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Opened 12 months ago
Closed 12 months ago
#16219 closed defect (fixed)
view sel: 'NoneType' object has no attribute 'get_scene_positions'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.6.3-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/model_vs_AllCrystal.cxs
Log from Tue Oct 29 15:20:43 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v3.cxs
> format session
Opened 7.cryosparc_P13_J203_map_sharp.mrc as #1, grid size 256,256,256, pixel
0.834, shown at level 0.0621, step 1, values float32
Opened cryosparc_P13_J196_map_sharp.mrc as #2, grid size 360,360,360, pixel
0.834, shown at level 0.127, step 2, values float32
Log from Wed Jun 19 21:42:35 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v2.cxs
Opened 7.cryosparc_P13_J203_map_sharp.mrc as #1, grid size 256,256,256, pixel
0.834, shown at level 0.0296, step 1, values float32
Log from Thu Jun 6 00:21:10 2024UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v1.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Redust" returned None
Log from Wed Mar 27 17:29:34 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon.cxs
Opened cryosparc_P13_J196_map_sharp.mrc as #1, grid size 360,360,360, pixel
0.834, shown at level 0.144, step 1, values float32
Log from Fri Jan 5 12:41:04 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_cartoon.cxs
Opened cryosparc_P13_J196_map_sharp.mrc as #1, grid size 360,360,360, pixel
0.834, shown at level 0.144, step 1, values float32
Log from Wed Nov 29 12:30:48 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_mesh_fit.cxs
Opened cryosparc_P13_J196_map_sharp.mrc as #1, grid size 360,360,360, pixel
0.834, shown at level 0.144, step 1, values float32
Log from Tue Nov 28 13:20:25 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_segments.cxs
Log from Tue Nov 28 13:09:14 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open
> /Users/evitatsiolaki/Dropbox/Synuclein/Evita/Southworth_Collab/Figures/Figure_1/panelB.cxs
Log from Mon Nov 20 17:35:51 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
> open /Users/evitatsiolaki/Downloads/2kho.pdb
2kho.pdb title:
NMR-RDC / xray structure of E. Coli HSP70 (DNAk) chaperone (1-605) complexed
with adp and substrate [more info...]
Chain information for 2kho.pdb #1
---
Chain | Description | UniProt
A | heat shock protein 70 | DNAK_ECOLI 1-605
> cartoon style modeHelix tube sides 20
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.
> lighting simple
> lighting soft
> lighting full
> set bgColor white
> graphics silhouettes true
> open /Users/evitatsiolaki/Downloads/4b9q.pdb
4b9q.pdb title:
Open conformation of atp-bound HSP70 homolog DNAk [more info...]
Chain information for 4b9q.pdb #2
---
Chain | Description | UniProt
A B C D | chaperone protein DNAk | DNAK_ECOLI 1-605
Non-standard residues in 4b9q.pdb #2
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
> hide #2.1 models
> hide #2.2 models
> select #2/B
4711 atoms, 4615 bonds, 8 pseudobonds, 744 residues, 3 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> select #2/C
4662 atoms, 4599 bonds, 7 pseudobonds, 712 residues, 3 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> select #2/D
4637 atoms, 4596 bonds, 8 pseudobonds, 687 residues, 3 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> cartoon style (#!2 & sel) modeHelix tube sides 20
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
Drag select of 90 atoms, 379 residues, 73 bonds
Drag select of 91 atoms, 644 residues, 73 bonds
Drag select of 22 residues
Drag select of 91 atoms, 644 residues, 73 bonds
> hide sel target a
> ui mousemode right "translate selected models"
Drag select of 3 residues
> view matrix models #2,1,0,0,-51.545,0,1,0,-100.69,0,0,1,-113.84
Drag select of 645 residues
> view matrix models
> #1,1,0,0,-7.8189,0,1,0,0.0096541,0,0,1,1.232,#2,1,0,0,-59.364,0,1,0,-100.68,0,0,1,-112.61
Drag select of 18 residues
Drag select of 12 residues
Drag select of 647 residues
> view matrix models
> #1,1,0,0,-14.002,0,1,0,2.5717,0,0,1,2.2657,#2,1,0,0,-65.547,0,1,0,-98.115,0,0,1,-111.57
Drag select of 15 residues
> select clear
Drag select of 659 residues
> view matrix models
> #1,1,0,0,-2.6935,0,1,0,13.084,0,0,1,1.4804,#2,1,0,0,-54.239,0,1,0,-87.602,0,0,1,-112.36
> select #2/A:68
5 atoms, 4 bonds, 1 residue, 1 model selected
> view matrix models #2,1,0,0,-77.257,0,1,0,-108.91,0,0,1,-109.86
> view matrix models #2,1,0,0,-107.83,0,1,0,-69.532,0,0,1,-105.59
> view matrix models #2,1,0,0,-102.45,0,1,0,-76.425,0,0,1,-104.62
> view matrix models #2,1,0,0,-102.58,0,1,0,-71.827,0,0,1,-107.66
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.82428,0.55133,0.12881,-144.06,-0.32582,0.27585,0.90429,-48.202,0.46303,-0.78736,0.40701,-36.652
> view matrix models
> #2,0.91577,-0.39482,0.073963,-64.092,0.019721,0.2281,0.97344,-87.616,-0.40121,-0.88999,0.21667,83.434
> view matrix models
> #2,0.87463,-0.28061,0.39532,-97.358,-0.29338,0.3428,0.89242,-56.772,-0.38594,-0.89652,0.2175,82.281
> view matrix models
> #2,0.1635,-0.9831,0.082305,70.539,-0.16485,0.055028,0.98478,-52.788,-0.97267,-0.17458,-0.15307,113.08
> view matrix models
> #2,0.7218,0.53931,0.43376,-157.84,-0.67994,0.43564,0.58982,3.0237,0.12913,-0.72067,0.68115,-29.565
> view matrix models
> #2,0.68182,0.5921,0.42958,-157.86,-0.47843,0.80517,-0.35043,28.042,-0.55338,0.033401,0.83226,-35.784
> view matrix models
> #2,0.44523,-0.18851,0.87535,-99.713,0.040445,0.98082,0.19066,-90.823,-0.8945,-0.049481,0.44431,42.178
> view matrix models
> #2,0.20494,-0.72701,0.65533,-6.068,0.27603,0.68529,0.67393,-131.27,-0.93904,0.042773,0.34112,47.556
> view matrix models
> #2,0.80536,-0.040749,0.59138,-128.16,-0.31758,0.81272,0.4885,-61.956,-0.50053,-0.58123,0.64159,30.142
> view matrix models
> #2,0.76695,0.064579,0.63845,-137.48,-0.412,0.81233,0.41276,-45.116,-0.49198,-0.57961,0.64963,28.372
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.76695,0.064579,0.63845,-137.1,-0.412,0.81233,0.41276,-48.084,-0.49198,-0.57961,0.64963,35.041
> view matrix models
> #2,0.76695,0.064579,0.63845,-136.67,-0.412,0.81233,0.41276,-46.332,-0.49198,-0.57961,0.64963,41.56
> ui mousemode right "rotate selected models"
Drag select of 7 residues
> ui tool show Matchmaker
> matchmaker #!2 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 2kho.pdb, chain A (#1) with 4b9q.pdb, chain D (#2), sequence
alignment score = 2917.9
RMSD between 169 pruned atom pairs is 0.773 angstroms; (across all 591 pairs:
42.902)
Drag select of 667 residues
> select clear
Drag select of 644 residues
> view matrix models
> #2,-0.45743,0.80364,0.38069,-21.841,0.83481,0.24059,0.49519,-70.413,0.30637,0.54432,-0.78093,-27.262
> view matrix models
> #2,0.83506,0.2406,0.49477,-122.26,0.032315,-0.9192,0.39245,130.73,0.54922,-0.31173,-0.77536,22.862
> view matrix models
> #2,0.51709,0.23975,0.82167,-115.33,-0.012201,-0.95781,0.28715,148.08,0.85584,-0.15851,-0.49235,-48.695
> view matrix models
> #2,0.1337,0.87049,0.47368,-100.5,0.39898,-0.48481,0.77832,18.464,0.90716,0.084931,-0.41212,-83.115
> view matrix models
> #2,0.87667,0.39933,0.2683,-121.76,0.020346,-0.58796,0.80864,66.599,0.48066,-0.70345,-0.52357,44.15
> view matrix models
> #2,0.35538,0.61326,0.70542,-121.37,-0.14331,-0.71002,0.68945,105.7,0.92367,-0.34611,-0.16444,-67.236
> view matrix models
> #2,0.17971,0.64953,0.73879,-108.28,-0.091838,-0.73666,0.67,104.13,0.97942,-0.18825,-0.072732,-95.408
> view matrix models
> #2,0.3516,0.6285,0.69381,-121.34,-0.10312,-0.71061,0.69598,100.8,0.93045,-0.31625,-0.18504,-68.91
> view matrix models
> #2,0.42318,0.5191,0.7426,-123.48,-0.20234,-0.74477,0.63591,119.87,0.88316,-0.41936,-0.21014,-52.294
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.42318,0.5191,0.7426,-139.25,-0.20234,-0.74477,0.63591,24.72,0.88316,-0.41936,-0.21014,-35.445
> select clear
> select add #2
18760 atoms, 18449 bonds, 29 pseudobonds, 2910 residues, 3 models selected
> view matrix models
> #2,0.42318,0.5191,0.7426,-161.18,-0.20234,-0.74477,0.63591,37.649,0.88316,-0.41936,-0.21014,-40.295
> select clear
> select add #2
18760 atoms, 18449 bonds, 29 pseudobonds, 2910 residues, 3 models selected
> view matrix models
> #2,0.42318,0.5191,0.7426,-163.6,-0.20234,-0.74477,0.63591,25.153,0.88316,-0.41936,-0.21014,-40.397
> view matrix models
> #2,0.42318,0.5191,0.7426,-167.28,-0.20234,-0.74477,0.63591,26.799,0.88316,-0.41936,-0.21014,-40.617
> select clear
> ui tool show Matchmaker
> matchmaker #!2 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 2kho.pdb, chain A (#1) with 4b9q.pdb, chain D (#2), sequence
alignment score = 2917.9
RMSD between 169 pruned atom pairs is 0.773 angstroms; (across all 591 pairs:
42.902)
> select add #2
18760 atoms, 18449 bonds, 29 pseudobonds, 2910 residues, 3 models selected
> view matrix models
> #2,-0.44059,-0.34143,0.83024,42.237,0.5323,0.64536,0.54788,-68.618,-0.72287,0.68332,-0.10259,10.306
> view matrix models
> #2,-0.44059,-0.34143,0.83024,36.3,0.5323,0.64536,0.54788,-66.904,-0.72287,0.68332,-0.10259,21.826
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.87277,-0.36841,0.32024,129.62,-0.39655,0.91767,-0.025037,59.156,-0.28466,-0.14884,-0.947,121.08
> view matrix models
> #2,-0.79329,0.6012,0.096137,52.671,0.30581,0.25693,0.91677,-38.642,0.52646,0.75667,-0.38767,-97.114
> view matrix models
> #2,0.0089612,0.9244,0.38132,-88.624,0.28205,-0.36819,0.88594,22.947,0.95936,0.099611,-0.26402,-95.817
> view matrix models
> #2,0.33316,0.13319,0.93342,-99.968,-0.44017,-0.8535,0.2789,197.62,0.83382,-0.50378,-0.22573,-30.96
> view matrix models
> #2,0.083488,0.56615,0.82006,-101.99,-0.15154,-0.80615,0.57198,136.71,0.98492,-0.17203,0.018493,-98.278
> view matrix models
> #2,0.23336,0.72517,0.64782,-118,-0.16963,-0.62564,0.76145,106.22,0.95748,-0.28758,-0.02299,-81.312
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.23336,0.72517,0.64782,-136.29,-0.16963,-0.62564,0.76145,0.18598,0.95748,-0.28758,-0.02299,-67.36
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.28138,0.84846,0.44826,-135.6,-0.067394,-0.44851,0.89123,-38.064,0.95723,-0.28099,-0.06902,-63.992
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.28138,0.84846,0.44826,-141.66,-0.067394,-0.44851,0.89123,-32.693,0.95723,-0.28099,-0.06902,-71.315
