,54.283,0.46388,0.16913,0.86961,-159.97,-0.79458,-0.35462,0.49283,87.485
> view matrix models
> #1,-0.4815,0.86935,0.11134,-4.9637,-0.0091028,0.12206,-0.99248,3.7566,-0.8764,-0.47889,-0.05086,32.831,#3,-0.25004,-0.061879,0.96626,-89.081,-0.061398,0.99696,0.047957,-105.48,-0.96629,-0.047335,-0.25308,155.39
> view matrix models
> #1,-0.41749,-0.53959,-0.73112,-7.8662,0.85426,-0.50734,-0.11338,-5.2491,-0.30975,-0.6719,0.67276,27.281,#3,-0.59254,0.65186,-0.47326,30.114,0.69675,0.11988,-0.70723,1.5599,-0.40428,-0.7488,-0.52522,207.67
> volume #3 level 0.4162
> select #1
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> ~select #1
Nothing selected
> hide #1 models
> show #!5 models
> select #5
10172 atoms, 10266 bonds, 18 pseudobonds, 689 residues, 2 models selected
> view matrix models
> #5,0.60095,0.4878,-0.63317,-39.606,-0.020679,-0.78242,-0.62241,124.87,-0.79902,0.38713,-0.46011,104.94
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.60095,0.4878,-0.63317,16.091,-0.020679,-0.78242,-0.62241,131.88,-0.79902,0.38713,-0.46011,96.088
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.65288,0.5752,-0.49284,-11.682,0.10423,-0.71268,-0.6937,119.57,-0.75026,0.40153,-0.52525,96.258
> view matrix models
> #5,-0.57822,0.57734,-0.5765,119.13,0.50925,-0.29667,-0.80787,49.208,-0.63744,-0.7607,-0.12247,160.47
> view matrix models
> #5,-0.68125,0.42463,-0.59631,146.53,0.64384,-0.040086,-0.76411,5.9709,-0.34837,-0.90448,-0.24609,158.19
> view matrix models
> #5,-0.76069,0.50356,-0.4096,128.09,0.51758,0.089718,-0.85092,14.278,-0.39174,-0.85929,-0.32888,166.24
> view matrix models
> #5,-0.64911,0.64229,-0.40757,102.99,0.52032,-0.015956,-0.85383,24.787,-0.55491,-0.76629,-0.32384,172.77
> view matrix models
> #5,-0.63302,0.61779,-0.4665,109.67,0.5512,-0.063435,-0.83196,24.254,-0.54357,-0.78378,-0.30037,171.05
> view matrix models
> #5,-0.59424,0.55471,0.58239,8.0382,0.028573,0.73821,-0.67397,-18.918,-0.80378,-0.38386,-0.45452,172.57
> view matrix models
> #5,-0.69766,0.71529,0.040413,56.154,0.29168,0.33511,-0.89589,16.89,-0.65436,-0.61324,-0.44243,179.25
> view matrix models
> #5,-0.61435,0.58933,-0.52466,116.4,0.58191,-0.11066,-0.80569,23.277,-0.53288,-0.80028,-0.27495,169.1
> view matrix models
> #5,-0.60119,0.52325,-0.60397,129.51,0.62294,-0.16651,-0.76434,20.631,-0.50051,-0.83576,-0.22585,164.53
> view matrix models
> #5,-0.57747,0.43243,-0.69249,144.95,0.67265,-0.22869,-0.70373,15.84,-0.46268,-0.87218,-0.15881,157.73
> view matrix models
> #5,-0.51675,0.2526,-0.81803,169.2,0.75484,-0.31642,-0.57454,3.5452,-0.40397,-0.91437,-0.027161,143.01
> view matrix models
> #5,-0.27356,0.38076,-0.88328,138.7,0.92768,-0.13816,-0.34686,-53.966,-0.25411,-0.9143,-0.31543,156.65
> view matrix models
> #5,-0.44269,0.5832,-0.6811,115.41,0.84801,0.025461,-0.52937,-44.171,-0.29139,-0.81193,-0.50583,169.08
> view matrix models
> #5,-0.48779,0.63123,-0.603,107.39,0.81585,0.083905,-0.57214,-42.527,-0.31056,-0.77104,-0.55592,171.9
> view matrix models
> #5,-0.50088,0.62234,-0.6015,109.43,0.80356,0.076163,-0.59033,-38.729,-0.32158,-0.77903,-0.53824,172.04
> view matrix models
> #5,-0.53704,0.59896,-0.594,114.61,0.76347,0.045653,-0.64423,-26.357,-0.35875,-0.79948,-0.4818,172.18
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.53704,0.59896,-0.594,42.206,0.76347,0.045653,-0.64423,-2.3457,-0.35875,-0.79948,-0.4818,205.39
Fit molecule placed_model_real_space_refined-coot-0-Ref106-Loops-1339Lys-
iffy.pdb (#5) to map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-
sharpened-flipz.mrc (#3) using 10172 atoms
average map value = 0.5277, steps = 84
shifted from previous position = 2.12
rotated from previous position = 8.21 degrees
atoms outside contour = 4575, contour level = 0.41617
Position of placed_model_real_space_refined-coot-0-Ref106-Loops-1339Lys-
iffy.pdb (#5) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
1.00000000 -0.00015559 0.00014476 -0.00501313
0.00015558 0.99999992 0.00037072 -0.05400621
-0.00014480 -0.00037070 0.99999992 0.04485719
Axis -0.86754536 0.33881229 0.36410339
Axis point 0.00000000 118.63400111 147.88306570
Rotation angle (degrees) 0.02448303
Shift along axis 0.00238380
> ui mousemode right select
> select clear
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/Chimera-X-AF2-Cosmic-
> andDeepEMhancer.cxs"
> show #1 models
> ui tool show Matchmaker
> matchmaker #1 to #5
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 placed_model_real_space_refined-coot-0-Ref106-Loops-1339Lys-
iffy.pdb, chain A (#5) with output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb, chain B (#1), sequence alignment
score = 1204.8
RMSD between 247 pruned atom pairs is 1.086 angstroms; (across all 366 pairs:
12.006)
Drag select of 587 residues
> select clear
[Repeated 1 time(s)]Drag select of 526 residues, 3
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
> select clear
> show #!2 models
> hide #!3 models
> hide #1 models
> hide #!5 models
> show #!3 models
> select #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.72517,-0.6879,-0.030371,-0.37635,-0.12943,-0.092856,-0.98723,215.48,0.6763,0.71984,-0.15637,-173.14
> volume #2 level 0.5697
> view matrix models
> #2,0.45728,-0.79016,-0.40811,123.65,-0.86249,-0.28213,-0.42014,271.58,0.21684,0.54411,-0.81051,40.689
> view matrix models
> #2,-0.47409,-0.86799,-0.14777,243.82,-0.63424,0.45307,-0.62647,142.45,0.61072,-0.20328,-0.76531,98.481
> view matrix models
> #2,-0.46878,-0.88289,0.027567,216.22,-0.71935,0.36346,-0.59197,165.87,0.51262,-0.29733,-0.80549,137.25
> view matrix models
> #2,-0.051678,-0.99863,0.007651,172.21,-0.91311,0.044147,-0.40531,221,0.40442,-0.027932,-0.91415,126.41
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.051678,-0.99863,0.007651,96.81,-0.91311,0.044147,-0.40531,211.05,0.40442,-0.027932,-0.91415,149.19
> view matrix models
> #2,-0.051678,-0.99863,0.007651,44.988,-0.91311,0.044147,-0.40531,263.17,0.40442,-0.027932,-0.91415,104.68
> view matrix models
> #2,-0.051678,-0.99863,0.007651,72.613,-0.91311,0.044147,-0.40531,294.37,0.40442,-0.027932,-0.91415,132.36
> view matrix models
> #2,-0.051678,-0.99863,0.007651,50.635,-0.91311,0.044147,-0.40531,280.55,0.40442,-0.027932,-0.91415,109.34
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.011971,-0.97675,-0.21405,73.662,-0.8602,0.099083,-0.50023,278.41,0.50981,0.19012,-0.83902,42.167
> view matrix models
> #2,0.66878,-0.17584,-0.72237,-85.458,-0.50076,-0.82471,-0.26286,340.05,-0.54952,0.53753,-0.6396,119.83
> view matrix models
> #2,0.64333,-0.22559,-0.7316,-71.227,-0.50268,-0.84523,-0.1814,330.28,-0.57744,0.48446,-0.65716,136.43
> view matrix models
> #2,0.55528,-0.40537,-0.72618,-26.918,-0.48397,-0.8676,0.11424,281.68,-0.67634,0.28802,-0.67794,189.74
> view matrix models
> #2,0.51817,-0.48513,-0.70438,-10.818,-0.46284,-0.85161,0.24605,253.48,-0.71923,0.19852,-0.66581,210.07
> view matrix models
> #2,-0.061603,-0.49538,-0.86649,111.61,-0.73213,-0.56762,0.37656,226.12,-0.67837,0.65758,-0.32771,67.768
> view matrix models
> #2,0.19116,-0.30973,-0.93141,49.658,-0.9034,-0.42658,-0.043553,299.68,-0.38383,0.84976,-0.36136,-7.2805
> view matrix models
> #2,0.4824,-0.18166,-0.85691,-31.882,-0.87354,-0.17237,-0.45521,319.86,-0.065013,0.96814,-0.24184,-99.124
> view matrix models
> #2,0.69523,-0.10912,-0.71046,-103.22,-0.66834,-0.46191,-0.58306,358.06,-0.26455,0.88019,-0.39406,-26.307
> view matrix models
> #2,0.49225,-0.30329,-0.81591,-19.349,-0.72375,-0.66338,-0.19005,336.03,-0.48362,0.68406,-0.54605,68.283
> view matrix models
> #2,0.43937,-0.006166,-0.89829,-48.289,-0.56896,-0.77575,-0.27296,344.3,-0.69516,0.63101,-0.34434,77.839
> view matrix models
> #2,0.37435,-0.12468,-0.91887,-13.916,-0.5138,-0.85279,-0.093607,318.7,-0.77193,0.50715,-0.3833,118.1
> view matrix models
> #2,0.34297,-0.19208,-0.9195,2.8779,-0.47564,-0.87962,0.0063419,300.45,-0.81003,0.43517,-0.39304,138.29
> view matrix models
> #2,0.31944,-0.24878,-0.91437,15.596,-0.44007,-0.89351,0.08936,283.23,-0.83923,0.37384,-0.3949,153.89
> view matrix models
> #2,0.37978,-0.11378,-0.91805,-16.81,-0.51953,-0.84735,-0.1099,321.41,-0.76541,0.51869,-0.38092,114.66
> view matrix models
> #2,0.15042,-0.2127,-0.96547,45.191,-0.70272,-0.70992,0.046916,301.04,-0.69538,0.6714,-0.25625,56.179
> view matrix models
> #2,0.1727,-0.18661,-0.96714,37.375,-0.72296,-0.69088,0.0042129,308.17,-0.66896,0.69847,-0.25422,46.907
> view matrix models
> #2,0.18545,-0.17232,-0.96743,32.901,-0.73348,-0.67943,-0.01958,311.87,-0.65393,0.71322,-0.25239,41.632
> view matrix models
> #2,0.21732,-0.13846,-0.96623,21.72,-0.75665,-0.64925,-0.077139,320.03,-0.61665,0.74786,-0.24586,28.549
> view matrix models
> #2,0.22885,-0.12682,-0.96517,17.671,-0.76402,-0.63781,-0.097352,322.62,-0.60324,0.75968,-0.24286,23.845
> view matrix models
> #2,0.23241,-0.12555,-0.96448,16.764,-0.76129,-0.64065,-0.10005,323.12,-0.60533,0.7575,-0.24447,24.829
> view matrix models
> #2,0.24243,-0.10094,-0.9649,10.973,-0.74194,-0.66011,-0.11736,326.25,-0.6251,0.74436,-0.23492,28.688
> view matrix models
> #2,0.32072,-0.13082,-0.9381,-0.98865,-0.71154,-0.687,-0.14746,331.02,-0.62518,0.71479,-0.31341,46.927
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.32072,-0.13082,-0.9381,38.569,-0.71154,-0.687,-0.14746,259.61,-0.62518,0.71479,-0.31341,97.061
> view matrix models
> #2,0.32072,-0.13082,-0.9381,66.933,-0.71154,-0.687,-0.14746,257.15,-0.62518,0.71479,-0.31341,82.451
> view matrix models
> #2,0.32072,-0.13082,-0.9381,67.512,-0.71154,-0.687,-0.14746,256.74,-0.62518,0.71479,-0.31341,78.085
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.35408,-0.17988,-0.91775,67.191,-0.7594,-0.62806,-0.16988,258.04,-0.54584,0.75709,-0.35898,65.606
> view matrix models
> #2,0.24101,-0.14196,-0.96008,85.971,-0.82233,-0.55527,-0.12433,248.02,-0.51545,0.81947,-0.25056,31.814
> ~select #2
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> select #2
2 models selected
> view matrix models
> #2,0.26925,-0.1644,-0.94894,83.422,-0.81336,-0.56644,-0.13265,249.89,-0.51571,0.80754,-0.28623,39.877
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.26925,-0.1644,-0.94894,82.351,-0.81336,-0.56644,-0.13265,254.38,-0.51571,0.80754,-0.28623,38.1
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.27786,-0.14516,-0.94959,77.751,-0.79961,-0.58278,-0.14489,257.02,-0.53237,0.79956,-0.278,40.79
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc in map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-
sharpened-flipz.mrc using 86490 points
correlation = 0.3917, correlation about mean = 0.004686, overlap = 7219
steps = 384, shift = 14.4, angle = 21.5 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc (#2) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
-0.47638552 -0.68270068 0.55405487 220.70486448
0.73558412 -0.65465512 -0.17419184 96.54428479
0.48163568 0.32457146 0.81405193 -135.31455288
Axis 0.33136643 0.04811358 0.94227457
Axis point 110.32248195 108.83728230 0.00000000
Rotation angle (degrees) 131.18514193
Shift along axis -49.72418851
> ui mousemode right select
> select clear
> show #!5 models
> hide #!3 models
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/Chimera-X-AF2-Cosmic-
> andDeepEMhancer.cxs"
> show #1 models
> hide #!5 models
> open "/Volumes/MEMO/Grad School/Side-
> ACC/J674-Models/cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
> sharpened.mrc"
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc as
#6, grid size 320,320,320, pixel 1.03, shown at level 0.112, step 2, values
float32
> select #6
2 models selected
> volume #6 step 1
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-71.045,0,1,0,-55.075,0,0,1,-9.7837
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.5798,0.79154,-0.1931,87.498,0.50449,0.16267,-0.84795,139.52,-0.63978,-0.58906,-0.49365,436.01
> volume #6 level 0.5807
> view matrix models
> #6,-0.56812,-0.14718,-0.80968,347.21,-0.73564,-0.3502,0.57983,197.25,-0.36889,0.92504,0.09068,36.678
> view matrix models
> #6,0.39106,-0.34285,0.85412,-42.791,0.26558,-0.84651,-0.4614,289.64,0.88121,0.40727,-0.23998,-22.264
> view matrix models
> #6,-0.62954,-0.46003,0.62614,178.95,0.76449,-0.51057,0.39353,12.98,0.13865,0.72642,0.67312,-105.12
> view matrix models
> #6,-0.64708,-0.41782,0.63775,172.62,0.74994,-0.49956,0.43362,6.9471,0.13742,0.75886,0.63659,-104.61
> view matrix models
> #6,-0.59978,-0.52777,0.60144,189.83,0.78726,-0.52367,0.32557,22.552,0.14313,0.66876,0.72958,-105.02
> view matrix models
> #6,-0.69481,-0.29297,0.65682,155.71,0.70542,-0.45547,0.54307,-11.169,0.14006,0.84066,0.52313,-100.8
> view matrix models
> #6,-0.66881,-0.36289,0.64885,164.86,0.73062,-0.48221,0.48339,-0.97389,0.13746,0.79736,0.58764,-103.34
> view matrix models
> #6,-0.53994,-0.38622,0.74787,132.08,0.83656,-0.34436,0.42614,-32.588,0.092953,0.85572,0.50902,-93.517
> view matrix models
> #6,-0.47393,-0.3691,0.79947,110.14,0.87431,-0.30529,0.37734,-37.53,0.10479,0.87782,0.46739,-92.508
> view matrix models
> #6,-0.44429,-0.42385,0.78928,116.45,0.88773,-0.32687,0.32417,-27.378,0.12059,0.84469,0.52149,-98.089
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.44429,-0.42385,0.78928,-59.303,0.88773,-0.32687,0.32417,-111.23,0.12059,0.84469,0.52149,-186.54
> view matrix models
> #6,-0.44429,-0.42385,0.78928,-35.008,0.88773,-0.32687,0.32417,-153.63,0.12059,0.84469,0.52149,-210.7
> color #6 #b2b2ff85 models
[Repeated 1 time(s)]
> hide #!2 models
> hide #1 models
> show #!3 models
> view matrix models
> #6,-0.44429,-0.42385,0.78928,-34.254,0.88773,-0.32687,0.32417,-160.01,0.12059,0.84469,0.52149,-216.97
> hide #!6 models
> ~select #6
Nothing selected
> show #!6 models
> select #6
2 models selected
> view matrix models
> #6,-0.44429,-0.42385,0.78928,-35.772,0.88773,-0.32687,0.32417,-87.773,0.12059,0.84469,0.52149,-281.34
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.80175,-0.59377,0.068094,167.8,0.52783,-0.65002,0.54668,-9.9367,-0.28034,0.47424,0.83457,-203.37
