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Opened 3 years ago
Last modified 3 years ago
#8900 assigned defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1160.88.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J226_014_volume_map_sharp.mrc
Opened cryosparc_P30_J226_014_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.3, shown at level 0.1, step 1, values float32
> volume #1 level 0.1568
> ui tool show "Hide Dust"
> surface dust #1 size 7.8
> volume #1 level 0.1279
> volume #1 level 0.146
> volume #1 level 0.1424
> open
> /home/Medalia/BWang/Downloads/cryosparc_P27_J107_012_volume_mask_refine.mrc
Opened cryosparc_P27_J107_012_volume_mask_refine.mrc as #2, grid size
512,512,512, pixel 0.65, shown at level 1, step 2, values float32
> volume #2 level 0.8205
> vop flip #2
Opened cryosparc_P27_J107_012_volume_mask_refine.mrc z flip as #3, grid size
512,512,512, pixel 0.65, shown at step 1, values float32
> ui mousemode right "translate selected models"
[Repeated 1 time(s)]
> select #3
2 models selected
> view matrix models #3,1,0,0,-0.024762,0,1,0,-31.53,0,0,1,-6.9355
> view matrix models
> #3,0.74535,0.35816,-0.5623,59.162,-0.09163,-0.7804,-0.61853,379.28,-0.66035,0.51255,-0.54885,231.45
> view matrix models
> #3,-0.074875,0.97806,-0.19442,33.228,0.54227,-0.12369,-0.83105,192.53,-0.83686,-0.16766,-0.52111,374
> view matrix models
> #3,0.41241,0.82314,-0.39034,8.4937,0.79562,-0.11673,0.59445,-52.033,0.44375,-0.55572,-0.70304,258.49
> view matrix models
> #3,-0.8165,-0.29963,-0.49351,417.54,-0.46393,0.8493,0.25192,34.365,0.34366,0.43465,-0.83246,121.7
> view matrix models
> #3,-0.86827,-0.10002,-0.4859,390.34,-0.26382,0.92257,0.28153,-15.095,0.42012,0.37263,-0.82743,119.27
> view matrix models
> #3,-0.85818,-0.26165,-0.44167,410.4,-0.41913,0.8539,0.30852,18.25,0.29642,0.44989,-0.84246,128.17
> view matrix models
> #3,-0.85818,-0.26165,-0.44167,428.27,-0.41913,0.8539,0.30852,47.94,0.29642,0.44989,-0.84246,179.58
> view matrix models
> #3,-0.85818,-0.26165,-0.44167,421.21,-0.41913,0.8539,0.30852,56.951,0.29642,0.44989,-0.84246,170.59
> view matrix models
> #3,-0.76869,-0.28069,-0.57475,428.81,-0.52447,0.79095,0.31516,84.054,0.36614,0.5437,-0.75521,130.63
> view matrix models
> #3,-0.74531,-0.44553,-0.49599,442.37,-0.49558,0.86786,-0.034877,115.67,0.44599,0.21981,-0.86762,189.63
> view matrix models
> #3,-0.74531,-0.44553,-0.49599,449.77,-0.49558,0.86786,-0.034877,100.06,0.44599,0.21981,-0.86762,193.8
> view matrix models
> #3,-0.74531,-0.44553,-0.49599,444.9,-0.49558,0.86786,-0.034877,149.95,0.44599,0.21981,-0.86762,260.76
> close #3
> select #2
2 models selected
> view matrix models #2,1,0,0,9.3424,0,1,0,-4.8486,0,0,1,12.816
> view matrix models
> #2,0.97659,0.1034,0.18864,-40.654,-0.05997,0.973,-0.22288,52.016,-0.2066,0.20635,0.95642,19.028
> view matrix models
> #2,0.97659,0.1034,0.18864,-33.833,-0.05997,0.973,-0.22288,58.856,-0.2066,0.20635,0.95642,7.0374
> view matrix models
> #2,0.88703,0.093791,0.45208,-67.737,-0.10205,0.99476,-0.0061464,20.682,-0.45028,-0.040682,0.89196,101.74
> view matrix models
> #2,0.88703,0.093791,0.45208,-68.732,-0.10205,0.99476,-0.0061464,13.085,-0.45028,-0.040682,0.89196,98.8
> view matrix models
> #2,0.88703,0.093791,0.45208,-76.689,-0.10205,0.99476,-0.0061464,14.173,-0.45028,-0.040682,0.89196,100.92
> view matrix models
> #2,0.88703,0.093791,0.45208,-64.366,-0.10205,0.99476,-0.0061464,17.044,-0.45028,-0.040682,0.89196,102.99
> view matrix models
> #2,0.88013,0.091885,0.46576,-65.517,-0.15037,0.98453,0.089918,8.3945,-0.4503,-0.14918,0.88033,123.98
> view matrix models
> #2,0.96311,-0.047375,0.26491,-16.687,0.011552,0.99075,0.13518,-27.66,-0.26886,-0.12714,0.95475,76.464
> view matrix models
> #2,0.96311,-0.047375,0.26491,-40.278,0.011552,0.99075,0.13518,-31.235,-0.26886,-0.12714,0.95475,74.761
> view matrix models
> #2,0.96311,-0.047375,0.26491,-37.609,0.011552,0.99075,0.13518,-30.504,-0.26886,-0.12714,0.95475,80.433
> view matrix models
> #2,0.96311,-0.047375,0.26491,-144.16,0.011552,0.99075,0.13518,26.971,-0.26886,-0.12714,0.95475,154.08
> close #2
> volume #1 level 0.2022
> surface undust #1
> volume #1 level 0.2691
> volume #1 level 0.2937
> volume #1 level 0.3219
> volume #1 level 0.343
> volume #1 level 0.3606
> open /home/Medalia/BWang/Downloads/cryosparc_P30_J242_mask.mrc
Opened cryosparc_P30_J242_mask.mrc as #2, grid size 256,256,256, pixel 1.3,
shown at level 1, step 1, values float32
> volume #2 level 0.9605
> volume #2 level 0.9372
> volume #2 level 0.2334
> volume #1 level 0.1318
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J243_010_volume_map_sharp.mrc
Opened cryosparc_P30_J243_010_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.3, shown at level 0.178, step 1, values float32
> volume #3 level 0.3286
> surface dust #1 size 7.8
> surface dust #3 size 7.8
> volume #3 level 0.2784
> open 6zhx
6zhx title:
Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's
acidic patch: nucleosome class. [more info...]