> view matrix models
> #2,0.28138,0.84846,0.44826,-143.64,-0.067394,-0.44851,0.89123,-33.458,0.95723,-0.28099,-0.06902,-72.297
> view matrix models
> #2,0.28138,0.84846,0.44826,-143.83,-0.067394,-0.44851,0.89123,-33.776,0.95723,-0.28099,-0.06902,-71.679
> view matrix models
> #2,0.28138,0.84846,0.44826,-143.25,-0.067394,-0.44851,0.89123,-34.755,0.95723,-0.28099,-0.06902,-72.954
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.39129,0.84465,0.36531,-147.84,-0.038848,-0.38145,0.92357,-46.689,0.91945,-0.37558,-0.11644,-56.239
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.39129,0.84465,0.36531,-148.55,-0.038848,-0.38145,0.92357,-40.59,0.91945,-0.37558,-0.11644,-56.23
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.027397,0.58851,0.80803,-123.49,-0.44362,-0.71722,0.53741,66.98,0.8958,-0.37318,0.24142,-84.452
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.027397,0.58851,0.80803,-123.15,-0.44362,-0.71722,0.53741,66.954,0.8958,-0.37318,0.24142,-85.373
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right "move picked models"
> view matrix models
> #2,0.027397,0.58851,0.80803,-129.16,-0.44362,-0.71722,0.53741,151.07,0.8958,-0.37318,0.24142,-95.565
> ui mousemode right "move picked models"
> ui mousemode right rotate
> select clear
> select add #2
18760 atoms, 18449 bonds, 29 pseudobonds, 2910 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.027397,0.58851,0.80803,-130.45,-0.44362,-0.71722,0.53741,183.03,0.8958,-0.37318,0.24142,-57.627
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.65369,0.55851,0.51065,-170.85,-0.21722,-0.50791,0.83357,114.07,0.72492,-0.65582,-0.2107,25.2
> view matrix models
> #2,0.96445,0.16606,0.20557,-143.39,-0.080347,-0.55681,0.82675,104.09,0.25176,-0.81387,-0.52367,117.98
> view matrix models
> #2,0.98581,0.16466,0.032721,-130.83,0.061168,-0.53381,0.84339,85.108,0.15634,-0.82942,-0.5363,130.9
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.98581,0.16466,0.032721,-125.17,0.061168,-0.53381,0.84339,67.284,0.15634,-0.82942,-0.5363,145.16
> select clear
> lighting flat
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> view
> view orient
[Repeated 3 time(s)]
> ui tool show "Selection Inspector"
> save fig1 transparentBackground true
Cannot determine format for 'fig1'
> save fig1 format png transparentBackground true
> save fig1 format png transparentBackground true models #1 #2
Cannot determine format for 'fig1'
> save fig1 format png transparentBackground true models all
Expected a keyword
> save fig1 format png transparentBackground true models #1
Expected a keyword
> save fig1 format png transparentBackground true
[Repeated 1 time(s)]
> save fig1 format jpeg transparentBackground true
The JPEG file format does not support transparency, use PNG or TIFF instead.
> save fig1 format PNG transparentBackground true
Unknown data format: 'PNG'
> save fig1 format png transparentBackground true
> save fig1.png format png transparentBackground true
> save
> /Users/evitatsiolaki/Dropbox/Synuclein/Evita/Southworth_Collab/Figures/Figure_1/panelB.jpg
> width 1472 height 863 supersample 3
> save
> /Users/evitatsiolaki/Dropbox/Synuclein/Evita/Southworth_Collab/Figures/Figure_1/panelB.cxs
Alignment identifier is 1/A
Alignment identifier is 1
> select #1/A:508-603
831 atoms, 834 bonds, 96 residues, 1 model selected
> color sel forest green
> select #2/B,D:605
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/A:508-602/B,D:508-605/C:508-603
2987 atoms, 2995 bonds, 387 residues, 1 model selected
> color sel forest green
> select #2/A-D:389
28 atoms, 24 bonds, 4 residues, 1 model selected
> select #2/A-D:389-490
2987 atoms, 3021 bonds, 2 pseudobonds, 399 residues, 2 models selected
> select #2/A-D:501-502
68 atoms, 64 bonds, 8 residues, 1 model selected
> select #2/A-D:389-502
3367 atoms, 3401 bonds, 2 pseudobonds, 447 residues, 2 models selected
> color (#!2 & sel) lime
> select #1/A:399
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:399-501
868 atoms, 877 bonds, 103 residues, 1 model selected
> color sel lime
> select clear
> select #2/A-D:384
16 atoms, 12 bonds, 4 residues, 1 model selected
> select #2/A-D:2-384
11520 atoms, 11665 bonds, 3 pseudobonds, 1518 residues, 2 models selected
> color (#!2 & sel) orange
> color (#!2 & sel) orange red
> color (#!2 & sel) orange
> select #1/A:381
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/A:201-381
1544 atoms, 1559 bonds, 181 residues, 1 model selected
> select #1/A:326-381
456 atoms, 460 bonds, 56 residues, 1 model selected
> select #1/A:4-381
3194 atoms, 3230 bonds, 378 residues, 1 model selected
> color sel orange
> select clear
> select #1/A:603
10 atoms, 9 bonds, 1 residue, 1 model selected
> color sel forest green
> select #2/A:387
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/A-D:385
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A-D:385-388
128 atoms, 124 bonds, 16 residues, 1 model selected
> color sel lime
> select clear
> select #1/A:4-328
2758 atoms, 2789 bonds, 325 residues, 1 model selected
> select #1/A:398
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/A:309-398
745 atoms, 751 bonds, 90 residues, 1 model selected
> color sel orange
> select #1/A:507
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/A:501-507
53 atoms, 52 bonds, 7 residues, 1 model selected
> color sel lime
> select clear
> select #2/A-D:507
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #2/A-D:502-507
152 atoms, 148 bonds, 24 residues, 1 model selected
> color sel lime
> select clear
> save fig1.png format png transparentBackground true
> save
> /Users/evitatsiolaki/Dropbox/Synuclein/Evita/Southworth_Collab/Figures/Figure_1/panelB.cxs
——— End of log from Mon Nov 20 17:35:51 2023 ———
opened ChimeraX session
> open /Users/evitatsiolaki/Downloads/cryosparc_P13_J201_map_sharp.mrc
Opened cryosparc_P13_J201_map_sharp.mrc as #3, grid size 360,360,360, pixel
0.834, shown at level 4.29e-05, step 2, values float32
> close #1
> close #2
> show target m
> volume #3 level -0.001762
> volume #3 level 0.005059
> surface dust #3 size 8.34
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> volume #3 step 1
> volume #3 level 0.1108
> open
> /Users/evitatsiolaki/Downloads/cryosparc_P13_J193_009_volume_mask_fsc.mrc
Opened cryosparc_P13_J193_009_volume_mask_fsc.mrc as #1, grid size
360,360,360, pixel 0.834, shown at level 1, step 2, values float32
> volume #1 level 1
> close #1
> ui tool show "Segment Map"
Segmenting cryosparc_P13_J201_map_sharp.mrc, density threshold 0.110785
Only showing 60 of 70 regions.
Showing 60 of 70 region surfaces
1271 watershed regions, grouped to 70 regions
Showing cryosparc_P13_J201_map_sharp.seg - 70 regions, 60 surfaces
> open
> /Users/evitatsiolaki/Desktop/paper_Evita/Erics_finalDimer/70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb
Summary of feedback from opening
/Users/evitatsiolaki/Desktop/paper_Evita/Erics_finalDimer/70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb
---
warnings | Ignored bad PDB record found on line 18844
# All scores below are weighted scores, not raw scores.
Ignored bad PDB record found on line 18845
#BEGIN_POSE_ENERGIES_TABLE 70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb
Ignored bad PDB record found on line 18846
label fa_atr fa_rep fa_sol fa_intra_rep fa_elec hbond_sr_bb hbond_lr_bb
hbond_bb_sc hbond_sc dslf_fa13 rama omega fa_dun p_aa_pp ref cart_bonded
elec_dens_fast total
Ignored bad PDB record found on line 18847
weights 0.8 0.44 0.75 0.004 0.7 1.17 1.17 1.17 1.1 1 0.2 0.5 0.56 0.32 1 0.5
25 NA
Ignored bad PDB record found on line 18848
pose -4716.01 438.691 2645.32 11.7217 -592.243 -435.347 -233.797 -120.513
-165.064 0 -88.6764 75.3859 1119.03 -168.536 -110.113 471.77 -8140.87 -10009.2
1217 messages similar to the above omitted
Chain information for 70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb #2
---
Chain | Description
A B | No description available
> fitmap #2 inMap #3
Fit molecule 70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb (#2) to map
cryosparc_P13_J201_map_sharp.mrc (#3) using 18840 atoms
average map value = 0.2601, steps = 36
shifted from previous position = 0.211
rotated from previous position = 0.182 degrees
atoms outside contour = 8478, contour level = 0.11078
Position of 70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb (#2) relative to
cryosparc_P13_J201_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99999568 -0.00035749 0.00291829 -0.18819442
0.00035399 0.99999922 0.00119918 -0.15861077
-0.00291872 -0.00119815 0.99999502 0.58245013
Axis -0.37752445 0.91919646 0.11204087
Axis point 199.80827751 0.00000000 66.01117393
Rotation angle (degrees) 0.18191809
Shift along axis -0.00948824
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-14.891,0,1,0,-5.6353,0,0,1,-0.33467
> view matrix models #3,1,0,0,-87.988,0,1,0,-25.028,0,0,1,-2.7074
> close #3
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> view matrix models
> #2,1,-0.00035749,0.0029183,-91.962,0.00035399,1,0.0011992,-30.429,-0.0029187,-0.0011981,1,-1.8738
> select subtract #2
Nothing selected
> select #1.11
1 model selected
> select add #1.23
2 models selected
> select add #1.25
3 models selected
> select add #1.13
4 models selected
> select add #1.53
5 models selected
Grouped 5 regions
> select add #1.10
2 models selected
> select add #1.54
3 models selected
> select add #1.26
4 models selected
> select add #1.29
5 models selected
> select add #1.30
6 models selected
> select add #1.27
7 models selected
Grouped 7 regions
> select #1.5
1 model selected
> select #1.44
1 model selected
> select add #1.5
2 models selected
> select add #1.16
3 models selected
> select add #1.42
4 models selected
> select add #1.9
5 models selected
> select add #1.2
6 models selected
> select add #1.43
7 models selected
> select add #1.19
8 models selected
> select subtract #1.19
7 models selected
Grouped 7 regions
> select add #1.60
2 models selected
Grouped 2 regions
> select clear
> select add #1.47
1 model selected
> select add #1.1
2 models selected
> select add #1.34
3 models selected
> select add #1.48
4 models selected
> select add #1.6
5 models selected
> select add #1.46