> view matrix models
> #6,-0.69301,-0.71941,0.046808,175.37,0.5998,-0.53934,0.59106,-47.815,-0.39997,0.43769,0.80527,-173.02
> view matrix models
> #6,-0.63749,-0.74464,0.1978,146.35,0.71891,-0.48257,0.50029,-62.149,-0.27708,0.46112,0.84297,-202.99
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.63749,-0.74464,0.1978,177.46,0.71891,-0.48257,0.50029,-131.94,-0.27708,0.46112,0.84297,-155.72
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 83114 points
correlation = 0.3725, correlation about mean = -0.005972, overlap = 6557
steps = 1092, shift = 9.29, angle = 11.4 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#6) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.96054423 -0.20881455 -0.18371541 9.35246194
-0.25721907 -0.91821739 -0.30118965 350.25117411
-0.10579789 0.33656108 -0.93569946 253.54706485
Axis 0.98981403 -0.12093104 -0.07512571
Axis point 0.00000000 154.82877113 155.88102988
Rotation angle (degrees) 161.20658801
Shift along axis -52.14694198
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.69552,-0.62628,0.35216,133.47,0.70402,-0.49612,0.50816,-129.03,-0.14353,0.60137,0.78597,-191.21
> view matrix models
> #6,-0.7785,-0.54458,0.31206,139.25,0.60368,-0.51359,0.60974,-126.25,-0.17178,0.66307,0.72858,-188.01
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.7785,-0.54458,0.31206,140.05,0.60368,-0.51359,0.60974,-128.92,-0.17178,0.66307,0.72858,-186.68
> view matrix models
> #6,-0.7785,-0.54458,0.31206,140.33,0.60368,-0.51359,0.60974,-131.03,-0.17178,0.66307,0.72858,-185.87
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.78369,-0.53603,0.31385,139.4,0.599,-0.51843,0.61026,-129.52,-0.16441,0.66625,0.72737,-187.42
> view matrix models
> #6,-0.82968,-0.52487,0.19012,164.9,0.48686,-0.51372,0.70644,-127.79,-0.27312,0.67868,0.68176,-164.65
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.82968,-0.52487,0.19012,173.11,0.48686,-0.51372,0.70644,-135.31,-0.27312,0.67868,0.68176,-158.07
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.82641,-0.54409,0.14493,183.2,0.47465,-0.53471,0.69913,-128.54,-0.3029,0.64656,0.70015,-150.7
> view matrix models
> #6,-0.84922,-0.46582,0.24867,156.61,0.49485,-0.53774,0.68261,-128.61,-0.18425,0.70274,0.68717,-177.44
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 83114 points
correlation = 0.3867, correlation about mean = -0.0005254, overlap = 6787
steps = 416, shift = 5.56, angle = 11.8 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#6) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.93394148 -0.29868391 0.19631942 -51.42406791
-0.21313104 -0.90630430 -0.36494891 352.56397989
0.28692951 0.29899916 -0.91009395 189.36840268
Axis 0.98283810 -0.13412953 0.12664337
Axis point 0.00000000 155.18257801 128.32891811
Rotation angle (degrees) 160.25888136
Shift along axis -73.84852048
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 83114 points
correlation = 0.3868, correlation about mean = -0.0004909, overlap = 6786
steps = 240, shift = 0.0166, angle = 0.0326 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#6) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.93394058 -0.29838199 0.19678230 -51.54984217
-0.21275606 -0.90647608 -0.36474102 352.48558760
0.28721060 0.29877981 -0.91007732 189.34708409
Axis 0.98283856 -0.13394669 0.12683319
Axis point 0.00000000 155.15211097 128.30465112
Rotation angle (degrees) 160.27212117
Shift along axis -73.86395541
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 83114 points
correlation = 0.3864, correlation about mean = 0.001228, overlap = 6784
steps = 2000, shift = 0.28, angle = 0.6 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#6) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#3)
coordinates:
Matrix rotation and translation
0.93754961 -0.29146666 0.18986308 -51.93616176
-0.20824209 -0.90749133 -0.36482155 351.91754300
0.27863242 0.30250081 -0.91151372 190.40181322
Axis 0.98377900 -0.13086540 0.12269122
Axis point 0.00000000 154.78862541 128.83951667
Rotation angle (degrees) 160.17412831
Shift along axis -73.78690623
> ~select #6
Nothing selected
> show #!5 models
> hide #!3 models
> hide #!5 models
> show #1 models
> ui mousemode right select
> save /Users/gcaballero/Desktop/AccM-Coparison-Aligned-All-Maps.cxs
> includeMaps true
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb, chain C (#1) with 6g2d.pdb, chain D
(#4), sequence alignment score = 2381.8
RMSD between 309 pruned atom pairs is 1.251 angstroms; (across all 1726 pairs:
14.841)
> hide #!6 models
> show #!6 models
> show #!4 models
> hide #!6 models
> hide #1 models
> show #1 models
> hide #1 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #1 models
> hide #!6 models
Drag select of 33 atoms, 7 bonds
> select clear
Window position QRect(1375,681 455x282) outside any known screen, using
primary screen
> hide #!4 models
> hide #1 models
> show #1 models
> save /Users/gcaballero/Desktop/AccM-Coparison-Aligned-All-Maps.cxs
——— End of log from Thu Feb 3 20:10:27 2022 ———
opened ChimeraX session
> close session
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
> format pdb
Chain information for output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb #1
---
Chain | Description
B C | No description available
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
Chain information for output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb #2
---
Chain | Description
B C | No description available
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
Chain information for output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb #3
---
Chain | Description
B C | No description available
> select #1 /B,C :1-622
9482 atoms, 9642 bonds, 1244 residues, 1 model selected
> color sel hot pink
> select up
9518 atoms, 9678 bonds, 1248 residues, 1 model selected
> select #1 /B,C :623-1828
18542 atoms, 18892 bonds, 2412 residues, 1 model selected
> cartoon hide sel
> select #2 /B,C :1246-1828
8810 atoms, 8998 bonds, 1166 residues, 1 model selected
> color sel forest green
> select #2 /B,C :1-1246
19232 atoms, 19554 bonds, 2492 residues, 1 model selected
> cartoon hide sel
> select #3 /B,C :624-1256
9890 atoms, 10058 bonds, 1266 residues, 1 model selected
> color sel orange
> select #3 /B,C :1-623,1257-1828
18134 atoms, 18474 bonds, 2390 residues, 1 model selected
> cartoon hide sel
> rename #1 AccM-Dimer-BCDomain
> rename #2 AccM-Dimer-BCCPDomain
> rename #3 AccM-Dimer-CTDomain
> select #3
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> save /Users/gcaballero/AccM-Manual-Fitting-Domains.cxs
> view matrix models
> #3,0.99999,0.0012704,0.0037442,-0.0045707,-0.0012779,1,0.0020177,-0.0029127,-0.0037416,-0.0020224,0.99999,-0.0013098
> select clear
> open "/Volumes/MEMO/Grad School/Side-
> ACC/J674-Models/cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
> sharpened.mrc"
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc as
#4, grid size 320,320,320, pixel 1.03, shown at level 0.112, step 2, values
float32
> open "/Volumes/MEMO/Grad School/Side-
> ACC/J668-models/cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-
> sharpened-flipz.mrc"
Opened cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-
flipz.mrc as #5, grid size 196,196,196, pixel 1.02, shown at level 0.174, step
1, values float32
> volume #5 level 0.4105
> volume #5 color #54fa48
> volume #5 color #54fa4883
> volume #5 color #54fa4882
> volume #4 color #fe9f91
> volume #4 color #fe9f9183
> volume #4 color #fe676083
> volume #4 color #fe676082
> volume #4 step 1
> ui mousemode right select
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-223.73,0,1,0,-262.26,0,0,1,-233.3
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.91498,0.1609,0.37003,-296.54,0.21466,0.5824,-0.78405,-100.77,-0.34166,0.79682,0.49834,-229.89
> view matrix models
> #4,0.51875,-0.85467,0.020815,-4.0902,0.37154,0.20345,-0.90585,-43.253,0.76997,0.47765,0.42309,-347.31
> view matrix models
> #4,0.31103,-0.019526,0.9502,-260.39,0.68055,0.70247,-0.20833,-290.76,-0.66341,0.71145,0.23178,-119.43
> volume #4 level 0.4485
> view matrix models
> #4,0.66082,0.38117,0.64655,-335.69,0.36509,0.58941,-0.72063,-135.05,-0.65576,0.71225,0.25033,-123.89
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.66082,0.38117,0.64655,-290.75,0.36509,0.58941,-0.72063,-32.235,-0.65576,0.71225,0.25033,-43.938
> view matrix models
> #4,0.66082,0.38117,0.64655,-285.03,0.36509,0.58941,-0.72063,-27.973,-0.65576,0.71225,0.25033,-46.736
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.48857,0.22069,0.84415,-262.3,0.54188,0.68154,-0.4918,-110.52,-0.68386,0.69771,0.21339,-33.538
> view matrix models
> #4,0.50209,0.28364,0.81698,-270.83,0.53663,0.63863,-0.55152,-92.34,-0.67818,0.71533,0.16844,-30.027
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.50209,0.28364,0.81698,-275.15,0.53663,0.63863,-0.55152,-95.798,-0.67818,0.71533,0.16844,-29.219
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.2628,0.21565,0.94044,-245.21,0.69109,0.63811,-0.33944,-155.95,-0.6733,0.73913,0.018659,-9.221
> view matrix models
> #4,0.37851,-0.060961,0.92359,-213.39,0.84221,0.4366,-0.31634,-149.46,-0.38395,0.89759,0.2166,-116.3
> view matrix models
> #4,0.48139,-0.0057788,0.87648,-231.73,0.7994,0.413,-0.43634,-118.52,-0.35946,0.91071,0.20343,-120.34
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.48139,-0.0057788,0.87648,-238.08,0.7994,0.413,-0.43634,-124.62,-0.35946,0.91071,0.20343,-124.57
> view matrix models
> #4,0.48139,-0.0057788,0.87648,-235.22,0.7994,0.413,-0.43634,-122.95,-0.35946,0.91071,0.20343,-128.4
> view matrix models
> #4,0.48139,-0.0057788,0.87648,-239.18,0.7994,0.413,-0.43634,-125.82,-0.35946,0.91071,0.20343,-126.11
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.34477,-0.020645,0.93846,-224.81,0.89186,0.31902,-0.32063,-143.8,-0.29277,0.94752,0.1284,-130.78
> view matrix models
> #4,0.1158,0.10689,0.9875,-217.92,0.8043,0.57328,-0.15637,-200.82,-0.58283,0.81236,-0.019584,-35.916
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.1158,0.10689,0.9875,-231.42,0.8043,0.57328,-0.15637,-214.36,-0.58283,0.81236,-0.019584,-14.752
> ~select #4
Nothing selected
> hide #!4 models
> select #5
2 models selected
> view matrix models #5,1,0,0,-44.042,0,1,0,-69.058,0,0,1,-144.94
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.61274,0.36255,-0.70221,30.9,0.76938,-0.070657,0.63487,-104.47,0.18056,-0.92928,-0.32223,66.356
> view matrix models
> #5,0.66586,0.15156,-0.73052,49.596,0.74243,-0.23122,0.62875,-85.104,-0.073612,-0.96102,-0.26649,89.161
> view matrix models
> #5,0.89041,0.0052007,-0.45514,13.365,0.45489,0.02449,0.89021,-108.92,0.015776,-0.99969,0.01944,54.581
> view matrix models
> #5,0.81269,-0.45676,-0.36181,57.649,0.26081,-0.27012,0.92683,-63.878,-0.52107,-0.84759,-0.1004,105.38
> view matrix models
> #5,0.59792,-0.18536,-0.77983,95.135,0.53801,-0.62837,0.56187,-18.101,-0.59417,-0.75551,-0.27599,121.6
> view matrix models
> #5,0.76327,-0.48347,-0.42857,72.146,0.34766,-0.25176,0.90319,-71.948,-0.54456,-0.83837,-0.024075,98.926
> view matrix models
> #5,0.84553,-0.079495,-0.52797,33.827,0.5296,-0.00066493,0.84825,-109.54,-0.067782,-0.99684,0.041538,60.362
> view matrix models
> #5,0.76223,0.014005,-0.64716,45.109,0.63995,-0.16661,0.75014,-93.852,-0.097319,-0.98592,-0.13596,80.544
> view matrix models
> #5,0.74923,0.042297,-0.66096,45.007,0.65419,-0.20309,0.72855,-89.401,-0.10342,-0.97825,-0.17983,84.915
> volume #5 level 0.5724
> view matrix models
> #5,0.74447,-0.11167,-0.65825,60.581,0.60448,-0.30589,0.73555,-74.892,-0.28349,-0.94549,-0.16023,97.599
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.74447,-0.11167,-0.65825,-0.32573,0.60448,-0.30589,0.73555,-108.03,-0.28349,-0.94549,-0.16023,139.85
> view matrix models
> #5,0.74447,-0.11167,-0.65825,14.498,0.60448,-0.30589,0.73555,-128.82,-0.28349,-0.94549,-0.16023,142.46
> view matrix models
> #5,0.74447,-0.11167,-0.65825,14.717,0.60448,-0.30589,0.73555,-129.26,-0.28349,-0.94549,-0.16023,142.57
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.74851,-0.0221,-0.66275,5.8309,0.59891,-0.40651,0.68997,-113.94,-0.28466,-0.91338,-0.29104,153.01
> view matrix models
> #5,0.67909,-0.11823,-0.72447,28.75,0.61029,-0.45749,0.64672,-105.51,-0.4079,-0.88132,-0.23852,156.68
> view matrix models
> #5,0.71673,-0.23089,-0.65802,29.372,0.56588,-0.35888,0.74228,-120.81,-0.40754,-0.90438,-0.12657,147.37
> view matrix models
> #5,0.69563,-0.29123,-0.65672,37.372,0.52593,-0.41629,0.74169,-111.03,-0.48939,-0.86133,-0.13642,152.26
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.69563,-0.29123,-0.65672,40.388,0.52593,-0.41629,0.74169,-105.41,-0.48939,-0.86133,-0.13642,158.03
> view matrix models
> #5,0.69563,-0.29123,-0.65672,42.099,0.52593,-0.41629,0.74169,-109.94,-0.48939,-0.86133,-0.13642,156.46
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.65447,-0.12189,-0.74619,38.548,0.5779,-0.55575,0.59764,-86.303,-0.48755,-0.82236,-0.29329,168.61
> view matrix models
> #5,0.64478,-0.12104,-0.75472,40.312,0.59011,-0.54874,0.59216,-87.656,-0.48582,-0.82718,-0.28239,167.79
> save /Users/gcaballero/AccM-Manual-Fitting-Domains.cxs
> ui tool show "Fit in Map"
> hide #1 models
> hide #2 models
> show #2 models
> hide #3 models
Fit molecule AccM-Dimer-CTDomain (#3) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.07292, steps = 136
shifted from previous position = 8.57
rotated from previous position = 6.88 degrees
atoms outside contour = 26895, contour level = 0.57241
Position of AccM-Dimer-CTDomain (#3) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.68164250 0.49324021 -0.54044204 104.83811064
-0.18494842 -0.59849091 -0.77948875 97.11460760
-0.70792484 0.63128656 -0.31673284 121.71716837
Axis 0.89615453 0.10638864 -0.43079986
Axis point 0.00000000 3.20511996 110.93846976
Rotation angle (degrees) 128.08214609
Shift along axis 51.84729905