Chain information for 6zhx #4
---
Chain | Description | UniProt
A E | Histone H3 | A0A310TTQ1_XENLA
B F | Histone H4 | H4_XENLA
C G | Histone H2A type 1 | H2A1_XENLA
D H | Histone H2B 1.1 | H2B11_XENLA
I | DNA (145-MER) Widom 601 sequence |
J | DNA (145-MER) Widom 601 sequence |
K L | Chromodomain-helicase-DNA-binding protein 1-like | CHD1L_HUMAN
> volume #3 level 0.4792
> ui mousemode right "translate selected models"
> select #4
12313 atoms, 12968 bonds, 370 pseudobonds, 1220 residues, 2 models selected
> view matrix models #4,1,0,0,19.778,0,1,0,-16.161,0,0,1,21.816
> view matrix models
> #4,0.40209,-0.44079,-0.80252,199.5,0.86073,0.48083,0.16716,-62.564,0.31219,-0.75797,0.57274,109.82
> view matrix models
> #4,0.14377,-0.58354,-0.79925,237.38,-0.89669,0.26485,-0.35467,175.54,0.41865,0.76768,-0.48518,56.126
> view matrix models
> #4,0.22684,-0.60479,-0.7634,228.09,-0.032124,-0.78805,0.61477,100.75,-0.9734,-0.11493,-0.19819,244.38
> view matrix models
> #4,0.22684,-0.60479,-0.7634,276.35,-0.032124,-0.78805,0.61477,110.52,-0.9734,-0.11493,-0.19819,234.98
> view matrix models
> #4,0.22684,-0.60479,-0.7634,273.08,-0.032124,-0.78805,0.61477,188.92,-0.9734,-0.11493,-0.19819,291.34
> view matrix models
> #4,0.22684,-0.60479,-0.7634,274.04,-0.032124,-0.78805,0.61477,188.65,-0.9734,-0.11493,-0.19819,290
> view matrix models
> #4,0.22684,-0.60479,-0.7634,272.2,-0.032124,-0.78805,0.61477,185.01,-0.9734,-0.11493,-0.19819,285.63
> view matrix models
> #4,0.22684,-0.60479,-0.7634,283.28,-0.032124,-0.78805,0.61477,185.41,-0.9734,-0.11493,-0.19819,288.59
> view matrix models
> #4,0.094262,-0.65652,-0.74839,299.27,-0.038776,-0.75359,0.6562,178.5,-0.99479,-0.032835,-0.096492,272.34
> view matrix models
> #4,0.094262,-0.65652,-0.74839,295.36,-0.038776,-0.75359,0.6562,179.3,-0.99479,-0.032835,-0.096492,274.16
> view matrix models
> #4,0.094262,-0.65652,-0.74839,295.26,-0.038776,-0.75359,0.6562,180.53,-0.99479,-0.032835,-0.096492,275.94
> view matrix models
> #4,0.094262,-0.65652,-0.74839,297.11,-0.038776,-0.75359,0.6562,180.82,-0.99479,-0.032835,-0.096492,276.02
> view matrix models
> #4,0.10573,-0.73017,-0.67503,295.92,-0.053425,-0.68203,0.72937,167.84,-0.99296,-0.041051,-0.11112,278.12
> view matrix models
> #4,0.10573,-0.73017,-0.67503,293.83,-0.053425,-0.68203,0.72937,167.38,-0.99296,-0.041051,-0.11112,277.23
> ui tool show "Fit in Map"
Fit molecule 6zhx (#4) to map cryosparc_P30_J243_010_volume_map_sharp.mrc (#3)
using 12313 atoms
average map value = 0.9007, steps = 80
shifted from previous position = 1.09
rotated from previous position = 7.58 degrees
atoms outside contour = 3263, contour level = 0.4792
Position of 6zhx (#4) relative to cryosparc_P30_J243_010_volume_map_sharp.mrc
(#3) coordinates:
Matrix rotation and translation
0.22608704 -0.70478966 -0.67242559 278.46586129
-0.00255115 -0.69072549 0.72311257 164.45756402
-0.97410376 -0.16177093 -0.15796210 292.12086209
Axis -0.75678975 0.25800791 0.60058404
Axis point 0.00000000 191.07714848 221.87716104
Rotation angle (degrees) 144.22316686
Shift along axis 7.13437196
> show sel cartoons
> style sel stick
Changed 12313 atom styles
> transparency #3.1 50
> volume #3 level 0.3161
> volume #3 level 0.1278
> volume #3 level 0.2408
> volume #3 level 0.1153
> volume #3 level 0.178
> volume #3 level 0.316
> volume #3 level 0.2658
> volume #3 level 0.2156