6 models selected
> select add #1.40
7 models selected
> select add #1.36
8 models selected
Grouped 8 regions
> select add #1.59
2 models selected
Grouped 2 regions
> select add #1.17
2 models selected
> select add #1.22
3 models selected
Grouped 3 regions
> select add #1.4
2 models selected
> select add #1.15
3 models selected
> select subtract #1.4
2 models selected
> select add #1.31
3 models selected
> select add #1.55
4 models selected
Grouped 4 regions
> select add #1.28
2 models selected
> select add #1.4
3 models selected
Grouped 3 regions
> select add #1.14
2 models selected
Grouped 2 regions
> select add #1.24
2 models selected
Grouped 2 regions
> select add #1.52
2 models selected
Grouped 2 regions
> select add #1.2
2 models selected
Grouped 2 regions
Ungrouped to 2 regions
> select subtract #1.2
1 model selected
> select add #1.58
2 models selected
> select add #1.49
3 models selected
Grouped 3 regions
> select add #1.39
2 models selected
Grouped 2 regions
> select add #1.19
2 models selected
Grouped 2 regions
> select add #1.38
2 models selected
Grouped 2 regions
> select add #1.32
2 models selected
Grouped 2 regions
> select add #1.8
2 models selected
Grouped 2 regions
> select add #1.3
2 models selected
Grouped 2 regions
> select add #1.7
2 models selected
Grouped 2 regions
> select add #1.20
2 models selected
Grouped 2 regions
> select add #1.45
2 models selected
Grouped 2 regions
> select add #1.33
2 models selected
Grouped 2 regions
> select add #1.21
2 models selected
Grouped 2 regions
> select add #1.41
2 models selected
Grouped 2 regions
> select add #1.35
2 models selected
Grouped 2 regions
> select add #1.18
2 models selected
Grouped 2 regions
> select add #1.50
2 models selected
Grouped 2 regions
> select add #1.51
2 models selected
Grouped 2 regions
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting full
> lighting shadows false
Alignment identifier is 1
> select /A-B:608
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /A-B:512-608
3138 atoms, 3152 bonds, 194 residues, 1 model selected
> color sel #bd92a9ff
> select /A-B:511
22 atoms, 20 bonds, 2 residues, 1 model selected
> select /A-B:507-511
166 atoms, 164 bonds, 10 residues, 1 model selected
> color sel #bd92a9ff
> select /A-B:506
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /A-B:381-506
3822 atoms, 3844 bonds, 252 residues, 1 model selected
> select /A-B:381-382
48 atoms, 46 bonds, 4 residues, 1 model selected
> select /A-B:381-393
400 atoms, 398 bonds, 26 residues, 1 model selected
> select /A-B:506
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /A-B:422-506
2598 atoms, 2616 bonds, 170 residues, 1 model selected
> select /A-B:421
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /A-B:409-421
426 atoms, 426 bonds, 26 residues, 1 model selected
> select /A-B:392
38 atoms, 36 bonds, 2 residues, 1 model selected
> select /A-B:392-506
3498 atoms, 3520 bonds, 230 residues, 1 model selected
> select /A-B:395-396
56 atoms, 54 bonds, 4 residues, 1 model selected
> select /A-B:395-399
142 atoms, 142 bonds, 10 residues, 1 model selected
> select /A-B:395-396
56 atoms, 54 bonds, 4 residues, 1 model selected
> select /A-B:395-506
3384 atoms, 3406 bonds, 224 residues, 1 model selected
> color sel #a07163ff
> select clear
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_segments.cxs
> ui tool show "Segment Map"
> select #1.1
1 model selected
> select add #1.12
2 models selected
> select subtract #1.12
1 model selected
> select add #1.12
2 models selected
Grouped 2 regions
> select clear
> select /A-B:393-394
76 atoms, 74 bonds, 4 residues, 1 model selected
> select /A-B:4-394
12152 atoms, 12248 bonds, 782 residues, 1 model selected
> color sel #b5dce4ff
> select clear
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_segments.cxs
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> view matrix models
> #2,1,-0.00035749,0.0029183,2.4452,0.00035399,1,0.0011992,0.90657,-0.0029187,-0.0011981,1,1.8913
> view matrix models
> #2,1,-0.00035749,0.0029183,1.6672,0.00035399,1,0.0011992,0.30637,-0.0029187,-0.0011981,1,1.8721
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
[Repeated 1 time(s)]
> select subtract #2
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
[Repeated 1 time(s)]
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> select add #1
18840 atoms, 18976 bonds, 1210 residues, 8 models selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> select clear
> hide #1.1 models
> hide #1.2 models
> hide #1.10 models
> hide #1.37 models
> hide #1.56 models
> hide #1.57 models
> show #1.57 models
> show #1.56 models
> show #1.37 models
> show #1.10 models
> hide #1.10 models
> ui tool show "Segment Map"
> show #1.1 models
> hide #1.1 models
> select #1.37
1 model selected
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 2 models selected
> select subtract #2
1 model selected
> hide #2 models
> select #1.56
1 model selected
> select add #1.37
2 models selected
> select add #1.57
3 models selected
> show #1.1 models
> select add #1.1
4 models selected
Grouped 4 regions
> show #1.2 models
> show #1.10 models
> select subtract #1.1
Nothing selected
> show #2 models
> hide #2 models
> show #2 models
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_segments.cxs
——— End of log from Tue Nov 28 13:09:14 2023 ———
opened ChimeraX session
Showing cryosparc_P13_J201_map_sharp.seg - 13 regions, 3 surfaces
> close #1
> open
> /Users/evitatsiolaki/Desktop/paper_Evita/Erics_finalDimer/Erics_final_model/cryosparc_P13_J196_map_sharp.mrc
Opened cryosparc_P13_J196_map_sharp.mrc as #1, grid size 360,360,360, pixel
0.834, shown at level 0.000168, step 2, values float32
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.9731,0.21337,0.086948,-39.894,-0.12059,0.79321,-0.59689,133.59,-0.19632,0.57035,0.7976,-26.125
> view matrix models
> #1,0.77028,0.58705,0.2491,-88.818,0.49039,-0.29558,-0.81985,237.31,-0.40766,0.75366,-0.51556,166.58
> view matrix models
> #1,0.61343,0.78355,0.098756,-73.39,0.7745,-0.62132,0.11879,108.95,0.15444,0.0036149,-0.988,263.69
> view matrix models
> #1,0.57349,0.70738,-0.41318,17.25,0.74498,-0.66012,-0.096114,149.83,-0.34074,-0.25269,-0.90556,360.47
> volume #1 level 0.1961
> view matrix models
> #1,0.61656,0.78709,0.018318,-66.546,0.78699,-0.61681,0.013954,120.38,0.022282,0.0058124,-0.99973,281.73
> view matrix models
> #1,0.60749,0.7895,0.087437,-76.028,0.78795,-0.61287,0.059365,112.76,0.10046,0.032832,-0.9944,265.19
Drag select of 7 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> ui mousemode right "translate selected models"
Drag select of 21 residues, 1 cryosparc_P13_J196_map_sharp.mrc
Drag select of 6 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> view matrix models
> #2,1,-0.00035749,0.0029183,9.0513,0.00035399,1,0.0011992,1.737,-0.0029187,-0.0011981,1,2.331,#1,0.60749,0.7895,0.087437,-68.644,0.78795,-0.61287,0.059365,114.19,0.10046,0.032832,-0.9944,265.65
Drag select of 5 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> view matrix models
> #2,1,-0.00035749,0.0029183,9.8651,0.00035399,1,0.0011992,0.6408,-0.0029187,-0.0011981,1,2.4096,#1,0.60749,0.7895,0.087437,-67.831,0.78795,-0.61287,0.059365,113.1,0.10046,0.032832,-0.9944,265.73
> select clear
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
Drag select of 24 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> view matrix models
> #2,1,-0.00035749,0.0029183,17.129,0.00035399,1,0.0011992,2.2714,-0.0029187,-0.0011981,1,2.8561,#1,0.60749,0.7895,0.087437,-60.567,0.78795,-0.61287,0.059365,114.73,0.10046,0.032832,-0.9944,266.17
Drag select of 15 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.83354,0.54031,-0.11519,-21.719,0.17532,-0.060985,0.98262,-4.0953,0.5239,-0.83925,-0.14556,209.32,#1,0.92003,0.32254,0.22252,-56.803,0.15985,0.20956,-0.96464,233.97,-0.35776,0.92307,0.14124,35.782
> view matrix models
> #2,0.72727,0.67874,0.10197,-57.299,0.67698,-0.73385,0.056346,154.92,0.11307,0.028053,-0.99319,261.75,#1,0.9869,0.16126,0.005431,-11.361,-0.16092,0.98619,-0.039257,34.342,-0.011686,0.037868,0.99921,-5.4026
> view matrix models
> #2,0.73667,0.67594,-0.020513,-41.169,0.67087,-0.72665,0.14801,141.96,0.085138,-0.12279,-0.98877,287.95,#1,0.97777,0.16618,0.12787,-28.523,-0.14951,0.98011,-0.13049,46.797,-0.14701,0.10847,0.98317,7.2293
> view matrix models
> #2,0.74191,0.65035,-0.16316,-18.313,0.66092,-0.75031,0.014577,165.52,-0.11294,-0.11865,-0.98649,316.75,#1,0.94608,0.1811,0.26859,-46.495,-0.18795,0.98218,-0.00018241,33.366,-0.26384,-0.05031,0.96325,52.634
> view matrix models
> #2,0.75434,0.65576,0.030783,-47.593,0.65624,-0.75196,-0.062541,177.01,-0.017865,0.067378,-0.99757,276.2,#1,0.9779,0.19426,0.077252,-25.094,-0.20005,0.97684,0.075955,24.742,-0.060707,-0.089731,0.99411,22.579
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 3 models selected
> select subtract #2
2 models selected
Drag select of 2 residues, 1 cryosparc_P13_J196_map_sharp.mrc
Drag select of 24 residues, 1 cryosparc_P13_J196_map_sharp.mrc
Drag select of 9 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> select clear
> select add #1
2 models selected
> ui mousemode right "translate selected models"
Drag select of 15 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> view matrix models
> #2,0.75434,0.65576,0.030783,-51.858,0.65624,-0.75196,-0.062541,175.29,-0.017865,0.067378,-0.99757,275.96,#1,0.9779,0.19426,0.077252,-29.359,-0.20005,0.97684,0.075955,23.013,-0.060707,-0.089731,0.99411,22.334
> view matrix models
> #2,0.75434,0.65576,0.030783,-43.133,0.65624,-0.75196,-0.062541,177.87,-0.017865,0.067378,-0.99757,276.48,#1,0.9779,0.19426,0.077252,-20.634,-0.20005,0.97684,0.075955,25.597,-0.060707,-0.089731,0.99411,22.857
> view matrix models
> #2,0.75434,0.65576,0.030783,-39.748,0.65624,-0.75196,-0.062541,179.28,-0.017865,0.067378,-0.99757,276.68,#1,0.9779,0.19426,0.077252,-17.249,-0.20005,0.97684,0.075955,27.003,-0.060707,-0.089731,0.99411,23.05
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 3 models selected
> select subtract #2
2 models selected
> view matrix models
> #1,0.9779,0.19426,0.077252,-21.444,-0.20005,0.97684,0.075955,24.842,-0.060707,-0.089731,0.99411,22.82