> ui mousemode right select
> select clear
Fit molecule AccM-Dimer-CTDomain (#3) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.07292, steps = 40
shifted from previous position = 0.012
rotated from previous position = 0.0231 degrees
atoms outside contour = 26893, contour level = 0.57241
Position of AccM-Dimer-CTDomain (#3) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.68177384 0.49306060 -0.54044026 104.82992046
-0.18524234 -0.59831878 -0.77955109 97.12257193
-0.70772149 0.63158996 -0.31658239 121.71811972
Axis 0.89618443 0.10623660 -0.43077518
Axis point 0.00000000 3.20756821 110.94772984
Rotation angle (degrees) 128.06562727
Shift along axis 51.83177024
Fit molecule AccM-Dimer-CTDomain (#3) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.07293, steps = 60
shifted from previous position = 0.0228
rotated from previous position = 0.0499 degrees
atoms outside contour = 26895, contour level = 0.57241
Position of AccM-Dimer-CTDomain (#3) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.68205149 0.49269468 -0.54042364 104.81462219
-0.18587077 -0.59792762 -0.77970162 97.13746670
-0.70728907 0.63224561 -0.31623989 121.71537243
Axis 0.89624592 0.10591929 -0.43072538
Axis point 0.00000000 3.21053980 110.96600170
Rotation angle (degrees) 128.02883744
Shift along axis 51.80250861
> rename #3 AccM-Dimer-BCCPCTDomain
> rename #2 AccM-Dimer-CTDomain
> rename #3 AccM-Dimer-BCCPDomain
Fit molecule AccM-Dimer-CTDomain (#2) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.07291, steps = 180
shifted from previous position = 8.57
rotated from previous position = 6.71 degrees
atoms outside contour = 26892, contour level = 0.57241
Position of AccM-Dimer-CTDomain (#2) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.68144669 0.49344153 -0.54050519 104.84820699
-0.18459165 -0.59877024 -0.77935879 97.09706463
-0.70820642 0.63086421 -0.31694481 121.70918705
Axis 0.89611031 0.10656385 -0.43084854
Axis point 0.00000000 3.20444526 110.92070366
Rotation angle (degrees) 128.10715773
Shift along axis 51.86437114
> select #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.070098,-0.85922,-0.50678,145.8,-0.073371,-0.5111,0.85639,-52.484,-0.99484,-0.022848,-0.098868,119.3
> ui mousemode right select
Fit molecule AccM-Dimer-CTDomain (#2) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.1215, steps = 264
shifted from previous position = 9.28
rotated from previous position = 11.1 degrees
atoms outside contour = 25651, contour level = 0.57241
Position of AccM-Dimer-CTDomain (#2) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.18742281 -0.23919964 -0.95270994 100.11094371
-0.84616335 -0.53190618 -0.03291510 99.45820364
-0.49887903 0.81231727 -0.30209332 130.66119594
Axis 0.74453626 -0.39976411 -0.53465355
Axis point 0.00000000 53.20968425 119.13707600
Rotation angle (degrees) 145.41533769
Shift along axis -35.08206565
> select clear
> show #3 models
> hide #!5 models
> show #!5 models
> hide #2 models
Fit molecule AccM-Dimer-BCCPDomain (#3) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.1215, steps = 172
shifted from previous position = 9.32
rotated from previous position = 11.3 degrees
atoms outside contour = 25654, contour level = 0.57241
Position of AccM-Dimer-BCCPDomain (#3) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.18748633 -0.23928831 -0.95267517 100.10364610
-0.84561682 -0.53279445 -0.03259255 99.42549494
-0.49978102 0.81170880 -0.30223789 130.65644430
Axis 0.74463917 -0.39943407 -0.53475688
Axis point -0.00000000 53.20121682 119.10361974
Rotation angle (degrees) 145.46428944
Shift along axis -35.04226666
> show #2 models
> show #1 models
> hide #1 models
Fit molecule AccM-Dimer-BCDomain (#1) to map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
using 28024 atoms
average map value = 0.1215, steps = 136
shifted from previous position = 5.09
rotated from previous position = 12 degrees
atoms outside contour = 25653, contour level = 0.57241
Position of AccM-Dimer-BCDomain (#1) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.18740357 -0.23916993 -0.95272118 100.11258952
-0.84606309 -0.53206945 -0.03285351 99.45342871
-0.49905626 0.81221909 -0.30206457 130.65889091
Axis 0.74454179 -0.39969642 -0.53469645
Axis point -0.00000000 53.20886465 119.13474032
Rotation angle (degrees) 145.42309804
Shift along axis -35.07601806
> show #1 models
> select clear
[Repeated 1 time(s)]
> hide #3 models
> hide #1 models
> show #!4 models
Drag select of 4 cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.06773,0.19303,0.97885,-237.07,0.75266,0.63414,-0.17713,-213.06,-0.65492,0.74874,-0.10233,21.651
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.06773,0.19303,0.97885,-233.32,0.75266,0.63414,-0.17713,-209.89,-0.65492,0.74874,-0.10233,22.009
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.03059,0.24848,0.96815,-235.11,0.7147,0.6717,-0.19498,-207.27,-0.69876,0.69791,-0.15704,46.972
> view matrix models
> #4,0.23247,-0.29619,0.92641,-166.82,0.8868,0.45572,-0.076825,-217.48,-0.39943,0.8394,0.36861,-113.26
> view matrix models
> #4,0.42121,-0.14142,0.89587,-219,0.87693,0.31559,-0.36249,-144.21,-0.23146,0.9383,0.25694,-138.96
> view matrix models
> #4,0.56344,-0.29651,0.77112,-194.51,0.43336,0.90073,0.029707,-238.62,-0.70338,0.31743,0.636,-18.419
> view matrix models
> #4,0.38619,0.41755,0.8225,-297.63,0.66775,0.48862,-0.56157,-107.13,-0.63638,0.7661,-0.090119,13.982
> view matrix models
> #4,-0.46853,0.75645,0.45636,-156.95,0.34936,0.6331,-0.69074,-59.081,-0.81143,-0.1642,-0.5609,281.15
> view matrix models
> #4,-0.48813,0.68634,0.53913,-155.44,0.13573,0.6699,-0.72994,-24.344,-0.86215,-0.28314,-0.42015,286.49
> view matrix models
> #4,-0.55142,0.70915,0.43936,-132.55,0.39663,0.68619,-0.60977,-89.352,-0.73391,-0.16198,-0.65965,284.63
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.55142,0.70915,0.43936,-92.16,0.39663,0.68619,-0.60977,-74.39,-0.73391,-0.16198,-0.65965,297.42
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.54003,0.65933,0.52311,-99.325,0.24249,0.71707,-0.65346,-47.515,-0.80595,-0.22604,-0.54712,301.43
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.54003,0.65933,0.52311,-103.44,0.24249,0.71707,-0.65346,-48.95,-0.80595,-0.22604,-0.54712,295.17
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.51666,0.66808,0.53548,-110.79,0.22509,0.7094,-0.6679,-42.41,-0.82608,-0.22455,-0.51689,293.14
> view matrix models
> #4,-0.038492,0.91805,0.39458,-207.9,-0.23312,0.37573,-0.89693,127.41,-0.97169,-0.12651,0.19955,180.7
> view matrix models
> #4,-0.71308,0.40134,0.57484,-39.504,-0.66267,-0.11818,-0.73953,256.01,-0.22887,-0.90827,0.35022,170.39
> view matrix models
> #4,-0.91203,0.074255,0.40335,77.655,-0.37011,0.27471,-0.88744,165.44,-0.1767,-0.95866,-0.22306,265.94
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.91203,0.074255,0.40335,82.611,-0.37011,0.27471,-0.88744,165.43,-0.1767,-0.95866,-0.22306,234.54
> hide #2 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.94306,0.15717,0.29314,91.64,-0.29698,-0.0009805,-0.95488,212.39,-0.14979,-0.98757,0.047601,190.19
> view matrix models
> #4,-0.83494,-0.41252,0.36428,160.66,-0.50903,0.32727,-0.7961,163.65,0.20919,-0.85013,-0.48324,196.6
> view matrix models
> #4,-0.98673,-0.15997,0.027845,197.55,-0.12828,0.66291,-0.73763,34.38,0.099537,-0.73141,-0.67463,225.67
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.98673,-0.15997,0.027845,205.35,-0.12828,0.66291,-0.73763,42.055,0.099537,-0.73141,-0.67463,229.51
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.7605,0.51431,0.39639,-8.9155,-0.021728,0.58995,-0.80715,48.959,-0.64898,-0.62245,-0.43748,292.41
> view matrix models
> #4,-0.68209,0.63957,0.35455,-36.273,-0.056805,0.43704,-0.89765,96.075,-0.72906,-0.63241,-0.26177,277.89
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.68209,0.63957,0.35455,-36.034,-0.056805,0.43704,-0.89765,96.656,-0.72906,-0.63241,-0.26177,279.7
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.61916,0.67903,0.39441,-59.654,-0.035963,0.47722,-0.87805,83.089,-0.78444,-0.55784,-0.27105,277.33
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3672, correlation about mean = -0.02649, overlap = 8598
steps = 636, shift = 22.7, angle = 25.7 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.51670463 0.69492868 0.50009043 -199.60144084
0.82729408 -0.55565852 -0.08263233 67.96207546
0.22045594 0.45641836 -0.86202172 167.03522389
Axis 0.86730514 0.44991768 0.21296919
Axis point 0.00000000 68.31834224 118.68666358
Rotation angle (degrees) 161.89485131
Shift along axis -106.96466097
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3673, correlation about mean = -0.0264, overlap = 8598
steps = 268, shift = 0.0163, angle = 0.0254 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.51671678 0.69517655 0.49973325 -199.58612172
0.82736298 -0.55555264 -0.08265444 67.94019649
0.22016870 0.45616973 -0.86222671 167.17209502
Axis 0.86731192 0.44999775 0.21277232
Axis point 0.00000000 68.30966671 118.72411229
Rotation angle (degrees) 161.90286930
Shift along axis -106.96089193
> save /Users/gcaballero/AccM-Manual-Fitting-Domains.cxs
> ui mousemode right select
> select clear
> hide #!4 models
> show #!4 models
> hide #!4 models
> volume #5 level 0.596
> show #!4 models
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> ~select #4
Nothing selected
> select #4
2 models selected
> view matrix models
> #4,-0.87378,0.1474,0.46345,41.562,-0.32882,0.52306,-0.78631,106,-0.35832,-0.83945,-0.40857,287.68
> view matrix models
> #4,-0.42812,-0.88956,0.15936,198.99,-0.014509,-0.16955,-0.98541,207.79,0.90361,-0.42419,0.059681,-66.045
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.42812,-0.88956,0.15936,194.96,-0.014509,-0.16955,-0.98541,204.75,0.90361,-0.42419,0.059681,-94.83
> view matrix models
> #4,-0.42812,-0.88956,0.15936,196.33,-0.014509,-0.16955,-0.98541,205.71,0.90361,-0.42419,0.059681,-91.697
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.39727,-0.89018,0.22307,180.86,-0.084673,-0.20648,-0.97478,221.67,0.91379,-0.40614,0.0066539,-87.647
> view matrix models
> #4,-0.45869,-0.86234,0.21441,187.43,0.0074692,-0.24502,-0.96949,212.53,0.88856,-0.4431,0.11883,-95.83
> view matrix models
> #4,-0.33154,-0.91409,0.23348,172.62,0.093564,-0.27812,-0.95598,202.07,0.93879,-0.2951,0.17773,-139.3
> view matrix models
> #4,-0.29676,-0.9502,0.09518,196.21,0.11426,-0.13428,-0.98433,178.6,0.94809,-0.28124,0.14842,-138.32
> view matrix models
> #4,-0.12037,-0.98423,0.12959,167.82,0.23309,-0.15491,-0.96004,158.9,0.96498,-0.08535,0.24806,-191.43
> view matrix models
> #4,-0.090754,-0.99123,0.096068,169.81,0.20842,-0.11323,-0.97146,157.59,0.97382,-0.068142,0.21687,-190.65
> view matrix models
> #4,-0.06341,-0.99276,0.10205,164.65,0.22679,-0.11392,-0.96726,154.04,0.97188,-0.03819,0.23237,-198.08
> ui mousemode right select
> select clear
> ui tool show "Fit in Map"
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3772, correlation about mean = -0.01576, overlap = 9143
steps = 2000, shift = 8.21, angle = 25.5 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.89176335 0.40444350 -0.20293736 229.03580371
0.28389246 0.84929244 0.44509260 -171.34505840
0.35236798 0.33930488 -0.87218633 164.55716486
Axis -0.18302274 -0.96073068 -0.20856469
Axis point 116.77735999 0.00000000 119.71995497
Rotation angle (degrees) 163.20180932
Shift along axis 88.37688082
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.4609,-0.86808,0.1844,197.76,0.13147,-0.27229,-0.95319,189.93,0.87766,-0.41508,0.23963,-126.63
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.4609,-0.86808,0.1844,196.92,0.13147,-0.27229,-0.95319,188.51,0.87766,-0.41508,0.23963,-126.83
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.31361,-0.92047,0.23319,174.02,0.37948,-0.34661,-0.85782,145.35,0.87043,-0.18053,0.458,-202.45
> view matrix models
> #4,-0.25669,-0.95227,0.16521,181.6,0.38913,-0.2583,-0.88423,132.94,0.88469,-0.16268,0.43686,-204.32
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.25669,-0.95227,0.16521,179.92,0.38913,-0.2583,-0.88423,129.95,0.88469,-0.16268,0.43686,-206.87
> ui tool show "Fit in Map"
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3764, correlation about mean = 0.0001404, overlap = 9015
steps = 188, shift = 4.25, angle = 10.6 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.89930956 0.28578780 -0.33101001 277.48268573
0.13724023 0.90311731 0.40687127 -149.62648426
0.41521972 0.32047534 -0.85140362 152.80310810
Axis -0.11282367 -0.97449468 -0.19398694
Axis point 130.11826658 0.00000000 120.60733505
Rotation angle (degrees) 157.48778726
Shift along axis 84.86179069
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.28465,-0.94989,0.12914,192.83,0.42251,-0.24524,-0.87255,122.71,0.8605,-0.19381,0.47115,-205.84
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.28465,-0.94989,0.12914,188.19,0.42251,-0.24524,-0.87255,118.93,0.8605,-0.19381,0.47115,-208.23
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3764, correlation about mean = 0.0001323, overlap = 9015
steps = 172, shift = 7.12, angle = 9.1 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.89935479 0.28571293 -0.33095177 277.49297280
0.13721516 0.90314709 0.40681361 -149.61732656
0.41513004 0.32045817 -0.85145382 152.83124260
Axis -0.11279412 -0.97450307 -0.19396201
Axis point 130.12194418 0.00000000 120.61240176
Rotation angle (degrees) 157.49269853
Shift along axis 84.85951363
> view matrix models
> #4,-0.39132,-0.91838,0.05876,217.13,0.35137,-0.20812,-0.91281,138.65,0.85053,-0.33656,0.40413,-173.44
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.39766,-0.91609,0.051373,218.99,0.33433,-0.19681,-0.92168,140.93,0.85445,-0.34934,0.38454,-168.61
> view matrix models
> #4,-0.41006,-0.91128,0.037673,222.45,0.30166,-0.17449,-0.93731,144.96,0.86073,-0.37299,0.34645,-159.22
> view matrix models