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 3 models selected
> select subtract #1
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> view matrix models
> #2,0.75434,0.65576,0.030783,-46.557,0.65624,-0.75196,-0.062541,177.41,-0.017865,0.067378,-0.99757,276.26
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.44843,0.63039,0.63365,-85.981,0.67563,-0.7032,0.22145,125.18,0.58518,0.32881,-0.74124,108.58
> view matrix models
> #2,0.79941,0.60076,0.0059221,-41.389,0.59883,-0.79596,-0.088591,196.48,-0.048508,0.074367,-0.99605,279.59
> select add #1
18840 atoms, 18976 bonds, 1210 residues, 3 models selected
> select subtract #1
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> view matrix models
> #2,0.79291,0.60504,0.072225,-50.862,0.60922,-0.78953,-0.074117,191.82,0.01218,0.10277,-0.99463,266.01
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.79291,0.60504,0.072225,-48.864,0.60922,-0.78953,-0.074117,191.67,0.01218,0.10277,-0.99463,282.46
> select add #1
18840 atoms, 18976 bonds, 1210 residues, 3 models selected
> select subtract #1
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> view matrix models
> #2,0.79291,0.60504,0.072225,-54.151,0.60922,-0.78953,-0.074117,191.29,0.01218,0.10277,-0.99463,281.37
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.77908,0.62685,-0.0096452,-43.241,0.62678,-0.77847,0.033751,171.04,0.013648,-0.03234,-0.99938,302.13
> view matrix models
> #2,0.7545,0.6551,-0.039771,-39.336,0.65511,-0.74808,0.10589,151.55,0.039614,-0.10594,-0.99358,308.42
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.7545,0.6551,-0.039771,-43.264,0.65511,-0.74808,0.10589,150.38,0.039614,-0.10594,-0.99358,307.45
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.6845,0.72848,0.027893,-53.779,0.72569,-0.68453,0.069231,135.67,0.069527,-0.027147,-0.99721,291.67
> view matrix models
> #2,0.66787,0.73832,-0.09399,-34.735,0.74369,-0.657,0.12359,120.79,0.029496,-0.15244,-0.98787,315.1
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.66787,0.73832,-0.09399,-28.866,0.74369,-0.657,0.12359,121.47,0.029496,-0.15244,-0.98787,316.37
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.66743,0.72806,-0.15645,-18.022,0.74196,-0.66808,0.056258,133.36,-0.063559,-0.15362,-0.98608,330.25
> view matrix models
> #2,0.66079,0.74987,0.032334,-48.219,0.74593,-0.66088,0.08256,127.79,0.083278,-0.030436,-0.99606,291.19
> view matrix models
> #2,0.67174,0.73949,-0.043741,-37.054,0.72793,-0.66988,-0.14621,165.67,-0.13742,0.066372,-0.98829,308.64
> view matrix models
> #2,0.66058,0.59618,0.4563,-87.814,0.66764,-0.74446,0.0061307,163.39,0.34335,0.30059,-0.88981,186.74
> view matrix models
> #2,0.68897,0.71887,-0.09243,-29.345,0.69271,-0.61559,0.37577,85.616,0.21323,-0.32292,-0.92209,304.65
> view matrix models
> #2,0.61121,0.77755,0.1478,-62.007,0.63168,-0.59175,0.50081,72.708,0.47687,-0.21274,-0.85284,238.29
> view matrix models
> #2,0.83712,0.51637,-0.18055,-8.153,0.52589,-0.85053,0.0057807,200.65,-0.15058,-0.099788,-0.98355,334.86
> fitmap #2 inMap #1
Fit molecule 70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb (#2) to map
cryosparc_P13_J196_map_sharp.mrc (#1) using 18840 atoms
average map value = 0.2525, steps = 104
shifted from previous position = 1.84
rotated from previous position = 7.57 degrees
atoms outside contour = 10928, contour level = 0.19606
Position of 70ATPdimer_HSPA1A-hm_INPUT_symm_multicyc_0001.pdb (#2) relative to
cryosparc_P13_J196_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.72384411 0.68996354 -0.00013645 -62.06873321
0.68996354 -0.72384412 -0.00005075 155.24728364
-0.00013378 -0.00005741 -0.99999999 300.29360526
Axis -0.92841649 -0.37154113 -0.00003364
Axis point -0.00000000 90.04351291 150.14777702
Rotation angle (degrees) 179.99979436
Shift along axis -0.06521712
> select subtract #2
Nothing selected
Drag select of 9 residues, 1 cryosparc_P13_J196_map_sharp.mrc
> select clear
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> surface dust #1 size 8.34
> volume #1 level 0.1438
> lighting full
> lighting shadows false
> lighting shadows true
> lighting soft
> volume style mesh
> volume #1 step 1
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_mesh_fit.cxs
——— End of log from Tue Nov 28 13:20:25 2023 ———
opened ChimeraX session
> open
> /Users/evitatsiolaki/Desktop/paper_Evita/Erics_finalDimer/Erics_final_model/HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-
> ATP.pdb
Chain information for HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-
ATP.pdb #3
---
Chain | Description
B D | No description available
> select add #3
18912 atoms, 19052 bonds, 1212 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.68477,0.70766,0.1741,-85.419,0.60141,-0.68367,0.41341,99.678,0.41158,-0.17839,-0.89374,252.99
> view matrix models
> #3,-0.33128,-0.13664,-0.93359,362.28,0.3479,-0.93743,0.013751,236.6,-0.87705,-0.32024,0.35809,277.33
> view matrix models
> #3,-0.89446,-0.1953,-0.40224,374.82,0.25618,-0.96112,-0.10303,271.68,-0.36648,-0.1952,0.90972,98.04
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.89446,-0.1953,-0.40224,390.24,0.25618,-0.96112,-0.10303,273.43,-0.36648,-0.1952,0.90972,97.322
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.95867,-0.24537,0.14403,324.32,0.26295,-0.95743,0.1191,238.08,0.10867,0.15205,0.98238,-37.18
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb
(#3) to map cryosparc_P13_J196_map_sharp.mrc (#1) using 18912 atoms
average map value = 0.2627, steps = 72
shifted from previous position = 1.52
rotated from previous position = 5.73 degrees
atoms outside contour = 9413, contour level = 0.14382
Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#3)
relative to cryosparc_P13_J196_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99999997 0.00020990 0.00005644 300.25690443
-0.00020990 -0.99999997 0.00009712 300.31161183
0.00005646 0.00009711 0.99999999 0.03859204
Axis -0.00002698 -0.00004874 -1.00000000
Axis point 150.14421040 150.14004914 0.00000000
Rotation angle (degrees) 179.98797373
Shift along axis -0.06132883
> hide #2 models
> hide #!1 models
> show #!1 models
> show #2 models
> select subtract #3
Nothing selected
> select add #2
18840 atoms, 18976 bonds, 1210 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.84187,0.5341,-0.077395,45.998,0.52916,-0.84511,-0.075977,230.18,-0.10599,0.023009,-0.9941,307.99
> view matrix models
> #2,0.84187,0.5341,-0.077395,62.336,0.52916,-0.84511,-0.075977,235.53,-0.10599,0.023009,-0.9941,307.33
> select clear
Alignment identifier is 1
> select #2/A-B:608 #3/B,D:608
48 atoms, 44 bonds, 4 residues, 2 models selected
> select #2/A-B:507-608 #3/B,D:507-608
6608 atoms, 6636 bonds, 408 residues, 2 models selected
> ui tool show "Color Actions"
> color sel #d9aac3ff
> select #2/A-B:506 #3/B,D:506
48 atoms, 44 bonds, 4 residues, 2 models selected
> select #2/A-B:395-506 #3/B,D:395-506
6768 atoms, 6812 bonds, 448 residues, 2 models selected
> color sel #b68070ff
> select #2/A-B:393-394 #3/B,D:393-394
152 atoms, 148 bonds, 8 residues, 2 models selected
> select #2/A-B:4-394 #3/B,D:4-394
24306 atoms, 24498 bonds, 1564 residues, 2 models selected
> color sel #b9e2eaff
> hide #!1 models
> select add #2
30994 atoms, 31226 bonds, 1992 residues, 2 models selected
> select subtract #2
12154 atoms, 12250 bonds, 782 residues, 1 model selected
> hide #2 models
> show #2 models
> show #!1 models
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_cartoon.cxs
> hide #3 models
> show #3 models
> select add #3
18912 atoms, 19052 bonds, 1212 residues, 1 model selected
> select subtract #3
Nothing selected
> hide #2 models
> show #2 models
> close #2
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_cartoon.cxs
——— End of log from Wed Nov 29 12:30:48 2023 ———
opened ChimeraX session
> hide #3 models
> show #3 models
> hide #!1 models
> select /B
9421 atoms, 9489 bonds, 605 residues, 1 model selected
> hide sel target a
> select /D
9421 atoms, 9489 bonds, 605 residues, 1 model selected
> hide sel target a
> select clear
Alignment identifier is 1
> select /B,D:608
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B,D:507-608
3304 atoms, 3318 bonds, 204 residues, 1 model selected
> select /B,D:506
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B,D:391-506
3536 atoms, 3558 bonds, 232 residues, 1 model selected
> select /B,D:390
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B,D:4-390
12002 atoms, 12098 bonds, 774 residues, 1 model selected
> select /B:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel #586c70ff
> color sel #add5dcff
> color sel #8dadb3ff
> select /B,D:608
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B,D:507-608
3304 atoms, 3318 bonds, 204 residues, 1 model selected
> select /B:507-608
1652 atoms, 1659 bonds, 102 residues, 1 model selected
> color sel #8dadb3ff
> color sel #947a88ff
[Repeated 1 time(s)]
> select clear
> select /B,D:506
24 atoms, 22 bonds, 2 residues, 1 model selected
> select /B,D:390-506
3560 atoms, 3582 bonds, 234 residues, 1 model selected
> select /B,D:391
38 atoms, 36 bonds, 2 residues, 1 model selected
> select /B,D:391-506
3536 atoms, 3558 bonds, 232 residues, 1 model selected
> color sel #a97c6fff
> color sel #8d6b60ff
> select clear
> select /D:391-506
1768 atoms, 1779 bonds, 116 residues, 1 model selected
> color sel #8d6b60ff
> color sel #f6c5b1ff
> select clear
Drag select of 5 residues
> select clear
> save fig2.png format png transparentBackground true
> save
> /Users/evitatsiolaki/Desktop/paper_Evita/Figures_All/Final_70dimer_cartoon.cxs
——— End of log from Fri Jan 5 12:41:04 2024 ———
opened ChimeraX session
> NBD — select /B:4-390
Unknown command: NBD — select /B:4-390
> select /B:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel #6cffffff
> color sel #6c7bffff
> color sel #6c7b80ff
> select /B:507-608
1652 atoms, 1659 bonds, 102 residues, 1 model selected
> color sel #807b80ff
> color sel #807280ff
> color sel #80727bff
> select /B:391-506
1768 atoms, 1779 bonds, 116 residues, 1 model selected
> color sel #80717bff
> color sel #80716bff
> select clear
> save fig1.png format png transparentBackground true
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v1.cxs
——— End of log from Wed Mar 27 17:29:34 2024 ———