> #4,-0.37872,-0.92253,0.074266,213.23,0.38593,-0.23035,-0.89331,133.65,0.84121,-0.30965,0.44327,-183.08
> view matrix models
> #4,-0.38225,-0.92142,0.069807,214.35,0.37615,-0.22416,-0.89903,135.12,0.84404,-0.3174,0.43228,-180.38
> view matrix models
> #4,-0.39222,-0.91806,0.057697,217.4,0.34894,-0.20652,-0.91411,138.99,0.85112,-0.3384,0.40135,-172.76
> view matrix models
> #4,-0.34963,-0.93259,0.089655,207.7,0.3228,-0.20974,-0.92294,145.24,0.87953,-0.29374,0.37437,-180.58
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.34963,-0.93259,0.089655,203.49,0.3228,-0.20974,-0.92294,142.46,0.87953,-0.29374,0.37437,-174.55
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.26462,-0.95617,0.12535,187.87,0.38246,-0.22338,-0.89656,130.77,0.88527,-0.18931,0.42481,-201.89
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.26462,-0.95617,0.12535,186.16,0.38246,-0.22338,-0.89656,129.58,0.88527,-0.18931,0.42481,-201.71
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3765, correlation about mean = 0.000152, overlap = 9015
steps = 164, shift = 5.25, angle = 8.76 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.89930186 0.28566951 -0.33113302 277.52794375
0.13728230 0.90330237 0.40644605 -149.57016256
0.41522249 0.32005899 -0.85155888 152.89998086
Axis -0.11279876 -0.97454379 -0.19375462
Axis point 130.12664157 0.00000000 120.63793132
Rotation angle (degrees) 157.48498122
Shift along axis 84.83278851
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.30546,-0.94699,0.099555,200.6,0.41181,-0.22565,-0.88289,122.76,0.85855,-0.22869,0.4589,-197.48
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.30546,-0.94699,0.099555,198.07,0.41181,-0.22565,-0.88289,120.93,0.85855,-0.22869,0.4589,-199.8
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 128452 points
correlation = 0.3828, correlation about mean = 0.01386, overlap = 8672
steps = 1712, shift = 3.32, angle = 12 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.85426091 0.34876145 -0.38549155 269.91770634
0.22716087 0.91744606 0.32663535 -147.84986269
0.46758553 0.19146322 -0.86296327 167.51958366
Axis -0.15497166 -0.97803273 -0.13941220
Axis point 125.71424183 0.00000000 127.41721965
Rotation angle (degrees) 154.14348867
Shift along axis 79.41813704
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.40856,-0.89843,0.16093,194.64,0.41322,-0.33928,-0.84507,132.11,0.81384,-0.27876,0.50987,-191.62
> view matrix models
> #4,-0.22512,-0.94338,0.24363,158.97,0.5507,-0.32947,-0.76693,95.186,0.80378,-0.038484,0.59369,-245.4
> view matrix models
> #4,-0.30155,-0.89834,0.31946,150.95,0.56165,-0.43812,-0.70185,101.35,0.77047,-0.03222,0.63667,-248.24
> view matrix models
> #4,0.15438,-0.9402,-0.30363,187.97,0.40195,0.3405,-0.85,17.415,0.90255,0.0091796,0.43048,-242.49
> view matrix models
> #4,0.054839,-0.99849,-0.0028918,164.15,0.45549,0.027594,-0.88981,69.38,0.88855,0.04748,0.45632,-251.13
> view matrix models
> #4,-0.049852,-0.97989,-0.1932,209.51,0.65958,0.11296,-0.7431,-2.7662,0.74998,-0.16447,0.64068,-222.76
> view matrix models
> #4,-0.057442,-0.9899,-0.12961,201.9,0.6306,0.064675,-0.77341,15.296,0.77398,-0.12616,0.62051,-229.91
> view matrix models
> #4,-0.13936,-0.99001,0.021421,190.07,0.61644,-0.10367,-0.78055,47.833,0.77497,-0.095576,0.62473,-236.05
> view matrix models
> #4,-0.11984,-0.98812,0.096192,174.16,0.55592,-0.14707,-0.81812,71.362,0.82255,-0.044569,0.56694,-242.95
> view matrix models
> #4,-0.24761,-0.96782,0.04491,199.85,0.464,-0.15915,-0.87142,97.182,0.85052,-0.19493,0.48848,-208.47
> view matrix models
> #4,-0.18954,-0.97961,0.066643,188.88,0.5064,-0.15568,-0.84813,85.85,0.84121,-0.127,0.52558,-224.86
> view matrix models
> #4,-0.20584,-0.97656,0.062948,191.6,0.50103,-0.16042,-0.85043,87.92,0.84059,-0.14351,0.52231,-221.37
> view matrix models
> #4,-0.23116,-0.97122,0.057319,195.72,0.49249,-0.16762,-0.85402,91.143,0.83906,-0.16919,0.51707,-215.81
> view matrix models
> #4,-0.27699,-0.9597,0.047486,202.78,0.4764,-0.18008,-0.86059,96.989,0.83446,-0.21576,0.50708,-205.37
> view matrix models
> #4,-0.2256,-0.97246,0.058545,194.83,0.49439,-0.16606,-0.85323,90.434,0.83946,-0.16354,0.51824,-217.05
> ui mousemode right select
> select clear
> save /Users/gcaballero/AccM-Manual-Fitting-Domains.cxs
——— End of log from Mon Feb 14 12:41:57 2022 ———
opened ChimeraX session
> ui mousemode right select
> select clear
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #1 models
> hide #1 models
> ui tool show "Fit to Segments"
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> BothModels-Rigid.cxs" includeMaps true
> ui tool show "Segment Map"
Window position QRect(1087,918 642x293) outside any known screen, using
primary screen
Segmenting cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc, density threshold 0.448479
Showing 56 region surfaces
1728 watershed regions, grouped to 56 regions
Showing cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.seg -
56 regions, 56 surfaces
> hide #!5 models
> select #6
57 models selected
> select clear
> select #6
57 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-66.555,0,1,0,-20.012,0,0,1,-45.442
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.21822,0.62847,0.7466,-163.86,-0.54936,0.71141,-0.43829,189.71,-0.80659,-0.31451,0.5005,218.88
> view matrix models
> #6,-0.63694,0.54093,0.54928,27.037,-0.60931,0.083255,-0.78855,362.39,-0.47228,-0.83694,0.27657,286.8
> view matrix models
> #6,-0.54208,0.8368,0.076871,36.66,-0.64766,-0.35775,-0.67272,425.24,-0.53544,-0.41445,0.73589,148.91
> view matrix models
> #6,-0.97914,-0.051973,0.19645,239.66,-0.086552,-0.768,-0.63458,398.17,0.18385,-0.63834,0.74748,69.33
> view matrix models
> #6,-0.71261,-0.62794,0.31285,271.29,0.2506,-0.64436,-0.7225,334.95,0.65527,-0.43646,0.61654,-22.575
> view matrix models
> #6,-0.86847,-0.47711,-0.13462,345.9,0.49413,-0.81125,-0.31259,255.16,0.039936,-0.338,0.9403,9.5196
> view matrix models
> #6,-0.79933,-0.55588,0.2282,287.1,0.33084,-0.72414,-0.60512,316.66,0.50162,-0.40819,0.76273,-23.198
> view matrix models
> #6,-0.31816,-0.87964,0.35357,240.85,0.5606,-0.47532,-0.67808,248.16,0.76452,-0.017526,0.64436,-113.73
> view matrix models
> #6,-0.33935,-0.93461,-0.10648,327.85,0.40609,-0.043459,-0.9128,237.44,0.84849,-0.353,0.39429,-29.82
> view matrix models
> #6,-0.31578,-0.9092,0.27137,258.82,0.53389,-0.4067,-0.74132,250.98,0.78438,-0.089213,0.61384,-99.742
> view matrix models
> #6,-0.016065,-0.95356,0.30078,212.15,0.53538,-0.26226,-0.80286,235.83,0.84446,0.14813,0.51473,-134.54
> view matrix models
> #6,0.16425,-0.9583,0.23386,193.94,0.60089,-0.090815,-0.79416,194.59,0.78227,0.27097,0.56091,-152.48
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.16425,-0.9583,0.23386,33.768,0.60089,-0.090815,-0.79416,88.122,0.78227,0.27097,0.56091,-223.1
> view matrix models
> #6,0.16425,-0.9583,0.23386,46.448,0.60089,-0.090815,-0.79416,74.911,0.78227,0.27097,0.56091,-222.32
> view matrix models
> #6,0.16425,-0.9583,0.23386,101.8,0.60089,-0.090815,-0.79416,57.426,0.78227,0.27097,0.56091,-277.04
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.42366,-0.85354,0.3033,169.95,0.4986,-0.49928,-0.7086,130.6,0.75625,-0.14898,0.6371,-213.02
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.42366,-0.85354,0.3033,177.99,0.4986,-0.49928,-0.7086,129.4,0.75625,-0.14898,0.6371,-214.71
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.56053,-0.8063,0.18889,211.31,0.41579,-0.47127,-0.77783,149.65,0.71619,-0.35746,0.59942,-166.56
> view matrix models
> #6,-0.58143,-0.79469,0.17438,215.19,0.40194,-0.46692,-0.78767,152.82,0.70738,-0.38788,0.5909,-158.59
> view matrix models
> #6,-0.087458,-0.87704,0.47239,99.026,0.76426,-0.36323,-0.53289,33.73,0.63895,0.31442,0.70205,-285.2
> view matrix models
> #6,-0.23152,-0.89613,0.37861,140.82,0.6782,-0.4277,-0.5976,69.18,0.69746,0.11842,0.70677,-262.21
> view matrix models
> #6,-0.34239,-0.90654,0.24688,182.18,0.61449,-0.41484,-0.67106,89.332,0.71076,-0.078056,0.6991,-229.37
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.34239,-0.90654,0.24688,182.59,0.61449,-0.41484,-0.67106,79.422,0.71076,-0.078056,0.6991,-247.7
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.4173,-0.87825,0.23355,192.37,0.54913,-0.44846,-0.70522,101.6,0.7241,-0.16604,0.66941,-230.03
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.4173,-0.87825,0.23355,185.67,0.54913,-0.44846,-0.70522,106.44,0.7241,-0.16604,0.66941,-219.54
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.16775,-0.9585,0.23051,158.47,0.48491,-0.2838,-0.82723,108.39,0.85832,-0.026989,0.5124,-240.49
> view matrix models
> #6,-0.0091792,-0.98033,0.19715,141.4,0.45618,-0.17955,-0.87158,102.26,0.88984,0.081934,0.44886,-254.29
> view matrix models
> #6,-0.081491,-0.99667,-0.0018805,187.77,0.42735,-0.033237,-0.90348,86.902,0.90041,-0.074429,0.42863,-225.91
> view matrix models
> #6,-0.081343,-0.99667,-0.0063501,188.45,0.44755,-0.030833,-0.89373,81.585,0.89055,-0.07554,0.44857,-227.24
> view matrix models
> #6,-0.14002,-0.99013,-0.0053827,196.95,0.51991,-0.068896,-0.85144,69.436,0.84267,-0.12202,0.52442,-223.19
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.14002,-0.99013,-0.0053827,196.64,0.51991,-0.068896,-0.85144,69.075,0.84267,-0.12202,0.52442,-227.25
> view matrix models
> #6,-0.14002,-0.99013,-0.0053827,193.33,0.51991,-0.068896,-0.85144,71.102,0.84267,-0.12202,0.52442,-224.74
> ui mousemode right select
> select clear
> ui tool show "Fit in Map"
> hide #!4 models
Smoothing and grouping, standard deviation 5 voxels
Showing 35 region surfaces
Got 35 regions after smoothing 5 voxels.
Smoothing and grouping, standard deviation 6 voxels
Showing 20 region surfaces
Got 20 regions after smoothing 6 voxels.
Smoothing and grouping, standard deviation 7 voxels
Showing 11 region surfaces
Got 11 regions after smoothing 7 voxels.
Smoothing and grouping, standard deviation 8 voxels
Showing 7 region surfaces
Got 7 regions after smoothing 8 voxels.
Smoothing and grouping, standard deviation 9 voxels
No new groups smoothing 9 voxels
Showing 6 region surfaces
Got 6 regions after smoothing 10 voxels.
Smoothing and grouping, standard deviation 11 voxels
No new groups smoothing 11 voxels
Showing 5 region surfaces
Got 5 regions after smoothing 12 voxels.
> select clear
Grouped 2 regions
> select clear
Grouped 3 regions
> select clear
[Repeated 1 time(s)]
> show #!4 models
> hide #!4 models
> select #4
2 models selected
> ~select #4
Nothing selected
> select #6
3 models selected
> ~select #6
Nothing selected
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> BothModels-Rigid-FitTOsegment.cxs"
——— End of log from Mon Feb 14 13:43:45 2022 ———
opened ChimeraX session
Showing cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.seg -
2 regions, 2 surfaces
> show #1 models
> hide #!6 models
> select #1 :623-1828
18542 atoms, 18892 bonds, 2412 residues, 1 model selected
> select #1 :1-622
9482 atoms, 9642 bonds, 1244 residues, 1 model selected
> select #1 :623-1828
18542 atoms, 18892 bonds, 2412 residues, 1 model selected
> select #1 :623-1828
18542 atoms, 18892 bonds, 2412 residues, 1 model selected
> cartoon sel
> delete #1 :623-1828
> show #2 models
> delete #2 :1-1246
> delete #3 /B,C :1-623,1257-1828
> show #3 models
> hide #3 models
> hide #2 models
> hide #1 models
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> BothModels-Rigid-FitTOsegment.cxs"
> show #1 models
> select #6.2
1 model selected
Simulating map res 8.000, grid 2.000
> molmap #1 8.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false
Opened AccM-Dimer-BCDomain map 8 as #7, grid size 59,71,83, pixel 2, shown at
level 0.0974, step 1, values float32
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened_masked
as #8, grid size 320,320,320, pixel 1.03, shown at step 1, values float32
Top score: 0.61084, z-score: 1.65157 (avg: 0.5920, stdev: 0.0114)
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!6 models
> show #2 models
> hide #2 models
> show #3 models
> hide #1 models
> hide #!6 models
> show #!6 models
> select #6
3 models selected
> ~select #6
Nothing selected
> select #6.2
1 model selected
Simulating map res 8.000, grid 2.000
> molmap #3 8.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false
Opened AccM-Dimer-BCCPDomain map 8 as #8, grid size 65,61,120, pixel 2, shown
at level 0.0792, step 1, values float32
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened_masked
as #9, grid size 320,320,320, pixel 1.03, shown at step 1, values float32
Top score: 0.44950, z-score: 1.69586 (avg: 0.4453, stdev: 0.0025)
> select #6.1
1 model selected
> select #2
8792 atoms, 8980 bonds, 1164 residues, 1 model selected
> ~select #2
Nothing selected
> show #2 models
> hide #3 models
Simulating map res 8.000, grid 2.000
> molmap #2 8.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false
Opened AccM-Dimer-CTDomain map 8 as #9, grid size 59,66,84, pixel 2, shown at
level 0.102, step 1, values float32
Please select a region to fit to
> select #6.1
1 model selected
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened_masked
as #10, grid size 320,320,320, pixel 1.03, shown at step 1, values float32
Top score: 0.64908, z-score: 3.00742 (avg: 0.6482, stdev: 0.0003)
> show #3 models
> hide #3 models
> show #1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select clear
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!7 models
> hide #6.2 models
> show #6.2 models
> hide #!7 models
> hide #2 models
> select #6.2
1 model selected
> select #6
3 models selected
> ~select #6
Nothing selected
> show #3 models
> hide #1 models
Saving 1 regions to mrc file...
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened_region_BC-BCCP-Domain.mrc as #10, grid size 91,107,92, pixel 1.03,
shown at step 1, values float32
Wrote cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened_region_BC-BCCP-Domain.mrc
Saving 1 regions to mrc file...
Opened cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened_region_CT-Domain.mrc as #11, grid size 84,92,88, pixel 1.03, shown
at step 1, values float32
Wrote cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened_region_CT-Domain.mrc
> volume #11 level 0.4497
> volume #11 level 0.4532
> hide #3 models
> hide #!6 models
> select #6
3 models selected
> ~select #6
Nothing selected
> volume #10 level 0.4462
> show #2 models
> volume #10 level 0.2313
> volume #11 level 0.1996
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!7 models
> hide #!7 models
> show #!6 models
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> BothModels-Rigid-FitTOsegment-trial.cxs"
> hide #!10 models
> hide #!11 models
> show #!7 models
> hide #!7 models
> show #1 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!6 models
> show #3 models
> hide #2 models
> show #2 models
> hide #1 models
> hide #3 models
> show #!5 models
> show #!4 models
> show #!6 models
> hide #!6 models
> show #3 models
> hide #3 models
> show #1 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> hide #!4 models
> hide #!5 models
> hide #2 models
> hide #1 models
> show #!11 models
> show #!10 models
> ui tool show "Fit in Map"
Window position QRect(1079,904 841x136) outside any known screen, using
primary screen
> show #1 models
> hide #!10 models
> show #!4 models
> hide #!11 models
> select #1
9482 atoms, 9642 bonds, 1244 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.44612,-0.20106,-0.87209,-3.9567,0.11691,-0.97918,0.16594,33.261,-0.8873,-0.027927,0.46034,-56.761
> view matrix models
> #1,-0.39495,-0.47631,-0.78559,-6.8626,0.91789,-0.2406,-0.31558,41.038,-0.038701,-0.84572,0.53223,-65.409
> view matrix models
> #1,-0.015756,-0.6852,-0.72819,-9.0556,0.75062,0.47301,-0.46133,48.589,0.66054,-0.55386,0.50687,-62.281
> view matrix models
> #1,0.12407,-0.18324,-0.97521,-3.768,0.75919,0.65037,-0.025613,50.581,0.63894,-0.73719,0.2198,-64.301
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.12407,-0.18324,-0.97521,-8.1933,0.75919,0.65037,-0.025613,32.691,0.63894,-0.73719,0.2198,-50.907
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.41216,-0.38861,-0.82408,-10.33,0.63956,0.76759,-0.042098,33.929,0.64892,-0.5097,0.56491,-48.404
> view matrix models
> #1,0.60797,-0.29471,-0.73723,-9.3022,0.69219,0.65158,0.31035,32.782,0.38891,-0.69899,0.60014,-50.42
> view matrix models
> #1,0.83375,-0.50055,-0.23306,-11.362,0.55145,0.77603,0.30606,34.099,0.027667,-0.3837,0.92304,-47.003
> view matrix models
> #1,0.79859,-0.44317,-0.40725,-10.795,0.58505,0.73041,0.35243,33.626,0.14128,-0.51971,0.84258,-48.465
> view matrix models
> #1,0.87514,-0.26291,-0.4062,-8.8733,0.41087,0.84717,0.33689,34.857,0.25555,-0.46172,0.84941,-47.841
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.87514,-0.26291,-0.4062,-12.503,0.41087,0.84717,0.33689,41.351,0.25555,-0.46172,0.84941,-52.993
Fit molecule AccM-Dimer-BCDomain (#1) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4) using
9482 atoms
average map value = 0.2262, steps = 112
shifted from previous position = 6.23
rotated from previous position = 10 degrees
atoms outside contour = 7489, contour level = 0.44848
Position of AccM-Dimer-BCDomain (#1) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4)
coordinates:
Matrix rotation and translation
0.34477340 -0.02662398 0.93830830 158.71992775
-0.91685681 0.20476659 0.34270137 177.00680542
-0.20125827 -0.97844867 0.04618770 115.89998308
Axis -0.67449840 0.58179299 -0.45449843
Axis point 0.00000000 211.37266887 -122.36237401
Rotation angle (degrees) 101.66190345
Shift along axis -56.75138003
> ~select #1
Nothing selected
> show #2 models
> show #3 models
> hide #3 models
> hide #1 models
> hide #2 models
> show #3 models
> select #3
9890 atoms, 10058 bonds, 1266 residues, 1 model selected
> view matrix models
> #3,0.10429,0.080884,-0.99125,3.4448,0.61509,0.77797,0.12819,-5.3919,0.78153,-0.62307,0.031384,-24.927
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.11641,-0.37752,-0.91865,5.9768,0.49267,0.82508,-0.27664,-5.7316,0.8624,-0.42039,0.28204,-25.99
> view matrix models
> #3,0.053096,-0.40375,-0.91333,6.0527,0.46411,0.81981,-0.33542,-5.7257,0.88418,-0.40608,0.23091,-26.039
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.053096,-0.40375,-0.91333,2.0123,0.46411,0.81981,-0.33542,1.5647,0.88418,-0.40608,0.23091,-33.773
> view matrix models
> #3,0.053096,-0.40375,-0.91333,-2.4416,0.46411,0.81981,-0.33542,0.91737,0.88418,-0.40608,0.23091,-35.272
> view matrix models
> #3,0.053096,-0.40375,-0.91333,0.53789,0.46411,0.81981,-0.33542,-4.699,0.88418,-0.40608,0.23091,-30.312
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.025208,-0.44662,-0.89437,0.74196,0.40306,0.82325,-0.39974,-4.7754,0.91483,-0.35041,0.20077,-30.582
> view matrix models
> #3,-0.50055,-0.38774,-0.77402,-0.16287,0.56547,0.53056,-0.63147,-2.9571,0.65551,-0.75376,-0.046319,-28.605
> view matrix models
> #3,-0.40334,-0.45807,-0.79214,0.33177,0.52772,0.59077,-0.61033,-3.3324,0.74755,-0.6642,0.0034547,-29.006
> view matrix models
> #3,-0.40054,-0.36005,-0.84257,-0.1994,0.51705,0.67035,-0.53225,-3.7927,0.75646,-0.64884,-0.082332,-29.071
> view matrix models
> #3,-0.32814,-0.34402,-0.87976,-0.20535,0.56306,0.67657,-0.47457,-3.785,0.75848,-0.65108,-0.028307,-29.063
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.32814,-0.34402,-0.87976,0.72826,0.56306,0.67657,-0.47457,6.7377,0.75848,-0.65108,-0.028307,-27.698
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.16404,-0.26929,-0.94899,0.50123,0.63053,0.71122,-0.31081,6.5982,0.75864,-0.64934,0.053128,-27.718
> view matrix models
> #3,-0.22145,-0.23543,-0.94633,0.25244,0.80474,0.50397,-0.31369,7.9288,0.55077,-0.83102,0.077856,-26.943
> view matrix models
> #3,-0.27827,-0.17449,-0.94452,-0.14492,0.87717,0.35447,-0.32391,8.8324,0.39133,-0.91864,0.054416,-26.628
> view matrix models
> #3,0.054276,-0.31874,-0.94629,1.0081,0.99222,0.12352,0.015307,10.187,0.112,-0.93976,0.32297,-26.846
> view matrix models
> #3,-0.18862,-0.18777,-0.96393,0.02713,0.89529,0.37049,-0.24736,8.7538,0.40358,-0.90966,0.09823,-26.67
> view matrix models
> #3,-0.19871,-0.29652,-0.93413,0.61225,0.87599,0.37368,-0.30496,8.7228,0.43949,-0.87889,0.1855,-26.812
> view matrix models
> #3,-0.20227,-0.35482,-0.91279,0.92726,0.8649,0.3725,-0.33645,8.7214,0.4594,-0.85752,0.23154,-26.914
> view matrix models
> #3,-0.1957,-0.38046,-0.90386,1.0746,0.9258,0.23229,-0.29823,9.5553,0.32341,-0.89515,0.30677,-26.862
> view matrix models
> #3,-0.062819,-0.41202,-0.90901,1.392,0.94106,0.27885,-0.19142,9.3013,0.33235,-0.86746,0.37022,-27.014
> view matrix models
> #3,-0.2527,-0.37487,-0.89197,0.98101,0.94219,0.11432,-0.31498,10.226,0.22005,-0.92,0.32431,-26.839
> view matrix models
> #3,-0.17028,-0.16041,-0.97225,-0.10303,0.97603,0.10828,-0.1888,10.279,0.13556,-0.98109,0.13813,-26.569
> view matrix models
> #3,-0.060039,-0.076374,-0.99527,-0.44516,0.79776,0.59563,-0.093831,7.3877,0.59998,-0.79962,0.025167,-27.056
> view matrix models
> #3,-0.071569,-0.10429,-0.99197,-0.30402,0.88454,0.45297,-0.11144,8.27,0.46095,-0.88541,0.059827,-26.737
> view matrix models
> #3,-0.077661,-0.31415,-0.94619,0.84106,0.85859,0.46132,-0.22364,8.2104,0.50675,-0.82975,0.2339,-27.017
> view matrix models
> #3,-0.077526,-0.35328,-0.9323,1.0553,0.85334,0.46004,-0.24529,8.2146,0.51555,-0.81459,0.2658,-27.095
> view matrix models
> #3,-0.075638,-0.4399,-0.89486,1.5302,0.84124,0.45366,-0.29412,8.243,0.53534,-0.77504,0.33575,-27.301
> view matrix models
> #3,-0.019729,-0.45391,-0.89083,1.6671,0.88505,0.40654,-0.22675,8.5414,0.46508,-0.7929,0.39371,-27.285
> view matrix models
> #3,-0.0084738,-0.29857,-0.95435,0.83049,0.89918,0.41529,-0.13791,8.4969,0.43751,-0.8593,0.26495,-26.932
Fit molecule AccM-Dimer-BCCPDomain (#3) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4) using
9890 atoms
average map value = 0.1384, steps = 144
shifted from previous position = 11
rotated from previous position = 15 degrees
atoms outside contour = 8611, contour level = 0.44848
Position of AccM-Dimer-BCCPDomain (#3) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4)
coordinates:
Matrix rotation and translation
0.87885544 -0.41606913 0.23345148 155.84070071
-0.20112546 0.12060704 0.97211239 168.67765511
-0.43262185 -0.90129929 0.02231406 148.92350657
Axis -0.93676137 0.33305641 0.10747821
Axis point 0.00000000 196.68145282 -20.87932214
Rotation angle (degrees) 89.37613576
Shift along axis -73.80034336
> ui mousemode right select
> select clear
> show #1 models
> hide #1 models
> ui mousemode right pivot
> select #3
9890 atoms, 10058 bonds, 1266 residues, 1 model selected
> ~select #3
Nothing selected
> select #1
9482 atoms, 9642 bonds, 1244 residues, 1 model selected
> select #3
9890 atoms, 10058 bonds, 1266 residues, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.05123,-0.17215,-0.98374,4.8588,0.82031,0.55458,-0.13977,12.333,0.56963,-0.81413,0.1128,-36.74
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.05123,-0.17215,-0.98374,4.2599,0.82031,0.55458,-0.13977,8.7705,0.56963,-0.81413,0.1128,-33.562
> view matrix models
> #3,-0.05123,-0.17215,-0.98374,3.525,0.82031,0.55458,-0.13977,7.898,0.56963,-0.81413,0.1128,-33.02
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.084634,-0.31869,-0.94407,4.2922,0.83772,0.49025,-0.24059,8.2844,0.5395,-0.81123,0.22548,-33.082
> view matrix models
> #3,-0.038875,-0.39393,-0.91832,4.7531,0.86862,0.44098,-0.22594,8.5875,0.49396,-0.80645,0.32503,-33.17
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.038875,-0.39393,-0.91832,4.0116,0.86862,0.44098,-0.22594,10.192,0.49396,-0.80645,0.32503,-28.252
Fit molecule AccM-Dimer-BCCPDomain (#3) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4) using
9890 atoms
average map value = 0.1599, steps = 304
shifted from previous position = 17.8
rotated from previous position = 35.2 degrees
atoms outside contour = 8312, contour level = 0.44848
Position of AccM-Dimer-BCCPDomain (#3) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4)
coordinates:
Matrix rotation and translation
0.93735231 -0.16985108 0.30417308 151.78665852
-0.32359166 -0.10100855 0.94078994 164.84453936
-0.12907011 -0.98027949 -0.14964299 140.74858748
Axis -0.97254148 0.21932938 -0.07783117
Axis point 0.00000000 157.14379656 -19.85329876
Rotation angle (degrees) 99.01248099
Shift along axis -122.41819853
> open "/Volumes/MEMO/Grad School/Side-ACC/AlphaFold-Cosmic/FL-
> Dimer/output_dir_prtn_adRlWfaz-acc-rhoddimer_unrelaxed_model_1_multimer.pdb"
Chain information for output_dir_prtn_adRlWfaz-acc-
rhoddimer_unrelaxed_model_1_multimer.pdb #12
---
Chain | Description
B C | No description available
> hide #3 models
> hide #!4 models
> select #12 /B,C :1-623,1257-1828
18134 atoms, 18474 bonds, 2390 residues, 1 model selected
> cartoon hide sel
> show #3 models
> hide #3 models
> hide #12 models
> show #!4 models
> show #3 models
> select #3
9890 atoms, 10058 bonds, 1266 residues, 1 model selected
> hide #!4 models
> show #12 models
> hide #12 models
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.041072,-0.07894,-0.99603,9.3334,0.094432,0.99272,-0.074783,16.231,0.99468,-0.090986,0.048227,-46.408
> view matrix models
> #3,0.13212,-0.17362,-0.97591,9.9509,-0.49562,0.84106,-0.21673,16.452,0.85843,0.51231,0.025069,-49.879
> view matrix models
> #3,0.39225,-0.15508,-0.90669,10.119,-0.91985,-0.06979,-0.386,21.041,-0.0034156,0.98543,-0.17003,-53.39
> view matrix models
> #3,0.31903,-0.050529,-0.9464,9.469,-0.91684,-0.26938,-0.29469,22.133,-0.24005,0.96171,-0.13227,-53.518
> view matrix models
> #3,0.17495,-0.33537,-0.9257,10.883,-0.95354,-0.29191,-0.074457,22.19,-0.24525,0.89572,-0.37086,-53.129
> view matrix models
> #3,-0.048572,-0.20262,-0.97805,9.917,-0.82596,-0.54246,0.1534,23.68,-0.56164,0.81528,-0.141,-53.054
> view matrix models
> #3,-0.017034,-0.096741,-0.99516,9.3691,-0.50025,-0.86095,0.092257,25.794,-0.86571,0.4994,-0.033729,-51.653
> view matrix models
> #3,0.015929,0.37762,-0.92582,6.7794,0.36911,-0.86276,-0.34555,26.794,-0.92925,-0.33622,-0.15313,-47.097
> view matrix models
> #3,-0.092775,-0.032973,-0.99514,8.936,0.3675,-0.93002,-0.0034461,27.12,-0.92538,-0.36603,0.0984,-46.96
> view matrix models
> #3,0.38135,-0.17298,-0.9081,10.206,0.41462,-0.84599,0.33526,26.664,-0.82623,-0.50437,-0.2509,-46.046
> view matrix models
> #3,0.37797,0.6116,-0.69505,5.8484,0.76102,-0.63278,-0.14296,25.921,-0.52724,-0.47491,-0.70461,-45.83
> view matrix models
> #3,0.47276,0.30417,-0.82703,7.6627,-0.008589,-0.9369,-0.34948,26.798,-0.88115,0.17232,-0.44032,-49.813
> view matrix models
> #3,0.087926,-0.057702,-0.99445,9.2664,-0.053243,-0.99717,0.053152,27.031,-0.9947,0.048275,-0.090749,-49.296
> view matrix models
> #3,0.23025,-0.10276,-0.96769,9.6644,-0.597,-0.80021,-0.057072,25.374,-0.76849,0.59085,-0.2456,-52.026
> view matrix models
> #3,-0.50011,-0.22268,-0.83684,9.5246,-0.49074,-0.72334,0.48575,24.995,-0.71349,0.6536,0.25247,-52.376
> view matrix models
> #3,0.40146,-0.31768,-0.85902,11.02,-0.77268,-0.62104,-0.13143,24.207,-0.49173,0.71651,-0.49479,-52.39
> view matrix models
> #3,0.3994,-0.30323,-0.86518,10.939,-0.73189,-0.67379,-0.10172,24.538,-0.55211,0.67384,-0.49104,-52.22
> view matrix models
> #3,0.16272,-0.29621,-0.94116,10.655,-0.68602,-0.71954,0.10785,24.813,-0.70915,0.62811,-0.32029,-52.158
> show #!4 models
> view matrix models
> #3,0.22621,-0.22902,-0.94677,10.354,-0.46584,-0.87905,0.10133,25.93,-0.85547,0.41812,-0.30554,-51.159
> view matrix models
> #3,0.072582,0.22108,-0.97255,7.7096,-0.50676,-0.8317,-0.22688,25.667,-0.85903,0.50932,0.051671,-51.711
> view matrix models
> #3,0.0065147,0.13175,-0.99126,8.1337,-0.80809,-0.58321,-0.082826,23.954,-0.58903,0.80157,0.10267,-53.039
> view matrix models
> #3,0.012331,0.18497,-0.98267,7.8453,-0.81452,-0.56818,-0.11717,23.869,-0.58,0.80185,0.14366,-53.036
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.012331,0.18497,-0.98267,4.4188,-0.81452,-0.56818,-0.11717,19.725,-0.58,0.80185,0.14366,-38.274
> view matrix models
> #3,0.012331,0.18497,-0.98267,-5.1649,-0.81452,-0.56818,-0.11717,11.074,-0.58,0.80185,0.14366,-31.932
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.50117,0.2616,-0.82486,-6.1592,-0.49723,-0.8672,0.02708,13.045,-0.70824,0.42372,0.56468,-30.037
> view matrix models
> #3,-0.59741,0.24585,-0.76332,-6.1836,-0.49242,-0.86373,0.10719,13.021,-0.63295,0.43991,0.63706,-30.055
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.59741,0.24585,-0.76332,-9.6656,-0.49242,-0.86373,0.10719,21.062,-0.63295,0.43991,0.63706,-22.741
Fit molecule AccM-Dimer-BCCPDomain (#3) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4) using
9890 atoms
average map value = 0.1234, steps = 240
shifted from previous position = 19.3
rotated from previous position = 15.4 degrees
atoms outside contour = 8712, contour level = 0.44848
Position of AccM-Dimer-BCCPDomain (#3) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4)
coordinates:
Matrix rotation and translation
-0.81826820 -0.04405206 0.57314621 182.65328389
0.56993580 -0.19209118 0.79892063 192.67349440
0.07490223 0.98038788 0.18228895 137.21258972
Axis 0.22368302 0.61415332 0.75682337
Axis point 66.69106191 57.99925994 0.00000000
Rotation angle (degrees) 156.06908401
Shift along axis 263.03319808
> view matrix models
> #3,-0.36526,0.25414,-0.89555,-1.6863,-0.56309,-0.82638,-0.0048442,25.636,-0.74129,0.50251,0.44494,-35.816
> view matrix models
> #3,-0.36526,0.25414,-0.89555,-6.0813,-0.56309,-0.82638,-0.0048442,24.544,-0.74129,0.50251,0.44494,-34.997
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.38874,0.44549,-0.80649,-7.1732,-0.60464,-0.78382,-0.14152,24.282,-0.69519,0.43262,0.57406,-34.579
> view matrix models
> #3,-0.36686,0.26487,-0.89177,-6.1427,-0.56522,-0.82485,-0.012473,24.534,-0.73888,0.49947,0.45231,-34.979
> view matrix models