opened ChimeraX session
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Evitas_finalDimer/final/7.cryosparc_P13_J203_map_sharp.mrc
Opened 7.cryosparc_P13_J203_map_sharp.mrc as #1, grid size 256,256,256, pixel
0.834, shown at level 0.00786, step 1, values float32
> select add #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,58.206,0,1,0,35.076,0,0,1,-6.6324
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.26125,-0.96288,-0.06789,270.88,-0.49058,-0.19302,0.84975,150.99,-0.83131,-0.18869,-0.5228,273.61
> view matrix models
> #1,0.37036,0.51201,0.77503,-26.326,-0.88034,-0.072727,0.46873,218.6,0.29636,-0.85589,0.42381,136.88
> view matrix models
> #1,0.26263,0.8292,0.49341,-25.571,-0.94312,0.11259,0.3128,218.08,0.20382,-0.5475,0.8116,63.935
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.26263,0.8292,0.49341,-11.674,-0.94312,0.11259,0.3128,197.51,0.20382,-0.5475,0.8116,67.692
> view matrix models
> #1,0.26263,0.8292,0.49341,1.59,-0.94312,0.11259,0.3128,209.35,0.20382,-0.5475,0.8116,94.676
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.12631,0.95335,0.27418,23.882,-0.9859,0.090056,0.14105,235.67,0.10978,-0.28813,0.95128,55.461
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.12631,0.95335,0.27418,20.531,-0.9859,0.090056,0.14105,231.15,0.10978,-0.28813,0.95128,56.806
> view matrix models
> #1,0.12631,0.95335,0.27418,22.624,-0.9859,0.090056,0.14105,231.69,0.10978,-0.28813,0.95128,63.82
> fitmap #3 inMap #1
Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb
(#3) to map 7.cryosparc_P13_J203_map_sharp.mrc (#1) using 18912 atoms
average map value = 0.2119, steps = 120
shifted from previous position = 2.98
rotated from previous position = 12.8 degrees
atoms outside contour = 3658, contour level = 0.0078577
Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#3)
relative to 7.cryosparc_P13_J203_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.24282944 0.97006900 0.00000374 -2.39772443
-0.97006899 -0.24282944 0.00012231 288.85235788
0.00011956 0.00002608 1.00000000 -42.16572751
Axis -0.00004960 -0.00005970 -1.00000000
Axis point 111.53251840 145.36237277 0.00000000
Rotation angle (degrees) 104.05359690
Shift along axis 42.14860220
> select clear
> surface dust #1 size 8.34
> volume #1 level 0.04404
> volume #1 level 0.06576
> volume #1 level 0.02957
> color zone #1 near #3 distance 5
> hide #3 models
> save fig1.png format png transparentBackground true
> hide #!1 models
> show #3 models
> select /D:391-506
1768 atoms, 1779 bonds, 116 residues, 1 model selected
> color sel #cda594ff
> color sel #b69384ff
> select clear
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v2.cxs
——— End of log from Thu Jun 6 00:21:10 2024 ———
opened ChimeraX session
> select /D:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel cyan
> color sel #00fdffff
[Repeated 1 time(s)]
> color sel #00ffffff
> select /C:4-390
Nothing selected
> select /B:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel light sea green
> color sel blue
> select /C:4-390
Nothing selected
> select /B:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel cyan
> color sel #3ffda0ff
[Repeated 1 time(s)]
> color sel #00fda0ff
[Repeated 1 time(s)]
> color sel #00ffa0ff
[Repeated 1 time(s)]
> color sel #00ffffff
> select /C:4-390
Nothing selected
> select /D:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel medium blue
> select clear
> select /D:4-390
6001 atoms, 6049 bonds, 387 residues, 1 model selected
> color sel #0071ffff
> color sel #005bffff
> color sel #005affff
> select /D:507-608
1652 atoms, 1659 bonds, 102 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #00f900ff
> color sel #00c700ff
> color sel #00ac00ff
[Repeated 1 time(s)]
> color sel #00aa00ff
> color sel #007700ff
[Repeated 1 time(s)]
> color sel #007c00ff
> color sel #007e00ff
> color sel #008000ff
> color sel #007700ff
[Repeated 2 time(s)]
> color sel #007800ff
> select /B:507-608
1652 atoms, 1659 bonds, 102 residues, 1 model selected
> color sel #00f900ff
> color sel #00f901ff
> color sel #00f90bff
> color sel #00f914ff
> color sel #00f915ff
> color sel #00f917ff
> color sel #00f918ff
> color sel #00f91aff
> color sel #00f91bff
> color sel #00f91dff
> color sel #00f91eff
> color sel #00f91fff
> color sel #00f921ff
> color sel #00f924ff
> color sel #00f926ff
> color sel #00f927ff
> color sel #00f929ff
> color sel #00f92aff
> color sel #00f92bff
> color sel #00f92cff
> color sel #00f92dff
> color sel #00f92eff
> color sel #00f92fff
[Repeated 1 time(s)]
> color sel #00f930ff
[Repeated 1 time(s)]
> color sel #00f931ff
> color sel #00f932ff
[Repeated 1 time(s)]
> color sel #00f934ff
> color sel #00f936ff
> color sel #00f938ff
> color sel #00f93aff
> color sel #00f93dff
> color sel #00f940ff
> color sel #00f943ff
> color sel #00f946ff
> color sel #00f949ff
> color sel #00f94bff
> color sel #00f94fff
> color sel #00f952ff
> color sel #00f955ff
> color sel #00f958ff
> color sel #00f95aff
> color sel #00f95cff
> color sel #00f95eff
> color sel #00f960ff
> color sel #00f962ff
> color sel #00f963ff
> color sel #00f964ff
> color sel #00f965ff
> color sel #00f966ff
> color sel #00f967ff
> color sel #00f968ff
[Repeated 2 time(s)]
> color sel #00f96aff
> color sel #00f96dff
> color sel #00f970ff
> color sel #00f973ff
> color sel #00f977ff
> color sel #00f97aff
> color sel #00f97dff
> color sel #00f980ff
> color sel #00f989ff
> color sel #00f98aff
> color sel #00f98cff
> color sel #00f98dff
[Repeated 1 time(s)]
> color sel #00f98eff
[Repeated 1 time(s)]
> color sel #00f98fff
> color sel #00f990ff
> color sel #00f991ff
[Repeated 1 time(s)]
> color sel #00f992ff
> color sel #00f993ff
> color sel #00f994ff
[Repeated 1 time(s)]
> color sel #00f995ff
> color sel #00f994ff
> color sel #00f98bff
> color sel #00f980ff
> color sel #00f967ff
> color sel #00f95dff
> color sel #00f94eff
> color sel #00f949ff
> color sel #00f947ff
> color sel #00f946ff
> color sel #00f945ff
[Repeated 1 time(s)]
> color sel #00f944ff
> color sel #00f942ff
> color sel #00f93fff
> color sel #00f93dff
> color sel #00f93bff
[Repeated 1 time(s)]
> color sel #00f93aff
> color sel #00f938ff
> color sel #00f930ff
> color sel #00f92bff
> color sel #00f924ff
> color sel #00f91bff
> color sel #00f918ff
> color sel #00f912ff
> color sel #00f90bff
> color sel #00f909ff
> color sel #00f908ff
[Repeated 1 time(s)]
> color sel #00f909ff
> color sel #00f912ff
> color sel #00f928ff
> color sel #00f947ff
> color sel #00f956ff
> color sel #00f965ff
> color sel #00f96eff
> color sel #00f974ff
> color sel #00f976ff
> color sel #00f978ff
> color sel #00f979ff
[Repeated 1 time(s)]
> color sel #00f97aff
> color sel #00f97bff
> color sel #00f97dff
> color sel #00f981ff
> color sel #00f983ff
> color sel #00f985ff
[Repeated 1 time(s)]
> color sel #00f984ff
[Repeated 2 time(s)]
> color sel #00f983ff
> color sel #00f982ff
> color sel #00f981ff
> color sel #00f980ff
[Repeated 1 time(s)]
> color sel #00f973ff
> color sel #00f960ff
> color sel #00f93aff
> color sel #00f925ff
> color sel #00f910ff
> color sel #00f900ff
[Repeated 1 time(s)]
> color sel #0af900ff
> color sel #11f900ff
> color sel #1ef900ff
> color sel #26f900ff
> color sel #2ff900ff
> color sel #35f900ff
> color sel #3ef900ff
> color sel #44f900ff
> color sel #49f900ff
> color sel #4ef900ff
> color sel #55f900ff
> color sel #5bf900ff
> color sel #5ff900ff
> color sel #63f900ff
> color sel #67f900ff
> color sel #69f900ff
> color sel #6cf900ff
> color sel #6ef900ff
[Repeated 1 time(s)]
> color sel #70f900ff
> color sel #72f900ff
> color sel #74f900ff
> color sel #76f900ff
> color sel #78f900ff
> color sel #79f900ff
> color sel #7bf900ff
> color sel #7cf900ff
> color sel #7df900ff
> color sel #7ef900ff
[Repeated 1 time(s)]
> color sel #80f900ff
> color sel #80fa00ff
> color sel #80ff00ff
[Repeated 1 time(s)]
> color sel #86ff00ff
> color sel #90ff00ff
> color sel #94ff00ff
> color sel #99ff00ff
> color sel #9fff00ff
> color sel #a1ff00ff
> color sel #a4ff00ff
> color sel #a7ff00ff
> color sel #a8ff00ff
> color sel #a9ff00ff
[Repeated 2 time(s)]
> color sel #a8ff00ff
> color sel #a3ff00ff
> color sel #9eff00ff
> color sel #9aff00ff
> color sel #93ff00ff
> color sel #8eff00ff
> color sel #8aff00ff
> color sel #88ff00ff
> color sel #87ff00ff
> color sel #86ff00ff
> color sel #85ff00ff
[Repeated 1 time(s)]
> color sel #84ff00ff
> color sel #81ff00ff
> color sel #80ff00ff
> color sel #73ff00ff
> color sel #55ff00ff
> color sel #2dff00ff
> color sel #08ff00ff
> color sel #00ff00ff
[Repeated 1 time(s)]
> color sel #00ff02ff
> color sel #00ff03ff
> color sel #00ff06ff
> color sel #00ff09ff
> color sel #00ff0cff
> color sel #00ff10ff
> color sel #00ff19ff
> color sel #00ff21ff
> color sel #00ff24ff
> color sel #00ff2bff
> color sel #00ff34ff
> color sel #00ff3bff
> color sel #00ff3eff
> color sel #00ff46ff
> color sel #00ff4bff
> color sel #00ff51ff
> color sel #00ff5aff
> color sel #00ff5fff
> color sel #00ff63ff
> color sel #00ff68ff
> color sel #00ff6bff
> color sel #00ff6eff
> color sel #00ff72ff
> color sel #00ff74ff
> color sel #00ff77ff
> color sel #00ff7aff
> color sel #00ff7cff
> color sel #00ff7eff
> color sel #00ff80ff
> color sel #00ff78ff
> color sel #73fa79ff
[Repeated 2 time(s)]
> color sel #73fa78ff
[Repeated 1 time(s)]
> color sel #64fa78ff
> select /D:391-506
1768 atoms, 1779 bonds, 116 residues, 1 model selected
> color sel #ff40ffff
> color sel #ff9300ff
[Repeated 2 time(s)]
> color sel #ff2600ff
> color sel #ff7e79ff
> color sel #ff9300ff
[Repeated 1 time(s)]
> color sel #ff7800ff
[Repeated 1 time(s)]
> color sel #ff7500ff
> color sel #ff7300ff
> color sel #ff6c00ff
> color sel #ff6b00ff
[Repeated 2 time(s)]
> color sel #ff6a00ff
> color sel #ff6900ff
> color sel #ff6600ff
> color sel #ff6400ff
> color sel #ff6100ff
> color sel #ff5f00ff
[Repeated 1 time(s)]
> color sel #ff5e00ff
> color sel #ff5d00ff
> color sel #ff5b00ff
> color sel #ff5a00ff
> color sel #ff5900ff
[Repeated 2 time(s)]
> color sel #ff6300ff
> color sel #ff6700ff
> color sel #ff7100ff
> color sel #ff7400ff
> color sel #ff7700ff
> color sel #ff7900ff
> color sel #ff7c00ff
> color sel #ff7d00ff
> color sel #ff8000ff
[Repeated 1 time(s)]
> color sel #f78000ff
> color sel #f68000ff