> #3,-0.14102,0.31745,-0.93773,-6.1842,-0.52331,-0.82795,-0.20159,24.62,-0.84039,0.4623,0.28288,-34.861
> view matrix models
> #3,0.098706,0.40386,-0.90948,-6.4069,-0.56717,-0.72814,-0.38489,24.046,-0.81766,0.55382,0.15719,-35.326
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.098706,0.40386,-0.90948,-1.4068,-0.56717,-0.72814,-0.38489,13.375,-0.81766,0.55382,0.15719,-24.98
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.21356,0.41602,-0.88392,-1.8125,-0.65778,-0.7302,-0.18475,13.264,-0.7223,0.54197,0.42959,-24.847
> view matrix models
> #3,0.14427,0.39407,-0.90768,-1.3041,-0.54217,-0.73587,-0.40566,13.447,-0.82779,0.55064,0.10749,-24.967
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.14427,0.39407,-0.90768,6.5394,-0.54217,-0.73587,-0.40566,15.573,-0.82779,0.55064,0.10749,-36.363
Fit molecule AccM-Dimer-BCCPDomain (#3) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4) using
9890 atoms
average map value = 0.1427, steps = 492
shifted from previous position = 18.5
rotated from previous position = 38.6 degrees
atoms outside contour = 8551, contour level = 0.44848
Position of AccM-Dimer-BCCPDomain (#3) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4)
coordinates:
Matrix rotation and translation
-0.78639844 0.58727570 0.19153261 150.16930326
0.13670164 -0.13692279 0.98110387 181.32790647
0.60240364 0.79772138 0.02739432 138.75934311
Axis -0.28799388 -0.64525431 -0.70760611
Axis point 48.52998940 18.65050377 0.00000000
Rotation angle (degrees) 161.43506920
Shift along axis -258.43741182
Fit molecule AccM-Dimer-BCCPDomain (#3) to map
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4) using
9890 atoms
average map value = 0.1427, steps = 60
shifted from previous position = 0.0219
rotated from previous position = 0.0174 degrees
atoms outside contour = 8555, contour level = 0.44848
Position of AccM-Dimer-BCCPDomain (#3) relative to
cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc (#4)
coordinates:
Matrix rotation and translation
-0.78640722 0.58728041 0.19148213 150.15910665
0.13684175 -0.13665357 0.98112188 181.33379105
0.60236038 0.79776408 0.02710088 138.74087561
Axis -0.28799954 -0.64536522 -0.70750265
Axis point 48.52172388 18.64304578 0.00000000
Rotation angle (degrees) 161.43803842
Shift along axis -258.43181300
> ui mousemode right select
> select clear
> show #1 models
> show #2 models
> show #12 models
> hide #12 models
> show #12 models
> select #12 /B,C :1-623,1257-1828
18134 atoms, 18474 bonds, 2390 residues, 1 model selected
> cartoon sel
> select clear
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> BothModels-Rigid-Manual-with-pred.cxs"
> ui tool show Matchmaker
> matchmaker #12 to #2
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 AccM-Dimer-CTDomain, chain C (#2) with output_dir_prtn_adRlWfaz-
acc-rhoddimer_unrelaxed_model_1_multimer.pdb, chain C (#12), sequence
alignment score = 7393.7
RMSD between 582 pruned atom pairs is 0.000 angstroms; (across all 582 pairs:
0.000)
> hide #12 models
> hide #!4 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #!4 models
> volume #4 level 0.3964
> volume #4 color #fe6760
> open "/Volumes/MEMO/Grad School/Side-ACC/Comparative
> Models/emd_4342-human6g2d.map"
Opened emd_4342-human6g2d.map as #13, grid size 450,450,450, pixel 1.06, shown
at level 0.00442, step 2, values float32
> hide #!13 models
> show #!13 models
> ui mousemode right "translate selected models"
> select #13
2 models selected
> view matrix models #13,1,0,0,-165.93,0,1,0,-24.618,0,0,1,-136.58
> ui mousemode right "rotate selected models"
> volume #13 step 1
> volume #13 level 0.01074
> volume #13 level 0.01221
> volume #13 level 0.01472
> volume #13 level 0.01663
> view matrix models
> #13,0.70752,-0.35049,-0.61366,112.02,0.40636,0.9122,-0.052488,-89.616,0.57817,-0.21223,0.78783,-180.27
> view matrix models
> #13,-0.18263,0.89309,-0.41115,-20.08,0.93141,0.29107,0.21853,-117.11,0.31484,-0.34303,-0.88499,248.44
> view matrix models
> #13,0.26657,0.65652,0.70563,-292.32,0.92453,0.032728,-0.37971,67.102,-0.27238,0.7536,-0.59825,63.185
> view matrix models
> #13,0.8727,0.35439,-0.33588,-155.16,-0.090586,-0.55844,-0.82458,542.59,-0.47979,0.75004,-0.45524,84.988
> view matrix models
> #13,0.8651,-0.017115,0.50131,-229.63,0.42951,-0.49095,-0.75795,388.72,0.25909,0.87102,-0.41737,-128.41
> view matrix models
> #13,0.90911,0.32605,-0.25926,-172.21,-0.064265,-0.50516,-0.86063,530.48,-0.41158,0.79907,-0.43829,53.345
> view matrix models
> #13,0.83952,0.37685,-0.39141,-141.65,-0.13535,-0.55261,-0.82237,551.4,-0.52621,0.74337,-0.41292,89.242
> view matrix models
> #13,0.85372,0.0036233,-0.52072,-27.98,-0.39985,-0.63603,-0.65999,602.48,-0.33358,0.77166,-0.54154,62.051
> view matrix models
> #13,0.79495,-0.0093712,-0.60661,6.3609,-0.51842,-0.52984,-0.6712,607.04,-0.31512,0.84804,-0.42606,15.919
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.79495,-0.0093712,-0.60661,-75.876,-0.51842,-0.52984,-0.6712,501.36,-0.31512,0.84804,-0.42606,85.327
> view matrix models
> #13,0.79495,-0.0093712,-0.60661,-55.201,-0.51842,-0.52984,-0.6712,390.33,-0.31512,0.84804,-0.42606,-64.52
> view matrix models
> #13,0.79495,-0.0093712,-0.60661,-63.589,-0.51842,-0.52984,-0.6712,378.53,-0.31512,0.84804,-0.42606,-62.31
> view matrix models
> #13,0.79495,-0.0093712,-0.60661,-55.134,-0.51842,-0.52984,-0.6712,377.4,-0.31512,0.84804,-0.42606,-52.289
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.82138,0.1148,-0.55871,-101.36,-0.34816,-0.67498,-0.65053,368.14,-0.4518,0.72885,-0.51444,27.098
> view matrix models
> #13,0.84263,-0.059206,-0.53522,-68.574,-0.39173,-0.74939,-0.53382,373.43,-0.36949,0.65948,-0.65465,52.41
> view matrix models
> #13,0.6783,-0.28574,-0.67695,54.299,-0.73195,-0.34353,-0.58842,366.26,-0.064416,0.89462,-0.44216,-120.27
> view matrix models
> #13,0.30285,-0.10886,-0.9468,154.49,-0.89118,-0.38444,-0.24086,344.87,-0.33776,0.91671,-0.21344,-106.11
> view matrix models
> #13,0.37654,0.029365,-0.92593,98.948,-0.80377,-0.48662,-0.34229,369.25,-0.46063,0.87312,-0.15963,-76.889
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.37654,0.029365,-0.92593,98.364,-0.80377,-0.48662,-0.34229,375.69,-0.46063,0.87312,-0.15963,-86.5
> ui mousemode right "rotate selected models"
> view matrix models
> #13,-0.17016,0.26728,-0.94848,175.12,-0.93011,-0.36147,0.065009,293.93,-0.32547,0.89325,0.31011,-217.43
> view matrix models
> #13,-0.19058,0.18784,-0.96353,202.41,-0.90425,-0.41565,0.097818,294.46,-0.38211,0.88992,0.24907,-190.91
> view matrix models
> #13,0.52857,-0.0382,-0.84803,63.066,-0.81835,-0.2885,-0.49707,361.63,-0.22567,0.95672,-0.18375,-158.17
> view matrix models
> #13,0.94757,0.075427,-0.31053,-171.96,-0.22578,-0.52966,-0.81761,343.21,-0.22615,0.84485,-0.48486,-70.604
> view matrix models
> #13,0.94155,-0.13632,-0.30805,-119.25,-0.32292,-0.62568,-0.71011,368.4,-0.095941,0.76808,-0.63313,-53.302
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.94155,-0.13632,-0.30805,-132.17,-0.32292,-0.62568,-0.71011,359.61,-0.095941,0.76808,-0.63313,-53.874
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.9491,-0.021727,-0.31423,-160.75,-0.26837,-0.57806,-0.7706,347.03,-0.1649,0.81571,-0.55446,-64.77
> view matrix models
> #13,0.9571,-0.031385,-0.28805,-165.52,-0.25661,-0.55348,-0.79235,342.55,-0.13456,0.83227,-0.53779,-79.386
> view matrix models
> #13,0.96777,0.010373,-0.25162,-185.55,-0.1839,-0.65353,-0.73423,338.06,-0.17206,0.75683,-0.63055,-33.48
> ui mousemode right "translate selected models"
> view matrix models
> #13,0.96777,0.010373,-0.25162,-172.5,-0.1839,-0.65353,-0.73423,335.42,-0.17206,0.75683,-0.63055,-25.804
> view matrix models
> #13,0.96777,0.010373,-0.25162,-178.5,-0.1839,-0.65353,-0.73423,335.6,-0.17206,0.75683,-0.63055,-28.772
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.83002,0.15903,-0.53457,-125.5,-0.26399,-0.73228,-0.62775,352.71,-0.49129,0.66217,-0.56583,57.606
> show #1 models
> hide #1 models
> show #!5 models
> ui mousemode right select
> select clear
> color #5 #54fa48 models transparency 0
> hide #!4 models
> volume #13 color grey
> volume #13 color #80808088
> volume #13 color #80808087
> ui tool show "Fit in Map"
Window position QRect(1079,904 841x136) outside any known screen, using
primary screen
> volume #13 level 0.03341
> select #13
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #13,0.82256,0.16846,-0.54315,-124.21,-0.27244,-0.72163,-0.63642,353.96,-0.49916,0.67147,-0.54769,53.401
> view matrix models
> #13,0.83528,0.15239,-0.52829,-126.46,-0.25803,-0.7398,-0.62138,351.77,-0.48552,0.65534,-0.57862,60.585
> view matrix models
> #13,0.79702,0.20068,-0.56964,-120.37,-0.30127,-0.68535,-0.66297,357.61,-0.52344,0.70002,-0.48578,39.209
> view matrix models
> #13,0.76056,0.19308,-0.61989,-99.193,-0.32841,-0.7092,-0.62384,361.69,-0.56008,0.67805,-0.47598,51.291
> view matrix models
> #13,0.79331,0.15609,-0.58847,-104.63,-0.29166,-0.75101,-0.59238,356.46,-0.53441,0.64157,-0.55026,69.689
> view matrix models
> #13,0.85482,0.087948,-0.51142,-118.97,-0.22196,-0.82886,-0.51354,342.15,-0.46906,0.5525,-0.689,104.99
> view matrix models
> #13,0.86016,0.29815,-0.41379,-192.13,-0.015065,-0.79612,-0.60495,303.83,-0.5098,0.52659,-0.68031,119.25
Fit map emd_4342-human6g2d.map in map
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 61379 points
correlation = 0.4732, correlation about mean = 0.238, overlap = 468
steps = 412, shift = 19.3, angle = 24.2 degrees
Position of emd_4342-human6g2d.map (#13) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
0.46597055 -0.08525728 0.88068306 -165.17463112
-0.86018065 0.18951532 0.47346932 164.80213775
-0.20726964 -0.97816928 0.01497189 410.63582936
Axis -0.73587740 0.55151454 -0.39283096
Axis point 0.00000000 268.32840066 170.80743239
Rotation angle (degrees) 99.48393883
Shift along axis 51.12858413
> ui mousemode right select
> select clear
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> ForFigures-140222.cxs"
> show #2 models
> show #1 models
> show #3 models
> hide #2 models
> hide #3 models
> show #12 models
> hide #1 models
> hide #12 models
> hide #!13 models
> hide #!5 models
> show #!4 models
> show #!13 models
> hide #!13 models
> hide #!4 models
> show #!13 models
> show #12 models
> hide #12 models
> show #!4 models
> hide #!4 models
> show #2 models
> show #3 models
> show #1 models
> show #12 models
> hide #12 models
> hide #!13 models
> hide #3 models
> hide #2 models
> hide #1 models
> show #!4 models
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting full
> save front-accM-dimer-map 3w 3h 900p
Cannot determine format for 'front-accM-dimer-map'
> save front-accM-dimer-map.TIFF pixelSize 0.4
> save front-accM-dimer-map.TIFF
> save front-accM-dimer-map.TIFF pixelSize 1
> save front-accM-dimer-map.TIFF pixelSize 0.1
> save front-accM-dimer-map.TIFF pixelSize 0.1 transparentBackground true
> turn y90
Expected an axis vector or a keyword
> turn y 90
> save front-accM-dimer-map-y90.TIFF pixelSize 0.1 transparentBackground true
> turn y 90
> save back-accM-dimer-map.TIFF pixelSize 0.1 transparentBackground true
> turn y 90
> save back-accM-dimer-map-y90.TIFF pixelSize 0.1 transparentBackground true
> turn y 90
> turn x 90
> save top-accM-dimer-map.TIFF pixelSize 0.1 transparentBackground true
> turn x 90
[Repeated 1 time(s)]
> save bottom-accM-dimer-map.TIFF pixelSize 0.1 transparentBackground true
> turn x 90
> show #!13 models
> hide #!4 models
> volume #13 level 0.0262
> volume #13 level 0.02075
> volume #13 level 0.01987
> volume #13 level 0.01869
> volume #13 level 0.01324
> volume #13 level 0.01486
> save Human-CitBound-Map.TIFF pixelSize 0.1 transparentBackground true
> show #!4 models
> undo
> ui tool show "Side View"
> save Human-CitBound-Map.TIFF pixelSize 0.1 transparentBackground true
> show #!4 models
> save Human-CitBound-Map-Imposed-AccM-Dimer.TIFF pixelSize 0.1
> transparentBackground true
> show #12 models
> hide #!4 models
> save Human-CitBound-Map-Imposed-AccM-Dimer-AF2.TIFF pixelSize 0.1
> transparentBackground true
> show #!4 models
> hide #!13 models
> save Imposed-AccM-Dimer-AF2.TIFF pixelSize 0.1 transparentBackground true
> hide #!4 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!4 models
> save Imposed-AccM-Dimer-AF2.TIFF pixelSize 0.1 transparentBackground true
> hide #!4 models
> show #!13 models
> save Human-CitBound-Map-Imposed-AccM-Dimer-AF2.TIFF pixelSize 0.1
> transparentBackground true
> show #!4 models
> hide #12 models
> save Human-CitBound-Map-Imposed-AccM-Dimer.TIFF pixelSize 0.1
> transparentBackground true
> hide #!13 models
> show #12 models
> hide #!4 models
> select #12 :1-622
9482 atoms, 9642 bonds, 1244 residues, 1 model selected
> color sel hot pink
> select #12 :623-1245
9732 atoms, 9892 bonds, 1246 residues, 1 model selected
> color sel orange
> select #12 :1256-1828
8654 atoms, 8834 bonds, 1146 residues, 1 model selected
> color sel forest green
> select #12
28024 atoms, 28536 bonds, 3656 residues, 1 model selected
> ~select #12
Nothing selected
> save AccM-Dimer-AF2-labelled.TIFF pixelSize 0.1 transparentBackground true
> show #!13 models
> hide #!13 models
> save AccM-Dimer-AF2-labelled.TIFF pixelSize 0.1 transparentBackground true
> show #!13 models
> save Human-CitBound-Map-Imposed-AccM-Dimer-AF2.TIFF pixelSize 0.1
> transparentBackground true
> hide #!13 models
> show #!4 models
> save Imposed-AccM-Dimer-AF2.TIFF pixelSize 0.1 transparentBackground true
> color #4 #fe676080 models
[Repeated 1 time(s)]
> save Imposed-AccM-Dimer-AF2-transparencyON.TIFF pixelSize 0.1
> transparentBackground true
> hide #12 models
> undo
> save Imposed-AccM-Dimer-AF2-transparencyON.TIFF pixelSize 0.1
> transparentBackground true
> hide #12 models
> show #2 models
> show #3 models
> show #1 models
> save Imposed-and-FITTED-AccM-Dimer-AF2-transparencyON.TIFF pixelSize 0.1
> transparentBackground true
> hide #3 models
> hide #2 models
> hide #1 models
> show #2 models
> save Imposed-and-FITTED-CT-AccM-Dimer-AF2-transparencyON.TIFF pixelSize 0.1
> transparentBackground true
> hide #2 models
> show #1 models
> save Imposed-and-FITTED-BC-AccM-Dimer-AF2-transparencyON.TIFF pixelSize 0.1
> transparentBackground true
> hide #1 models
> show #3 models
> save Imposed-and-FITTED-BCCP-AccM-Dimer-AF2-transparencyON.TIFF pixelSize
> 0.1 transparentBackground true
> hide #3 models
> show #1 models
> show #2 models
> show #3 models
> save Imposed-and-FITTED-ALL-AccM-Dimer-AF2-transparencyON.TIFF pixelSize 0.1
> transparentBackground true
> turn y 90
[Repeated 3 time(s)]
> hide #3 models
> hide #2 models
> hide #1 models
> show #2 models
> save Imposed-and-FITTED-CT-Focused-AccM-Dimer-AF2-transparencyON.TIFF
> pixelSize 0.1 transparentBackground true
> turn x 90
> save TOP-Imposed-and-FITTED-CT-Focused-AccM-Dimer-AF2-transparencyON.TIFF
> pixelSize 0.1 transparentBackground true
> hide #2 models
> show #3 models
> turn x 90
[Repeated 2 time(s)]
> save FRONT-Imposed-and-FITTED-BCCP-Focused-AccM-Dimer-
> AF2-transparencyON.TIFF pixelSize 0.1 transparentBackground true
> turn y 90
[Repeated 3 time(s)]
> turn x 90
> save TOP-Imposed-and-FITTED-BCCP-Focused-AccM-Dimer-AF2-transparencyON.TIFF
> pixelSize 0.1 transparentBackground true
> undo
> hide #3 models
> show #1 models
> save FRONT-Imposed-and-FITTED-BC-Focused-AccM-Dimer-AF2-transparencyON.TIFF
> pixelSize 0.1 transparentBackground true
> turn y 90
> save SIDE-Imposed-and-FITTED-BC-Focused-AccM-Dimer-AF2-transparencyON.TIFF
> pixelSize 0.1 transparentBackground true
> turn y 90
[Repeated 2 time(s)]
> turn x 90
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> ForFigures-140222-fig1.cxs"
> view
> hide #1 models
> show #3 models
> hide #3 models
> show #!5 models
> ui tool show "Fit in Map"
Back buffer dpr of 1 doesn't match <_NSViewBackingLayer: 0x60003ad6d680>
contents scale of 2 - updating layer to match.
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x60003ad6d680>
contents scale of 1 - updating layer to match.
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 149099 points
correlation = 0.3732, correlation about mean = 0.007213, overlap = 9796
steps = 212, shift = 5.78, angle = 12.3 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.89907865 0.27921894 -0.33718594 280.03054538
0.12967824 0.90549698 0.40405293 -148.04980433
0.41814009 0.31954968 -0.85032162 152.13844832
Axis -0.10909135 -0.97510495 -0.19305289
Axis point 130.89183037 0.00000000 120.61244154
Rotation angle (degrees) 157.21308817
Shift along axis 84.44441996
Fit map cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-sharpened.mrc in
map cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc
using 149099 points
correlation = 0.3732, correlation about mean = 0.00721, overlap = 9795
steps = 80, shift = 0.0293, angle = 0.0259 degrees
Position of cryosparc_P23_J674_002_volume_map_half_A_deepEMhancer-
sharpened.mrc (#4) relative to
cryosparc_P23_J668_007_volume_map_half_A_deepEMhancer-sharpened-flipz.mrc (#5)
coordinates:
Matrix rotation and translation
-0.89914592 0.27930955 -0.33693142 279.96885889
0.12968769 0.90533383 0.40441530 -148.10479418
0.41799248 0.31993251 -0.85025024 152.09035588
Axis -0.10911828 -0.97506247 -0.19325213
Axis point 130.87766034 0.00000000 120.58921554
Rotation angle (degrees) 157.22485397
Shift along axis 84.46991949
> select #5
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right select
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.35292,-0.93323,0.067339,211.14,0.38844,-0.21161,-0.89685,126.13,0.85122,-0.29035,0.43718,-182.42
> view matrix models
> #4,-0.34784,-0.93572,0.058675,212.19,0.38861,-0.20085,-0.89925,124.65,0.85322,-0.28999,0.43349,-182.2
> view matrix models
> #4,-0.30019,-0.95124,0.07095,205.1,0.43162,-0.20179,-0.8792,114.5,0.85064,-0.2333,0.47115,-197.82
> view matrix models
> #4,-0.29831,-0.95232,0.06402,206.13,0.42633,-0.19295,-0.88375,114.59,0.85397,-0.23634,0.46356,-196.57
> ui mousemode right select
> select clear
> color #5 #62ac4e models transparency 0
> color #5 #365e2b models transparency 0
> color #5 #6ec158 models transparency 0
> color #5 #5ea54b models transparency 0
> color #5 #67b653 models transparency 0
> color #4 #fe6760b4 models
> color #4 #fe6760b3 models
> volume #5 level 0.5502
> volume #5 level 0.5931
> volume #4 level 0.3855
> show #2 models
> hide #2 models
> volume #4 level 0.481
> volume #5 level 0.6504
Window position QRect(-1259,-101 654x459) outside any known screen, using
primary screen
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> ForFigures-160222-fig2.cxs"
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting flat
[Repeated 2 time(s)]
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> save Bean-Superimposed-FL-AccM-Dimer-8A-FULL.TIFF pixelSize 0.1
> transparentBackground true
> hide #!4 models
> ui tool show "Side View"
> volume #5 level 0.6476
> show #!4 models
> hide #!4 models
> show #!4 models
> save Bean-Superimposed-FL-AccM-Dimer-8A-SIDE.TIFF pixelSize 0.1
> transparentBackground true
> turn Y 90
> hide #!4 models
> show #!4 models
> save Bean-Superimposed-FL-AccM-Dimer-8A-SIDEy90.TIFF pixelSize 0.1
> transparentBackground true
> turn Y 90
[Repeated 1 time(s)]
> hide #!4 models
> turn Y 90
> show #!4 models
> turn x 90
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save Bean-Superimposed-FL-AccM-Dimer-8A-TOP.TIFF pixelSize 0.1
> transparentBackground true
> hide #!4 models
> save Bean-4A-TOP.TIFF pixelSize 0.1 transparentBackground true
> turn x 90
[Repeated 1 time(s)]
> save Bean-4A-BOTTOM.TIFF pixelSize 0.1 transparentBackground true
> show #!4 models
> undo
> show #!4 models
> hide #!4 models
> show #!4 models
> save Bean-4A-Superimposed-FL-AccM-Dimer-8A-BOTTOM.TIFF pixelSize 0.1
> transparentBackground true
> hide #!4 models
> save Bean-4A-BOTTOM.TIFF pixelSize 0.1 transparentBackground true
> turn x 90
[Repeated 1 time(s)]
> save Bean-4A-TOP.TIFF pixelSize 0.1 transparentBackground true
> show #!4 models
> save Bean-4A-Superimposed-FL-AccM-Dimer-8A-TOP.TIFF pixelSize 0.1
> transparentBackground true
> turn x 90
[Repeated 2 time(s)]
> hide #!4 models
> show #!4 models
> save Bean-Superimposed-FL-AccM-Dimer-8A-SIDE.TIFF pixelSize 0.1
> transparentBackground true
> hide #!4 models
> save Bean-4A-SIDE.TIFF pixelSize 0.1 transparentBackground true
> turn Y 90
> show #!4 models
> save Bean-Superimposed-FL-AccM-Dimer-8A-SIDEy90.TIFF pixelSize 0.1
> transparentBackground true
> hide #!4 models
> save Bean-4A-SIDEy90.TIFF pixelSize 0.1 transparentBackground true
Window position QRect(-1259,-101 654x459) outside any known screen, using
primary screen
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> ForFigures-160222-fig2.cxs"
Window position QRect(1091,899 817x96) outside any known screen, using primary
screen
> ui tool show "Side View"
> select clear
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Building/Side-
> ACC_fit_loops_151_real_space_refined_001-coot-0211-ChainA-1425.pdb"
Chain information for Side-
ACC_fit_loops_151_real_space_refined_001-coot-0211-ChainA-1425.pdb #14
---
Chain | Description
A | No description available
B | No description available
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Building/placed_model_real_space_refined-
> coot-1-dimer-rd10-unknot.pdb"
Chain information for placed_model_real_space_refined-coot-1-dimer-
rd10-unknot.pdb #15
---
Chain | Description
A B | No description available
> color #15 #8ae388 transparency 0
> color #15 #e3cc18 transparency 0
> color #14 #83ed59 transparency 0
> color #14 #ed323c transparency 0
> color #14 #ed2b21 transparency 0
> view
> select clear
> select #14
10384 atoms, 10486 bonds, 13 pseudobonds, 727 residues, 2 models selected
> select #15
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> select #14
10384 atoms, 10486 bonds, 13 pseudobonds, 727 residues, 2 models selected
> select #15
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> select #14
10384 atoms, 10486 bonds, 13 pseudobonds, 727 residues, 2 models selected
> select #15
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> select clear
[Repeated 13 time(s)]
> select #15
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #15,1,0,0,8.5871,0,1,0,-65.136,0,0,1,-263.53
> view matrix models #15,1,0,0,-29.606,0,1,0,-20.923,0,0,1,-12.195
> view matrix models #15,1,0,0,7.1572,0,1,0,-39.029,0,0,1,-162.41
> ui mousemode right "rotate selected models"
> view matrix models
> #15,0.82108,0.20131,-0.53414,63.294,0.40374,0.45669,0.79274,-111.72,0.40352,-0.86655,0.2937,-38.971
> view matrix models
> #15,0.51991,0.36557,-0.77205,102.98,0.82403,0.023515,0.56605,-85.672,0.22509,-0.93049,-0.28901,48.93
> view matrix models
> #15,0.35648,0.41617,-0.83649,121.3,0.92876,-0.060465,0.36572,-65.856,0.10162,-0.90727,-0.40808,71.961
> view matrix models
> #15,0.78629,0.34391,-0.51329,50.243,0.53756,0.028754,0.84273,-87.798,0.30458,-0.93856,-0.16226,27.941
> view matrix models
> #15,0.82951,0.33121,-0.44967,40.24,0.45692,0.060506,0.88745,-87.797,0.32114,-0.94162,-0.10115,19.912
> view matrix models
> #15,0.61261,0.61257,-0.49946,39.246,0.42029,0.2827,0.86223,-103.58,0.66937,-0.73813,-0.084271,-37.07
> view matrix models
> #15,0.35193,0.76364,-0.5413,54.777,0.32068,0.44493,0.83618,-106.99,0.87938,-0.46786,-0.088297,-84.627
> view matrix models
> #15,-0.033002,0.80962,-0.58603,93.544,0.12097,0.58527,0.80176,-97.292,0.99211,-0.04443,-0.11725,-135.04
> view matrix models
> #15,-0.16299,0.82505,-0.54104,100.08,0.35059,0.56102,0.7499,-112.15,0.92224,-0.067454,-0.3807,-96.968
> view matrix models
> #15,-0.14691,0.81241,-0.56428,102.27,0.31775,0.57899,0.75087,-110.77,0.93672,-0.068994,-0.3432,-102.36
> view matrix models
> #15,0.017298,0.8103,-0.58576,88.418,0.40925,0.52879,0.74357,-114.1,0.91226,-0.25258,-0.32246,-83.836
> view matrix models
> #15,0.047356,0.84276,-0.53621,76.756,0.37178,0.48337,0.79255,-111.17,0.92711,-0.23688,-0.29043,-90.39
> view matrix models
> #15,0.034791,0.97141,-0.23485,32.224,0.46751,0.19187,0.86291,-99.301,0.8833,-0.13981,-0.44747,-78.549
> view matrix models
> #15,-0.15378,0.96754,-0.20057,47.712,0.36433,0.2442,0.89868,-98.126,0.91848,0.065122,-0.39006,-108.82
> view matrix models
> #15,-0.3444,0.92159,-0.17905,69.004,0.24714,0.27298,0.92973,-92.682,0.90571,0.27595,-0.32178,-136.07
> view matrix models
> #15,-0.60111,0.77976,-0.17505,108.4,0.064801,0.26587,0.96183,-77.254,0.79653,0.56682,-0.21035,-166.4
> view matrix models
> #15,-0.39856,0.65324,-0.64376,152.01,-0.25643,0.59455,0.76207,-56.162,0.88057,0.46881,-0.069455,-180.4
> view matrix models
> #15,-0.23358,0.75336,-0.61473,122.35,-0.13603,0.60068,0.78783,-71.623,0.96278,0.26764,-0.037826,-171.97
> view matrix models
> #15,-0.0086177,0.82129,-0.57045,88.238,0.0081578,0.57051,0.82125,-86.672,0.99993,0.0024236,-0.011616,-152.05
> view matrix models
> #15,0.13716,0.8308,-0.5394,69.324,0.091542,0.53159,0.84204,-93.389,0.98631,-0.16487,-0.0031413,-134.9
> view matrix models
> #15,0.099245,0.80121,-0.5901,81.61,0.17587,0.56957,0.80291,-101.34,0.9794,-0.18346,-0.08438,-123.47
> view matrix models
> #15,0.011978,0.78607,-0.61802,94.897,0.32543,0.58136,0.74573,-111.21,0.94549,-0.21006,-0.24885,-99.451
> ui mousemode right "translate selected models"
> view matrix models
> #15,0.011978,0.78607,-0.61802,-29.624,0.32543,0.58136,0.74573,-171.97,0.94549,-0.21006,-0.24885,-48.554
> ui mousemode right select
> select clear
[Repeated 5 time(s)]
> select #14
10384 atoms, 10486 bonds, 13 pseudobonds, 727 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,1.7042,0,1,0,8.0648,0,0,1,28.604
> view matrix models #14,1,0,0,-11.731,0,1,0,-59.813,0,0,1,-215.69
Window position QRect(1091,860 817x135) outside any known screen, using
primary screen
> view matrix models #14,1,0,0,-13.585,0,1,0,-46.315,0,0,1,-149.41
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.97016,-0.066249,-0.23323,19.746,0.12724,0.95796,0.25716,-81.009,0.20639,-0.27916,0.9378,-135.84
> view matrix models
> #14,0.89342,-0.062617,-0.44483,48.59,0.28321,0.84716,0.44957,-105.12,0.34869,-0.52764,0.7746,-108.66
> view matrix models
> #14,0.62916,0.062697,-0.77475,96.076,0.65854,0.48648,0.57416,-119.33,0.4129,-0.87144,0.26478,-28.878
> view matrix models
> #14,0.34948,0.14094,-0.92628,131.65,0.89286,0.24958,0.37485,-98.822,0.28401,-0.95804,-0.038622,23.53
> view matrix models
> #14,0.8583,0.32833,-0.39436,7.9365,0.31503,0.26949,0.91002,-97.492,0.40506,-0.90531,0.12787,-10.781
> view matrix models
> #14,0.9228,0.37337,0.095032,-52.81,-0.21735,0.30085,0.92857,-49.278,0.31811,-0.87754,0.35878,-28.357
> view matrix models
> #14,0.33253,0.80982,0.48334,-76.874,0.0057045,-0.51422,0.85764,17.008,0.94308,-0.28243,-0.17561,-95.877
> view matrix models
> #14,0.070042,0.99753,-0.0059449,-19.577,0.41851,-0.023975,0.9079,-78.326,0.90551,-0.066079,-0.41915,-88.937
> view matrix models
> #14,0.069384,0.86455,-0.49774,43.81,0.35486,0.44492,0.82227,-110.06,0.93234,-0.23368,-0.27592,-89.463
> view matrix models
> #14,-0.069851,0.86987,-0.48831,56.241,0.23857,0.48987,0.83852,-104.57,0.96861,-0.057926,-0.24175,-114.11
> view matrix models
> #14,-0.062016,0.74256,-0.6669,86.341,0.21365,0.66258,0.71787,-107.04,0.97494,-0.097966,-0.19974,-115.02
> view matrix models
> #14,-0.0071824,0.33083,-0.94366,150.13,0.15774,0.93225,0.32563,-88.46,0.98745,-0.14652,-0.058882,-125.76
> view matrix models
> #14,-0.046546,0.40224,-0.91435,143.95,0.19959,0.90063,0.38604,-95.636,0.97877,-0.16452,-0.1222,-116.65
> view matrix models
> #14,-0.10798,0.57988,-0.80752,121.49,0.28745,0.79578,0.53302,-108.91,0.95169,-0.17456,-0.25261,-99.672
> view matrix models
> #14,-0.10618,0.55016,-0.82828,126.39,0.27931,0.81595,0.50617,-107.38,0.95431,-0.1776,-0.2403,-100.88
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.10618,0.55016,-0.82828,32.125,0.27931,0.81595,0.50617,-178.87,0.95431,-0.1776,-0.2403,-44.698
> hide #15 models
> view matrix models
> #14,-0.10618,0.55016,-0.82828,52.716,0.27931,0.81595,0.50617,-185.39,0.95431,-0.1776,-0.2403,-49.364
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.089506,0.57803,-0.81109,46.516,0.26623,0.79861,0.53976,-185.77,0.95974,-0.16763,-0.22537,-52.422
> view matrix models
> #14,-0.073516,0.62374,-0.77816,37.004,0.25421,0.76622,0.59015,-186.46,0.96435,-0.15444,-0.21489,-55.266
> view matrix models
> #14,-0.065674,0.93456,-0.34968,-38.412,0.27093,0.35398,0.89515,-178.01,0.96036,-0.03595,-0.27644,-60.432
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.065674,0.93456,-0.34968,-35.156,0.27093,0.35398,0.89515,-174.36,0.96036,-0.03595,-0.27644,-58.986
> hide #!14 models
> show #15 models
> select #15
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> select #14
10384 atoms, 10486 bonds, 13 pseudobonds, 727 residues, 2 models selected
> select #15
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> view matrix models
> #15,0.011978,0.78607,-0.61802,6.8576,0.32543,0.58136,0.74573,-194.83,0.94549,-0.21006,-0.24885,-40.387
> view matrix models
> #15,0.011978,0.78607,-0.61802,4.3654,0.32543,0.58136,0.74573,-193.65,0.94549,-0.21006,-0.24885,-40.727
> ui mousemode right "rotate selected models"
> view matrix models
> #15,-0.021161,0.78066,-0.6246,8.937,0.34637,0.59177,0.72789,-194.83,0.93786,-0.20094,-0.28292,-37.151
> view matrix models
> #15,-0.051184,0.78508,-0.61727,10.695,0.30747,0.60045,0.73819,-192.94,0.95018,-0.15201,-0.27212,-44.452
> view matrix models
> #15,-0.0095147,0.82587,-0.56379,-3.3902,0.29214,0.54151,0.7883,-190.99,0.95633,-0.15721,-0.24642,-47.356
> view matrix models
> #15,0.017411,0.68738,-0.72609,25.492,0.24147,0.70181,0.67019,-189.04,0.97025,-0.187,-0.15377,-55.896
> view matrix models
> #15,0.3025,0.88746,-0.34772,-64.342,-0.030175,0.37354,0.92712,-157.16,0.95267,-0.26996,0.13978,-77.926
> view matrix models
> #15,0.15351,0.92419,-0.34972,-52.903,0.07947,0.34122,0.93662,-165.93,0.98495,-0.17157,-0.021065,-73.407
> view matrix models
> #15,0.14063,0.89548,-0.42229,-40.815,0.098869,0.4117,0.90594,-171.56,0.98511,-0.16915,-0.030639,-72.619
> view matrix models
> #15,0.10555,0.86419,-0.49197,-26.568,0.13169,0.47823,0.86831,-177.37,0.98566,-0.15644,-0.063331,-70.372
> view matrix models
> #15,0.039987,0.74559,-0.66521,10.767,0.17984,0.6495,0.73879,-185.15,0.98288,-0.14918,-0.10812,-65.926
> view matrix models
> #15,0.041239,0.75717,-0.65191,8.0317,0.17979,0.6362,0.75029,-185.07,0.98284,-0.14815,-0.1099,-65.83
> view matrix models
> #15,0.0085649,0.74793,-0.66372,13.512,0.20813,0.64788,0.73276,-187.15,0.97806,-0.14441,-0.15011,-61.331
> view matrix models
> #15,-0.03248,0.81899,-0.57289,0.58722,0.21977,0.56502,0.79527,-186.87,0.97501,-0.10007,-0.19834,-60.187
> view matrix models
> #15,-0.080057,0.88919,-0.45048,-15.05,0.23949,0.45585,0.85723,-184.7,0.96759,-0.039258,-0.24945,-59.937
> ui mousemode right "translate selected models"
> view matrix models
> #15,-0.080057,0.88919,-0.45048,-19.194,0.23949,0.45585,0.85723,-180.42,0.96759,-0.039258,-0.24945,-60.588
Window position QRect(-1286,-25 654x459) outside any known screen, using
primary screen
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> ForFigures-160222-fig2-OnlyBeans.cxs"
> show #!7 models
> hide #!7 models
> select #7
2 models selected
> select down
2 models selected
> select down
2 models selected
> close #7-11,13
> close #6
> close #12
> close #15
> close #14
> open #6
'#6' has no suffix
> undo
[Repeated 1 time(s)]
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Building/placed_model_real_space_refined-
> coot-1-dimer-rd10-unknot.pdb"
Chain information for placed_model_real_space_refined-coot-1-dimer-
rd10-unknot.pdb #6
---
Chain | Description
A B | No description available
> open "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Building/Side-
> ACC_fit_loops_151_real_space_refined_001-coot-0211-ChainA-1425.pdb"
Chain information for Side-
ACC_fit_loops_151_real_space_refined_001-coot-0211-ChainA-1425.pdb #7
---
Chain | Description
A | No description available
B | No description available
> color #7 #ed1e15 transparency 0
> color #7 #c11811 transparency 0
> color #6 #dbd22e transparency 0
> color #6 #bbdb28 transparency 0
> color #6 #dbb117 transparency 0
> color #6 #dbce10 transparency 0
> color #6 #dbca0f transparency 0
> hide #!7 models
> hide #6 models
Back buffer dpr of 2 doesn't match <_NSViewBackingLayer: 0x60003b6a8c00>
contents scale of 1 - updating layer to match.