> color sel #ed8000ff
> color sel #ea8000ff
> color sel #e68000ff
> color sel #e38000ff
> color sel #e18000ff
> color sel #de8000ff
> color sel #db8000ff
> color sel #da8000ff
> color sel #d88000ff
> color sel #d68000ff
> color sel #d48000ff
> color sel #d28000ff
> color sel #cf8000ff
> color sel #cd8000ff
> color sel #ca8000ff
> color sel #c88000ff
> color sel #c68000ff
> color sel #c48000ff
> color sel #c38000ff
> color sel #c08000ff
> color sel #be8000ff
> color sel #bc8000ff
> color sel #ba8000ff
> color sel #b88000ff
> color sel #b78000ff
> color sel #b58000ff
> color sel #b28000ff
> color sel #b18000ff
> color sel #b08000ff
[Repeated 4 time(s)]
> color sel #b18000ff
[Repeated 1 time(s)]
> color sel #b28000ff
[Repeated 1 time(s)]
> color sel #b38000ff
> color sel #b48000ff
> color sel #b88000ff
> color sel #bd8000ff
> color sel #bf8000ff
> color sel #c28000ff
> color sel #c48000ff
> color sel #c68000ff
> color sel #c88000ff
> color sel #ca8000ff
> color sel #cc8000ff
> color sel #ce8000ff
> color sel #cf8000ff
> color sel #d08000ff
> color sel #d18000ff
> color sel #d28000ff
> color sel #d38000ff
[Repeated 2 time(s)]
> color sel #d18000ff
[Repeated 1 time(s)]
> color sel #d08000ff
> color sel #cf8000ff
[Repeated 1 time(s)]
> color sel #ce8000ff
[Repeated 2 time(s)]
> color sel #cd8000ff
[Repeated 1 time(s)]
> color sel #cc8000ff
[Repeated 2 time(s)]
> color sel #cd8000ff
> color sel #ce8000ff
[Repeated 1 time(s)]
> color sel #cd8000ff
[Repeated 1 time(s)]
> color sel #cc8000ff
[Repeated 1 time(s)]
> color sel #cb8000ff
> color sel #ca8000ff
[Repeated 1 time(s)]
> color sel #c98000ff
[Repeated 2 time(s)]
> color sel #c88000ff
> color sel #c78000ff
[Repeated 3 time(s)]
> color sel #c88000ff
[Repeated 1 time(s)]
> color sel #c98000ff
[Repeated 1 time(s)]
> color sel #ca8000ff
[Repeated 2 time(s)]
> color sel #ca8004ff
> color sel #ca8007ff
> color sel #ca800bff
> color sel #ca800cff
> color sel #ca800dff
[Repeated 2 time(s)]
> color sel #ca800eff
[Repeated 1 time(s)]
> color sel #ca800fff
> color sel #ca8010ff
[Repeated 2 time(s)]
> color sel #ca8012ff
> color sel #ca8014ff
> color sel #ca8016ff
> color sel #ca8019ff
> color sel #ca801bff
> color sel #ca801dff
> color sel #ca801fff
> color sel #ca8020ff
> color sel #ca8021ff
> color sel #ca8022ff
> color sel #ca8023ff
> color sel #ca8024ff
> color sel #ca8025ff
> color sel #ca8026ff
> color sel #ca8027ff
[Repeated 1 time(s)]
> color sel #ca8028ff
> color sel #ca802aff
> color sel #ca802cff
> color sel #ca802dff
> color sel #ca802eff
> color sel #ca8030ff
[Repeated 2 time(s)]
> color sel #ca8032ff
[Repeated 1 time(s)]
> color sel #c88032ff
> select /B:391-506
1768 atoms, 1779 bonds, 116 residues, 1 model selected
> color sel orange
> ui tool show "Color Actions"
> color sel #c8806fff
> color sel #c8807dff
> color sel #c88036ff
> color sel #c88000ff
> color sel #c89500ff
> color sel #c8a600ff
> color sel #c8b900ff
> color sel #c8b800ff
> color sel #c8b700ff
> color sel #c8b600ff
[Repeated 2 time(s)]
> color sel #c8b500ff
> color sel #c8b400ff
> color sel #c8b200ff
> color sel #c8b100ff
[Repeated 2 time(s)]
> color sel #c8b000ff
> color sel #c8af00ff
[Repeated 1 time(s)]
> color sel #c8ae00ff
[Repeated 1 time(s)]
> color sel #ffd479ff
> color sel #ff7e79ff
> color sel #ffd479ff
> color sel #fffb00ff
> color sel #fffc00ff
> color sel #ffff00ff
> color sel #fffd00ff
> color sel #fff900ff
> color sel #fff200ff
> color sel #ffef00ff
> color sel #ffec00ff
> color sel #ffe900ff
> color sel #ffe600ff
> color sel #ffe300ff
> color sel #ffdf00ff
> color sel #ffdb00ff
> color sel #ffd800ff
> color sel #ffd600ff
> color sel #ffd500ff
> color sel #ffd300ff
> color sel #ffd200ff
> color sel #ffd100ff
> color sel #ffd000ff
[Repeated 1 time(s)]
> color sel #ffcf00ff
[Repeated 1 time(s)]
> color sel #ffcd00ff
> color sel #ffcc00ff
> color sel #ffca00ff
> color sel #ffc800ff
> color sel #ffc700ff
> color sel #ffc600ff
> color sel #ffc500ff
[Repeated 1 time(s)]
> color sel #ff8000ff
> color sel #ff0000ff
> color sel #ff8000ff
> color sel #ff8080ff
[Repeated 1 time(s)]
> color sel #ff8086ff
> color sel #ff8088ff
> color sel #ff808cff
[Repeated 1 time(s)]
> color sel #ff808dff
[Repeated 1 time(s)]
> color sel #ff808eff
> color sel #ff8090ff
> color sel #ff8092ff
> color sel #ff8094ff
> color sel #ff8095ff
> color sel #ff8096ff
> color sel #ff8098ff
> color sel #ff8099ff
> color sel #ff809bff
> color sel #ff809cff
> color sel #ff809dff
> color sel #ff809fff
> color sel #ff80a0ff
> color sel #ff80a2ff
> color sel #ff80a3ff
> color sel #ff80a4ff
> color sel #ff80a5ff
> color sel #ff80a6ff
> color sel #ff80a7ff
> color sel #ff80a8ff
[Repeated 1 time(s)]
> color sel #ff80a9ff
[Repeated 1 time(s)]
> color sel #ff80aaff
> color sel #ff80abff
> color sel #ff80acff
> color sel #ff80adff
> color sel #ff80aeff
> color sel #ff80adff
[Repeated 1 time(s)]
> color sel #ff80aaff
> color sel #ff80a9ff
> color sel #ff80a7ff
> color sel #ff80a6ff
> color sel #ff80a5ff
> color sel #ff80a4ff
> color sel #ff80a3ff
> color sel #ff80a1ff
> color sel #ff80a0ff
> color sel #ff809eff
> color sel #ff809cff
> color sel #ff809bff
> color sel #ff8099ff
> color sel #ff8097ff
> color sel #ff8095ff
> color sel #ff8093ff
> color sel #ff8091ff
> color sel #ff808fff
> color sel #ff808eff
> color sel #ff808dff
[Repeated 1 time(s)]
> color sel #ff808cff
[Repeated 1 time(s)]
> color sel #ff808bff
[Repeated 1 time(s)]
> color sel #ff808aff
[Repeated 1 time(s)]
> color sel #ff8088ff
> color sel #ff8087ff
> color sel #ff8086ff
[Repeated 1 time(s)]
> color sel #ff8085ff
[Repeated 2 time(s)]
> color sel #ff8084ff
> color sel #ff8083ff
> color sel #ff8082ff
> color sel #ff8080ff
> color sel #ff8076ff
> color sel #ff8074ff
> color sel #ff8072ff
> color sel #ff8071ff
> color sel #ff8070ff
[Repeated 1 time(s)]
> color sel #ff806fff
[Repeated 1 time(s)]
> color sel #ff806cff
> color sel #ff806aff
> color sel #ff8069ff
> color sel #ff8068ff
[Repeated 1 time(s)]
> color sel #ff8067ff
[Repeated 1 time(s)]
> color sel #ff8065ff
> color sel #ff8064ff
> color sel #ff8063ff
[Repeated 1 time(s)]
> color sel #ff8062ff
> color sel #ff8061ff
> color sel #ff8060ff
[Repeated 1 time(s)]
> color sel #ff805fff
> color sel #ff805eff
[Repeated 2 time(s)]
> color sel #ff805fff
[Repeated 1 time(s)]
> color sel #ff8060ff
> color sel #ff8061ff
> color sel #ff8063ff
> color sel #ff8067ff
> color sel #ff806aff
> color sel #ff806cff
> color sel #ff806fff
> color sel #ff8071ff
> color sel #ff8073ff
> color sel #ff8074ff
> color sel #ff8075ff
> color sel #ff8076ff
> color sel #ff8077ff
> color sel #ff8078ff
> color sel #ff8079ff
[Repeated 2 time(s)]
> color sel #ff807aff
> color sel #ff807dff
[Repeated 1 time(s)]
> color sel #ff7e79ff
[Repeated 1 time(s)]
> color sel #ff7e78ff
[Repeated 1 time(s)]
> color sel #ff8078ff
> select clear
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v3.cxs
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v3.cxs
> save fig1.png format png transparentBackground true
> show #!1 models
> color zone #1 near #3 distance 5
> select clear
> hide #3 models
> save fig1.png format png transparentBackground true
> volume #1 level 0.06214
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Erics_finalDimer/Erics_final_model/cryosparc_P13_J193_009_volume_map_sharp.mrc
Opened cryosparc_P13_J193_009_volume_map_sharp.mrc as #2, grid size
360,360,360, pixel 0.834, shown at level 0.298, step 2, values float32
> surface dust #1 size 8.34
> surface dust #2 size 8.34
> volume #2 level 0.8273
> close #2
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Erics_finalDimer/Erics_final_model/cryosparc_P13_J196_map_sharp.mrc
Opened cryosparc_P13_J196_map_sharp.mrc as #2, grid size 360,360,360, pixel
0.834, shown at level 0.000168, step 2, values float32
> surface dust #1 size 8.34
> surface dust #2 size 8.34
> volume #2 level 0.02955
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,16.164,0,1,0,1.4079,0,0,1,-4.6115
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.93247,0.091632,0.34944,-40.459,-0.16059,0.97161,0.17374,3.4713,-0.3236,-0.21812,0.92071,88.867
> fitmap #2 inMap #1
Fit map cryosparc_P13_J196_map_sharp.mrc in map
7.cryosparc_P13_J203_map_sharp.mrc using 15902 points
correlation = 0.7946, correlation about mean = 0.5771, overlap = 1701
steps = 68, shift = 2.36, angle = 5.04 degrees
Position of cryosparc_P13_J196_map_sharp.mrc (#2) relative to
7.cryosparc_P13_J203_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.24386720 -0.96980864 0.00002542 215.77502880
0.96980859 0.24386717 -0.00033044 -75.43096607
0.00031427 0.00010523 0.99999995 -42.28756803
Axis 0.00022462 -0.00014892 0.99999996
Axis point 156.26981096 100.66293508 0.00000000
Rotation angle (degrees) 75.88510380
Shift along axis -42.22786577
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #3 models
> fitmap #3 inMap #2
Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb
(#3) to map cryosparc_P13_J196_map_sharp.mrc (#2) using 18912 atoms
average map value = 0.2627, steps = 40
shifted from previous position = 0.0303
rotated from previous position = 0.0623 degrees
atoms outside contour = 2419, contour level = 0.029551
Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#3)
relative to cryosparc_P13_J196_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
-1.00000000 0.00006244 0.00007244 300.26309200
-0.00006245 -1.00000000 -0.00006508 300.31222558
0.00007244 -0.00006508 1.00000000 0.06280715
Axis -0.00003202 0.00003453 -1.00000000
Axis point 150.13623342 150.15142621 0.00000000
Rotation angle (degrees) 179.99642203
Shift along axis -0.06205069
> color zone #2 near #3 distance 5
> volume #2 level 0.07199
> hide #3 models
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> select clear
> save fig1.png format png transparentBackground true
> volume #2 level 0.1275
> save fig1.png format png transparentBackground true
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/Final_70dimer_cartoon_v3.cxs
——— End of log from Wed Jun 19 21:42:35 2024 ———
opened ChimeraX session
> close #1
> close #2
> show #3 models
> rename #3 id #1
> open 4b9q fromDatabase pdb format mmcif
4b9q title:
Open conformation of ATP-bound Hsp70 homolog DnaK [more info...]
Chain information for 4b9q #2
---
Chain | Description | UniProt
A B C D | CHAPERONE PROTEIN DNAK | DNAK_ECOLI 1-605
Non-standard residues in 4b9q #2
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
4b9q mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
> select #2/B,D
9348 atoms, 9211 bonds, 16 pseudobonds, 1431 residues, 3 models selected
> hide (#!2 & sel) target a
> cartoon hide (#!2 & sel)
> select #2/A,C
9412 atoms, 9238 bonds, 13 pseudobonds, 1479 residues, 3 models selected
> view matrix models #2,1,0,0,42.698,0,1,0,56.11,0,0,1,-18.777
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.10508,-0.82492,0.55539,147.38,-0.077433,0.55,0.83157,23.781,-0.99144,-0.13039,-0.0060826,182.84
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.10508,-0.82492,0.55539,152.09,-0.077433,0.55,0.83157,51.623,-0.99144,-0.13039,-0.0060826,256.18
> view matrix models
> #2,0.10508,-0.82492,0.55539,163.08,-0.077433,0.55,0.83157,50.536,-0.99144,-0.13039,-0.0060826,257.65
> ui tool show Matchmaker
> matchmaker #!2 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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4b9q, chain A (#2), sequence alignment score = 1745.9
RMSD between 454 pruned atom pairs is 0.883 angstroms; (across all 590 pairs:
4.477)
> hide #!2 models
> select add #2
18760 atoms, 18449 bonds, 29 pseudobonds, 2910 residues, 3 models selected
Cell requested for row 0 is out of bounds for table with 4 rows! Resizing
table model.
> select subtract #2
Nothing selected
> open 5e84 fromDatabase pdb format mmcif
5e84 title:
ATP-bound state of BiP [more info...]
Chain information for 5e84 #3
---
Chain | Description | UniProt
A B C D E F | 78 kDa glucose-regulated protein | GRP78_HUMAN 25-629
Non-standard residues in 5e84 #3
---
ATP — adenosine-5'-triphosphate
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
5e84 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| author_and_software_defined_assembly
4| author_and_software_defined_assembly
5| author_and_software_defined_assembly
6| author_and_software_defined_assembly
> select #2/F,D
4637 atoms, 4596 bonds, 8 pseudobonds, 687 residues, 3 models selected
> select #3/F,D
9489 atoms, 9608 bonds, 21 pseudobonds, 1233 residues, 2 models selected
> select #3/A,B,C,E
18995 atoms, 19222 bonds, 44 pseudobonds, 2477 residues, 2 models selected
> hide (#!3 & sel) target a
> select #3/F,D
9489 atoms, 9608 bonds, 21 pseudobonds, 1233 residues, 2 models selected
> hide (#!3 & sel) target a
> cartoon (#!3 & sel)
> color #3 #ff8ad8ff
> color #3 #73fa79ff
> view matrix models #3,1,0,0,68.828,0,1,0,-1.1376,0,0,1,-16.675
> view matrix models #3,1,0,0,191.98,0,1,0,47.117,0,0,1,175.77
> view matrix models #3,1,0,0,156.18,0,1,0,38.439,0,0,1,177.48
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.42297,-0.47482,0.77178,240.48,-0.90037,-0.31625,0.29887,188.86,0.10217,-0.8213,-0.56127,192.28
> view matrix models
> #3,0.29651,-0.031991,0.95449,208.75,-0.78868,-0.57183,0.22584,207.67,0.53858,-0.81975,-0.19479,197.86
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.29651,-0.031991,0.95449,217.13,-0.78868,-0.57183,0.22584,233.47,0.53858,-0.81975,-0.19479,210.64
> view matrix models
> #3,0.29651,-0.031991,0.95449,202.99,-0.78868,-0.57183,0.22584,230.24,0.53858,-0.81975,-0.19479,217.55
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #!3 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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 5e84, chain F (#3), sequence alignment score = 2217.5
RMSD between 482 pruned atom pairs is 0.739 angstroms; (across all 598 pairs:
3.613)
> matchmaker #!3 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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 5e84, chain F (#3), sequence alignment score = 2217.5
RMSD between 482 pruned atom pairs is 0.739 angstroms; (across all 598 pairs:
3.613)
> ui tool show Matchmaker
> matchmaker #!2-3 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4b9q, chain A (#2), sequence alignment score = 1745.9
RMSD between 454 pruned atom pairs is 0.883 angstroms; (across all 590 pairs:
4.477)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 5e84, chain F (#3), sequence alignment score = 2217.5
RMSD between 482 pruned atom pairs is 0.739 angstroms; (across all 598 pairs:
3.613)
> matchmaker #!2-3 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4b9q, chain A (#2), sequence alignment score = 1745.9
RMSD between 454 pruned atom pairs is 0.883 angstroms; (across all 590 pairs:
4.477)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 5e84, chain F (#3), sequence alignment score = 2217.5
RMSD between 482 pruned atom pairs is 0.739 angstroms; (across all 598 pairs:
3.613)
> show #!2 models
> open 4JNE fromDatabase pdb format mmcif
Summary of feedback from opening 4JNE fetched from pdb
---
note | Fetching compressed mmCIF 4jne from http://files.rcsb.org/download/4jne.cif
4jne title:
Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP
[more info...]
Chain information for 4jne #4
---
Chain | Description | UniProt
A B | Hsp70 CHAPERONE DnaK | DNAK_ECOLI 2-610
Non-standard residues in 4jne #4
---
ATP — adenosine-5'-triphosphate
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
SO4 — sulfate ion
5 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> color #4 #0096ffff
> select add #3
28484 atoms, 28830 bonds, 65 pseudobonds, 3710 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.265,-0.22123,0.93852,233.14,-0.80681,-0.58388,0.090176,229.39,0.52804,-0.78111,-0.33323,209.92
> view matrix models
> #3,0.265,-0.22123,0.93852,221.67,-0.80681,-0.58388,0.090176,225.22,0.52804,-0.78111,-0.33323,204.36
> select subtract #3
Nothing selected
> select add #4
10672 atoms, 9366 bonds, 12 pseudobonds, 2616 residues, 2 models selected
> view matrix models #4,1,0,0,108.36,0,1,0,49.116,0,0,1,37.275
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> view matrix models #4,1,0,0,166.98,0,1,0,84.659,0,0,1,77.303
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.42181,-0.75699,-0.49905,257.84,-0.89777,0.42572,0.11306,136.73,0.12687,0.49571,-0.85917,88.383
> view matrix models
> #4,-0.54921,-0.54102,0.63691,218.73,-0.76764,0.62784,-0.12861,126.44,-0.3303,-0.55956,-0.76013,164.52
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.54921,-0.54102,0.63691,190.1,-0.76764,0.62784,-0.12861,122.19,-0.3303,-0.55956,-0.76013,173.61
> view matrix models
> #4,-0.54921,-0.54102,0.63691,209.94,-0.76764,0.62784,-0.12861,138.78,-0.3303,-0.55956,-0.76013,221.58
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.16928,-0.56953,0.80435,199.12,-0.8337,0.51802,0.19133,139.6,-0.52563,-0.6382,-0.56251,226.41
> select add #1
29584 atoms, 28418 bonds, 12 pseudobonds, 3828 residues, 3 models selected
> ui tool show Matchmaker
> matchmaker #!4 & sel to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4jne, chain A (#4), sequence alignment score = 1704.4
RMSD between 450 pruned atom pairs is 0.896 angstroms; (across all 586 pairs:
4.096)
> matchmaker #!4 & sel to #1/B & sel pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4jne, chain A (#4), sequence alignment score = 1704.4
RMSD between 450 pruned atom pairs is 0.896 angstroms; (across all 586 pairs:
4.096)
> hide #!4 models
> select subtract #4
18912 atoms, 19052 bonds, 1212 residues, 1 model selected
> open 6ASY fromDatabase pdb format mmcif
Summary of feedback from opening 6ASY fetched from pdb
---
note | Fetching compressed mmCIF 6asy from http://files.rcsb.org/download/6asy.cif
6asy title:
BiP-ATP2 [more info...]