> show #6 models
> select #6
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> view matrix models #6,1,0,0,-63.991,0,1,0,-11.638,0,0,1,-137.39
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.94071,-0.085737,-0.32819,-13.634,0.27265,0.76671,0.58121,-79.092,0.2018,-0.63624,0.74463,-66.078
> view matrix models
> #6,0.82647,-0.15339,-0.54168,27.873,0.52215,0.56861,0.63565,-90.181,0.2105,-0.80818,0.55003,-28.5
> view matrix models
> #6,0.75747,0.039722,-0.65165,27.491,0.65254,-0.014647,0.75761,-58.261,0.020549,-0.9991,-0.037015,73.713
> view matrix models
> #6,0.99857,-0.043697,-0.030686,-56.129,0.01959,-0.23479,0.97185,3.5887,-0.049671,-0.97106,-0.2336,99.412
> view matrix models
> #6,0.89777,-0.23295,0.37382,-71.347,-0.37122,0.056669,0.92682,18.446,-0.23708,-0.97084,-0.035598,96.483
> view matrix models
> #6,0.84941,0.44612,0.28192,-124.33,-0.44429,0.31622,0.83822,9.4951,0.2848,-0.83725,0.46681,-23.928
> view matrix models
> #6,0.54576,0.83693,-0.041133,-97.725,-0.59757,0.42315,0.68107,31.304,0.58741,-0.34712,0.73106,-132.03
> view matrix models
> #6,0.47173,0.82859,-0.30151,-61.039,-0.15103,0.41283,0.8982,-36.023,0.86871,-0.37817,0.31989,-112.11
> view matrix models
> #6,0.10315,0.91377,-0.39293,-22.722,-0.3073,0.40498,0.86114,-15.57,0.94601,0.031923,0.32258,-161.1
> view matrix models
> #6,0.035347,0.96354,-0.26523,-34.873,-0.21054,0.26662,0.94052,-20.09,0.97695,0.022597,0.21229,-151.21
> view matrix models
> #6,0.059797,0.84929,-0.52453,2.4348,-0.1877,0.52566,0.82973,-36.151,0.9804,0.048837,0.19084,-151.84
> view matrix models
> #6,-0.043017,0.88264,-0.46808,3.2111,0.067767,0.47002,0.88005,-61.623,0.99677,0.0061362,-0.080032,-119.61
> view matrix models
> #6,0.14647,0.85441,-0.49852,-9.5825,0.14591,0.47978,0.86517,-68.783,0.97839,-0.19946,-0.054394,-100.03
> view matrix models
> #6,0.19607,0.79551,-0.57334,-0.47826,-0.00013252,0.58471,0.81124,-58.778,0.98059,-0.15899,0.11475,-122.77
> view matrix models
> #6,0.19836,0.80933,-0.55285,-4.3255,-0.0046865,0.56484,0.82519,-57.861,0.98012,-0.16109,0.11583,-122.63
> view matrix models
> #6,0.19104,0.80573,-0.56062,-2.3852,0.013141,0.56899,0.82224,-59.736,0.98149,-0.16445,0.098111,-120.5
> view matrix models
> #6,0.13547,0.81664,-0.56103,2.1229,-0.01017,0.56736,0.82341,-57.37,0.99073,-0.10584,0.085164,-125.87
> view matrix models
> #6,0.13412,0.85671,-0.49805,-8.6278,0.0014887,0.50242,0.86462,-56.55,0.99096,-0.1167,0.066107,-122.72
> view matrix models
> #6,0.12455,0.92911,-0.34821,-31.281,0.058228,0.34349,0.93735,-54.288,0.9905,-0.13703,-0.011317,-112.18
> view matrix models
> #6,0.017562,0.94142,-0.33678,-23.067,0.014222,0.33656,0.94155,-49.657,0.99974,-0.021325,-0.0074785,-125.09
> view matrix models
> #6,-0.16012,0.93415,-0.31894,-6.5297,-0.055821,0.31402,0.94777,-41.083,0.98552,0.16956,0.0018631,-143.76
> view matrix models
> #6,0.041823,0.93974,-0.33932,-25.045,0.024079,0.33857,0.94063,-50.742,0.99883,-0.047511,-0.0084679,-122.27
> view matrix models
> #6,0.013828,0.94162,-0.33639,-22.756,0.012711,0.33623,0.9417,-49.488,0.99982,-0.017297,-0.00732,-125.52
> view matrix models
> #6,-0.0020754,0.82783,-0.56097,14.746,-0.011368,0.56092,0.82779,-57.086,0.99993,0.0080949,0.0082464,-129.76
> view matrix models
> #6,-0.011726,0.84432,-0.53571,11.302,0.020874,0.53584,0.84406,-59.58,0.99971,-0.0012852,-0.023907,-125.29
> view matrix models
> #6,-0.040961,0.7891,-0.61289,28.176,0.056673,0.61426,0.78707,-64.766,0.99755,-0.0024949,-0.069882,-119.93
> view matrix models
> #6,-0.036468,0.89049,-0.45353,0.18111,0.1485,0.45362,0.87873,-67.91,0.98824,-0.035303,-0.14878,-107.1
> view matrix models
> #6,0.114,0.86461,-0.48934,-8.3584,0.21084,0.46028,0.86238,-73.018,0.97085,-0.20148,-0.12982,-90.829
> view matrix models
> #6,0.16112,0.86633,-0.47278,-15.049,0.10548,0.46118,0.88102,-64.614,0.98128,-0.19182,-0.017073,-105.16
> view matrix models
> #6,0.023725,0.88935,-0.45661,-5.3847,0.048413,0.45518,0.88908,-59.193,0.99855,-0.043199,-0.032257,-120.07
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.023725,0.88935,-0.45661,-73.083,0.048413,0.45518,0.88908,-90.956,0.99855,-0.043199,-0.032257,-76.082
> show #!7 models
> select #7
10384 atoms, 10486 bonds, 13 pseudobonds, 727 residues, 2 models selected
> view matrix models #7,1,0,0,-61.589,0,1,0,-9.488,0,0,1,-148.91
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.98495,-0.11382,-0.13007,-35.486,0.14288,0.95965,0.24221,-44.394,0.097255,-0.25715,0.96146,-129.05
> view matrix models
> #7,0.97579,-0.14926,-0.15984,-28.002,0.18893,0.94348,0.27232,-50.448,0.11016,-0.29593,0.94884,-125.18
> view matrix models
> #7,0.90074,-0.25174,-0.35396,9.4872,0.40678,0.77464,0.48421,-76.938,0.1523,-0.58013,0.80016,-85.891
> view matrix models
> #7,0.88324,-0.25847,-0.39125,15.703,0.4439,0.72978,0.51999,-79.811,0.15113,-0.63295,0.7593,-76.343
> view matrix models
> #7,0.86678,-0.22603,-0.44453,19.533,0.48024,0.61858,0.62188,-82.713,0.13441,-0.75251,0.64472,-51.076
> view matrix models
> #7,0.85709,-0.15751,-0.4905,18.34,0.50454,0.44912,0.73738,-79.979,0.10415,-0.87948,0.46441,-17.026
> view matrix models
> #7,0.79007,-0.1075,-0.60352,31.549,0.60937,0.24509,0.75406,-71.789,0.066853,-0.96352,0.25914,15.982
> view matrix models
> #7,0.65154,-0.022642,-0.75828,52.678,0.75856,0.0069123,0.65157,-52.5,-0.0095114,-0.99972,0.021679,51.396
> view matrix models
> #7,0.99432,-0.088777,0.058637,-58.126,-0.047731,0.12033,0.99159,-17.802,-0.095086,-0.98876,0.11541,49.319
> view matrix models
> #7,0.8764,-0.48091,0.025368,-3.8018,-0.055817,-0.049117,0.99723,-0.65141,-0.47833,-0.87539,-0.069889,95.18
> view matrix models
> #7,0.8009,-0.3231,-0.50414,41.877,0.42857,-0.2787,0.85945,-12.145,-0.4182,-0.9044,-0.084738,93.573
> view matrix models
> #7,0.73855,-0.27936,-0.6136,54.883,0.5395,-0.30095,0.78637,-13.579,-0.40434,-0.91181,-0.07155,91.585
> view matrix models
> #7,0.58621,-0.49333,-0.64264,94.432,0.50198,-0.40145,0.76607,2.2717,-0.63591,-0.77167,0.012307,92.216
> view matrix models
> #7,0.21885,-0.73818,-0.63811,155.15,0.38109,-0.53736,0.75234,29.324,-0.89826,-0.40783,0.16371,66.72
> view matrix models
> #7,-0.10295,-0.79936,-0.59197,188.74,0.258,-0.59622,0.76023,46.706,-0.96064,-0.074466,0.26761,29.104
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.10295,-0.79936,-0.59197,118.93,0.258,-0.59622,0.76023,12.461,-0.96064,-0.074466,0.26761,89.01
> view matrix models
> #7,-0.10295,-0.79936,-0.59197,169.18,0.258,-0.59622,0.76023,-64.284,-0.96064,-0.074466,0.26761,99.129
> view matrix models
> #7,-0.10295,-0.79936,-0.59197,164.47,0.258,-0.59622,0.76023,-65.545,-0.96064,-0.074466,0.26761,90.501
> select #6
8604 atoms, 8782 bonds, 1140 residues, 1 model selected
> view matrix models
> #6,0.023725,0.88935,-0.45661,-24.841,0.048413,0.45518,0.88908,-169.92,0.99855,-0.043199,-0.032257,-74.271
Window position QRect(-1286,-25 654x459) outside any known screen, using
primary screen
> save "/Users/gcaballero/Library/Mobile Documents/com~apple~CloudDocs/Grad
> School/Side-ACC/cryoEM-Apo/Acc-Chimera-Sessions/With-WDpass/AccM-Fitting-
> ForFigures-160222-fig2-OnlyBeans.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1829, in take_snapshot
'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe1fbc611f0> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x7fe1ae7f3850> ->
<chimerax.segger.fit_dialog.Fit object at 0x7fe179464fd0> ->
<chimerax.map.volume.Volume object at 0x7fe17a722940> 'AccM-Dimer-CTDomain map
8'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fe1fbc611f0> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x7fe1ae7f3850> -> <chimerax.segger.fit_dialog.Fit object at 0x7fe179464fd0>
-> <chimerax.map.volume.Volume object at 0x7fe17a722940> 'AccM-Dimer-CTDomain
map 8': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe1fbc611f0> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x7fe1ae7f3850> ->
<chimerax.segger.fit_dialog.Fit object at 0x7fe179464fd0> ->
<chimerax.map.volume.Volume object at 0x7fe17a722940> 'AccM-Dimer-CTDomain map
8'
Window position QRect(-1101,118 284x173) outside any known screen, using
primary screen
ValueError: error processing: 'tools' -> -> -> -> 'AccM-Dimer-CTDomain map 8':
Error while saving session data for 'tools' -> -> -> -> 'AccM-Dimer-CTDomain
map 8'
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 283, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume.py", line 1829, in take_snapshot
'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 329, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 286, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe1fbc611f0> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x7fe1ae7f3850> ->
<chimerax.segger.fit_dialog.Fit object at 0x7fe179464fd0> ->
<chimerax.map.volume.Volume object at 0x7fe17a722940> 'AccM-Dimer-CTDomain map
8'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider
what(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save
show_save_file_dialog(session)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 89, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 890, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 619, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7fe1fbc611f0> -> <chimerax.segger.fit_dialog.FitSegmentsDialog object at
0x7fe1ae7f3850> -> <chimerax.segger.fit_dialog.Fit object at 0x7fe179464fd0>
-> <chimerax.map.volume.Volume object at 0x7fe17a722940> 'AccM-Dimer-CTDomain
map 8': Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7fe1fbc611f0> ->
<chimerax.segger.fit_dialog.FitSegmentsDialog object at 0x7fe1ae7f3850> ->
<chimerax.segger.fit_dialog.Fit object at 0x7fe179464fd0> ->
<chimerax.map.volume.Volume object at 0x7fe17a722940> 'AccM-Dimer-CTDomain map
8'
ValueError: error processing: 'tools' -> -> -> -> 'AccM-Dimer-CTDomain map 8':
Error while saving session data for 'tools' -> -> -> -> 'AccM-Dimer-CTDomain
map 8'
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 264, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Window position QRect(-1009,190 100x30) outside any known screen, using
primary screen
OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) HD Graphics 5300
OpenGL vendor: Intel Inc.Hardware:
Hardware Overview:
Model Name: MacBook
Model Identifier: MacBook8,1
Processor Name: Dual-Core Intel Core M
Processor Speed: 1.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 427.140.8.0.0
SMC Version (system): 2.25f87
Software:
System Software Overview:
System Version: macOS 11.6 (20G165)
Kernel Version: Darwin 20.6.0
Time since boot: 3 days 42 minutes
Graphics/Displays:
Intel HD Graphics 5300:
Chipset Model: Intel HD Graphics 5300
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x161e
Revision ID: 0x0009
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2304 x 1440 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2410:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Framebuffer Depth: 24-Bit Color (ARGB8888)
Display Serial Number: C592M15NARHL
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (5)
comment:1 by , 4 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → self.positions is None |
comment:2 by , 4 years ago
| Summary: | self.positions is None → Segger fit dialog tried to save a closed volume model in a session |
|---|
comment:3 by , 4 years ago
comment:4 by , 4 years ago
Deleting the segmented map after fitting an atomic model into one of the segments causes this error. It is a bug in the Segger session save code.
comment:5 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
Fixed session save when segmented map deleted. But Segger is likely to produce a variety of errors if used with the segmented map deleted. Still this fix will allow saving the session and restoring it.
Note:
See TracTickets
for help on using tickets.
Similar to #4766 where Segger was trying to save a fit PDB model that had been closed in a session.