Chain information for 6asy #5
---
Chain | Description | UniProt
A B | 78 kDa glucose-regulated protein | GRP78_HUMAN 25-629
Non-standard residues in 6asy #5
---
ATP — adenosine-5'-triphosphate
GOL — glycerol (glycerin; propane-1,2,3-triol)
PO4 — phosphate ion
SO4 — sulfate ion
170 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select add #5
29739 atoms, 28782 bonds, 3661 residues, 2 models selected
> select subtract #1
10827 atoms, 9730 bonds, 2449 residues, 1 model selected
> view matrix models
> #5,0.98897,0.14438,-0.033129,-2.8981,-0.14316,0.98902,0.03662,1.0738,0.038052,-0.031474,0.99878,0.42049
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.98897,0.14438,-0.033129,57.104,-0.14316,0.98902,0.03662,38.94,0.038052,-0.031474,0.99878,-23.163
> view matrix models
> #5,0.98897,0.14438,-0.033129,74.572,-0.14316,0.98902,0.03662,50.732,0.038052,-0.031474,0.99878,1.5782
> view matrix models
> #5,0.98897,0.14438,-0.033129,128.83,-0.14316,0.98902,0.03662,102.27,0.038052,-0.031474,0.99878,71.772
> view matrix models
> #5,0.98897,0.14438,-0.033129,174.18,-0.14316,0.98902,0.03662,142.83,0.038052,-0.031474,0.99878,129.73
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.1071,0.44579,-0.88871,177.81,0.30385,0.83641,0.45618,141.03,0.94668,-0.31889,-0.045875,134.78
> view matrix models
> #5,-0.74543,0.16748,0.6452,182.59,0.63358,0.47882,0.6077,145.97,-0.20716,0.86179,-0.46304,118.52
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.74543,0.16748,0.6452,186.92,0.63358,0.47882,0.6077,128.31,-0.20716,0.86179,-0.46304,140.42
> view matrix models
> #5,-0.74543,0.16748,0.6452,176.22,0.63358,0.47882,0.6077,129.84,-0.20716,0.86179,-0.46304,146.27
> ui tool show Matchmaker
> matchmaker #5 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 6asy, chain B (#5), sequence alignment score = 2179.6
RMSD between 463 pruned atom pairs is 0.696 angstroms; (across all 598 pairs:
2.651)
> matchmaker #5 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 6asy, chain B (#5), sequence alignment score = 2179.6
RMSD between 463 pruned atom pairs is 0.696 angstroms; (across all 598 pairs:
2.651)
> show #!4 models
> show #!3 models
> show #!2 models
> select add #2
29587 atoms, 28179 bonds, 29 pseudobonds, 5359 residues, 4 models selected
> select add #3
58071 atoms, 57009 bonds, 94 pseudobonds, 9069 residues, 6 models selected
> select add #4
68743 atoms, 66375 bonds, 106 pseudobonds, 11685 residues, 8 models selected
> select add #1
87655 atoms, 85427 bonds, 106 pseudobonds, 12897 residues, 9 models selected
> tile
5 models tiled
> tile off
> select subtract #2
68895 atoms, 66978 bonds, 77 pseudobonds, 9987 residues, 6 models selected
> select subtract #3
40411 atoms, 38148 bonds, 12 pseudobonds, 6277 residues, 4 models selected
> select subtract #5
29584 atoms, 28418 bonds, 12 pseudobonds, 3828 residues, 3 models selected
> select subtract #4
18912 atoms, 19052 bonds, 1212 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
18760 atoms, 18449 bonds, 29 pseudobonds, 2910 residues, 3 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.2117,0.3892,0.89649,34.201,0.37367,-0.81536,0.44222,92.327,0.90308,0.42861,0.027176,19.925
> view matrix models
> #2,-0.2117,0.3892,0.89649,72.783,0.37367,-0.81536,0.44222,117.5,0.90308,0.42861,0.027176,39.452
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.51406,0.36677,0.77539,117.15,-0.71623,-0.68095,-0.15273,276.35,0.47198,-0.63387,0.61274,107.97
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.51406,0.36677,0.77539,116.29,-0.71623,-0.68095,-0.15273,279.37,0.47198,-0.63387,0.61274,88.429
> select subtract #2
Nothing selected
> select add #3
28484 atoms, 28830 bonds, 65 pseudobonds, 3710 residues, 2 models selected
> view matrix models
> #3,-0.2117,0.3892,0.89649,4.0108,0.37367,-0.81536,0.44222,135.83,0.90308,0.42861,0.027176,41.581
> view matrix models
> #3,-0.2117,0.3892,0.89649,160.33,0.37367,-0.81536,0.44222,248.51,0.90308,0.42861,0.027176,64.795
> view matrix models
> #3,-0.2117,0.3892,0.89649,149.95,0.37367,-0.81536,0.44222,242.47,0.90308,0.42861,0.027176,98.552
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.97327,-0.17019,0.15421,151.21,-0.17004,-0.98533,-0.014267,251.11,0.15438,-0.012335,-0.98794,114.92
> view matrix models
> #3,0.81809,-0.56259,0.11925,189.19,-0.5739,-0.81198,0.10642,247.25,0.036956,-0.15549,-0.98715,130.44
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.81809,-0.56259,0.11925,199.14,-0.5739,-0.81198,0.10642,234.75,0.036956,-0.15549,-0.98715,125.85
> select subtract #3
Nothing selected
> select add #4
10672 atoms, 9366 bonds, 12 pseudobonds, 2616 residues, 2 models selected
> view matrix models
> #4,-0.2117,0.3892,0.89649,113.44,0.37367,-0.81536,0.44222,184.85,0.90308,0.42861,0.027176,69.047
> view matrix models
> #4,-0.2117,0.3892,0.89649,103.11,0.37367,-0.81536,0.44222,175.96,0.90308,0.42861,0.027176,81.165
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.83119,-0.55595,-0.0064723,201.9,0.54221,-0.81311,0.21178,176,-0.123,0.17252,0.9773,96.777
> select subtract #4
Nothing selected
> select add #5
10827 atoms, 9730 bonds, 2449 residues, 1 model selected
> view matrix models
> #5,-0.42256,0.063541,0.90411,13.825,0.16047,-0.97654,0.14363,157.19,0.89202,0.20577,0.40244,-51.465
> view matrix models
> #5,-0.40413,0.1132,0.90767,12.557,0.16086,-0.96805,0.19235,156.76,0.90045,0.22374,0.37301,-51.796
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.40413,0.1132,0.90767,55.68,0.16086,-0.96805,0.19235,76.961,0.90045,0.22374,0.37301,105.27
> view matrix models
> #5,-0.40413,0.1132,0.90767,156.87,0.16086,-0.96805,0.19235,153.11,0.90045,0.22374,0.37301,114.47
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.30813,0.80709,-0.50365,147.53,0.71403,0.54604,0.43818,114.09,0.62866,-0.2246,-0.74454,131.88
> ui mousemode right zoom
> ui tool show Matchmaker
> matchmaker #5#!2-4 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 6asy, chain B (#5), sequence alignment score = 2179.6
RMSD between 463 pruned atom pairs is 0.696 angstroms; (across all 598 pairs:
2.651)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4b9q, chain A (#2), sequence alignment score = 1745.9
RMSD between 454 pruned atom pairs is 0.883 angstroms; (across all 590 pairs:
4.477)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 5e84, chain F (#3), sequence alignment score = 2217.5
RMSD between 482 pruned atom pairs is 0.739 angstroms; (across all 598 pairs:
3.613)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4jne, chain A (#4), sequence alignment score = 1704.4
RMSD between 450 pruned atom pairs is 0.896 angstroms; (across all 586 pairs:
4.096)
> matchmaker #5#!2-4 to #1/B pairing bs
Parameters
---
Chain pairing | bs
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 HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 6asy, chain B (#5), sequence alignment score = 2179.6
RMSD between 463 pruned atom pairs is 0.696 angstroms; (across all 598 pairs:
2.651)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4b9q, chain A (#2), sequence alignment score = 1745.9
RMSD between 454 pruned atom pairs is 0.883 angstroms; (across all 590 pairs:
4.477)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 5e84, chain F (#3), sequence alignment score = 2217.5
RMSD between 482 pruned atom pairs is 0.739 angstroms; (across all 598 pairs:
3.613)
Matchmaker HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb,
chain B (#1) with 4jne, chain A (#4), sequence alignment score = 1704.4
RMSD between 450 pruned atom pairs is 0.896 angstroms; (across all 586 pairs:
4.096)
> hide sel target a
> select clear
Drag select of 24 atoms, 239 residues, 18 bonds, 4 pseudobonds
> select clear
> color #1 #919191ff
> color #2 #ff8ad8ff
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/model_vs_AllCrystal.cxs
——— End of log from Tue Oct 29 15:20:43 2024 ———
opened ChimeraX session
> close #2
> close #3
> close #4
> select add #1
18912 atoms, 19052 bonds, 1212 residues, 1 model selected
> select add #5
29739 atoms, 28782 bonds, 3661 residues, 2 models selected
> hide sel target a
> cartoon style sel modeHelix tube sides 20
> select subtract #1
10827 atoms, 9730 bonds, 2449 residues, 1 model selected
> select subtract #5
Nothing selected
> open
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/sequence_Alignment_files/hHsp70_6asy.aln
Summary of feedback from opening
/Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/sequence_Alignment_files/hHsp70_6asy.aln
---
notes | Alignment identifier is hHsp70_6asy.aln
Associated HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb chain
B to hHsp70 with 0 mismatches
Associated HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb chain
D to hHsp70 with 0 mismatches
Associated 6asy chain A to 6ASY_1|Chains with 0 mismatches
Associated 6asy chain B to 6ASY_1|Chains with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment hHsp70_6asy.aln
Opened 2 sequences from hHsp70_6asy.aln
> ui tool show "Render/Select by Attribute"
> color byattribute r:seq_conservation target csab palette
> -1.343,darkcyan:-0.3,white:0.743,darkgoldenrod
29739 atoms, 3661 residues, atom seq_conservation range -1.34 to 0.743
> color byattribute r:seq_conservation target csab palette
> -1.343,darkcyan:-0.3,white:0.743,darkgoldenrod
29739 atoms, 3661 residues, atom seq_conservation range -1.34 to 0.743
> hide #1 models
> save 6asy.png supersample 3 transparentBackground true
> turn y 1 90 models all center #1
> save 6asy_90.png supersample 3 transparentBackground true
> turn y 1 270 models all center #1
> show #1 models
> save
> /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/sequence_Alignment_files/hHsp70_6asy_conservation.cxs
> ui mousemode right "color key"
> ui mousemode right zoom
> ui mousemode right "color key"
> key delete
> ui mousemode right zoom
> ui mousemode right "color key"
> key delete
> ui mousemode right zoom
> color byattribute r:seq_conservation target csab palette
> -1.343,darkcyan:-0.3,white:0.743,darkgoldenrod key true
> key lipophilicity :-1.34 :-0.30 :0.74 showTool true
> ui mousemode right "color key"
29739 atoms, 3661 residues, atom seq_conservation range -1.34 to 0.743
> key colorTreatment distinct
> key colorTreatment blended
> ui mousemode right zoom
> ui mousemode middle 'color key'
> key labelColor #bfbfbf
> key labelColor default
> key bold true
> key numericLabelSpacing equal
> key labelOffset -1.0
> key labelOffset -2.0
> key labelOffset -3.0
> key labelOffset -2.0
> key labelOffset -1.0
> key border false
> key border true
> key borderWidth 1.0
> key borderWidth 0.0
> key borderWidth 1.0
> key ticks true
> key ticks false
> ui mousemode middle translate
> hide #1 models
> hide #5 models
> select clear
[Repeated 1 time(s)]
> select add #2
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-0.42811,0,1,0,-2.6034,0,0,1,32.988
> view matrix models #2,1,0,0,-13.975,0,1,0,25.925,0,0,1,64.958
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> select subtract #2
Nothing selected
> select add #2
1 model selected
> hide #2 models
> select subtract #2
Nothing selected
> show #2 models
> select add #2
1 model selected
> ui mousemode right "color key"
> ui mousemode right "translate selected models"
> view sel
Traceback (most recent call last):
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1386, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 401, in try_shortcut
self.run_shortcut(keys)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 419, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 338, in run
f(s)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 997, in view_selected
run(session, 'view' if session.selection.empty() else 'view sel')
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 535, in run
run_command(session, command, **kw)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/view.py", line 86, in view
view_objects(objects, v, clip, cofr, pad)
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/view.py", line 99, in view_objects
b = disp.bounds()
^^^^^^^^^^^^^
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/objects.py", line 291, in bounds
sb = copies_bounding_box(ib, m.parent.get_scene_positions())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'get_scene_positions'
AttributeError: 'NoneType' object has no attribute 'get_scene_positions'
File
"/private/var/folders/t6/9_28vzh575g6r_dzv5f29lvc0000gn/T/AppTranslocation/E50C6826-F722-4CB4-B814-434EC1331313/d/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/objects.py", line 291, in bounds
sb = copies_bounding_box(ib, m.parent.get_scene_positions())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac15,3
Model Number: MR7K3LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.81.1
OS Loader Version: 8422.141.2.700.1
Software:
System Software Overview:
System Version: macOS 13.6.3 (22G436)
Kernel Version: Darwin 22.6.0
Time since boot: 35 days, 14 hours, 32 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (4)
comment:1 by , 12 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → view sel: 'NoneType' object has no attribute 'get_scene_positions' |
comment:2 by , 12 months ago
| Cc: | added |
|---|
comment:3 by , 12 months ago
Need to take a look at how common the unintended use of the 3D position of a 2D label or color key is. If I open a PDB and create a 2D label and then try the view command on the 2D label it "works" without error and the model disappears from view
open 8xps
2dlabel text something
view #2
On the other hand just "view" seems to work taking account of only the atomic model, whereas "view #1,2" shows the atomic model off in the corner as does "view all".
The move and turn commands with the "model #2" option move and rotate the label which is not intended.
comment:4 by , 12 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed in daily build, not in 1.9.
I decided to go for a narrow fix just making sure the Objects.bounds() method does not use 2D labels or color keys. I added an attribute to those Model types has_scene_bounds = False to indicate that they should be excluded. This fixes the view command when these 2D model types are specified.
The user in this report seems to not know what they are doing selecting the color key and then trying "view sel" on it. It is unclear what they were trying to do -- maybe they did not understand how to move it with the move label mouse mode.
Note:
See TracTickets
for help on using tickets.
The user selected a colorkey model "select #2" then tried "view sel" which produces the error because a colorkey is a 2D model. I'm a bit surprised we haven't seen this kind of error more often where a command tries to use the 3D position of a 2D label or color key. Frighteningly it looks like those models get include as if they were in 3D without errors in most cases. For some reason in the above case the Objects model_instances contains the colorkey and the Objects.bounds() method then tries to use the parent of that model which is None.