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J241_011_volume_map_sharp.mrc
Opened cryosparc_P30_J241_011_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.3, shown at level 0.178, step 1, values float32
> surface dust #5 size 7.8
> volume #5 level 0.2009
> transparency #3.1#5.1 0
> transparency #3.1#5.1 50
> volume #5 level 0.2123
> volume #5 level 0.216
> volume #5 level 0.3066
> ui tool show "Surface Zone"
> surface zone #5 nearAtoms sel distance 7.8
> surface unzone #5
> ui mousemode right select
> select /L:9@CB
1 atom, 1 residue, 1 model selected
> select /L:9@CB
1 atom, 1 residue, 1 model selected
> select /L:9@CB
1 atom, 1 residue, 1 model selected
> surface zone #5 nearAtoms sel distance 7.8
Drag select of 35 atoms, 24 residues, 30 bonds
Drag select of 19 atoms, 15 residues, 18 bonds
> ui mousemode right select
> surface zone #5 nearAtoms sel distance 10
[Repeated 1 time(s)]
> open 6zhx
6zhx title:
Cryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's
acidic patch: nucleosome class. [more info...]
Chain information for 6zhx #6
---
Chain | Description | UniProt
A E | Histone H3 | A0A310TTQ1_XENLA
B F | Histone H4 | H4_XENLA
C G | Histone H2A type 1 | H2A1_XENLA
D H | Histone H2B 1.1 | H2B11_XENLA
I | DNA (145-MER) Widom 601 sequence |
J | DNA (145-MER) Widom 601 sequence |
K L | Chromodomain-helicase-DNA-binding protein 1-like | CHD1L_HUMAN
Drag select of 177 atoms, 30 residues, 5 pseudobonds, 164 bonds, 5
cryosparc_P30_J241_011_volume_map_sharp.mrc
> select clear
Drag select of 44 atoms, 13 residues, 40 bonds
> surface zone #5 nearAtoms sel distance 10
> select #4/L:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/L:11
8 atoms, 7 bonds, 1 residue, 1 model selected
> surface zone #5 nearAtoms sel distance 10
[Repeated 1 time(s)]
No atoms selected for zoning
[Repeated 1 time(s)]
> ui mousemode right select
> select #4/C:24@CG
1 atom, 1 residue, 1 model selected
No atoms selected for zoning
[Repeated 8 time(s)]Drag select of 20 atoms, 4 residues, 1 pseudobonds, 24
bonds, 5 cryosparc_P30_J241_011_volume_map_sharp.mrc
> select clear
Drag select of 1 atoms, 1 residues, 5
cryosparc_P30_J241_011_volume_map_sharp.mrc
> select clear
No atoms selected for zoning
Drag select of 23 atoms, 1 residues, 1 pseudobonds, 22 bonds, 5
cryosparc_P30_J241_011_volume_map_sharp.mrc
> surface zone #5 nearAtoms sel distance 20
No atoms selected for zoning
Drag select of 36 atoms, 25 residues, 32 bonds
> surface zone #5 nearAtoms sel distance 20
> select clear
Drag select of 1191 atoms, 191 residues, 39 pseudobonds, 1091 bonds, 5
cryosparc_P30_J241_011_volume_map_sharp.mrc
> open
> /home/Medalia/BWang/Downloads/cryosparc_P27_J113_class_00_00192_volume.mrc
Opened cryosparc_P27_J113_class_00_00192_volume.mrc as #7, grid size
120,120,120, pixel 2.77, shown at level 0.0705, step 1, values float32
> volume #7 level 0.107
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J245_010_volume_map_sharp.mrc
Opened cryosparc_P30_J245_010_volume_map_sharp.mrc as #8, grid size
512,512,512, pixel 0.65, shown at level 0.0649, step 2, values float32
> volume #8 level 0.1189
> volume #8 step 1
> surface dust #8 size 3.9
Drag select of 134 atoms
> hide #!6 models
> select #6
12313 atoms, 12968 bonds, 370 pseudobonds, 1220 residues, 2 models selected
> ~select #6
Nothing selected
> surface dust #8 size 3.89
> surface dust #8 size 3.88
> surface dust #8 size 3.87
> volume #8 level 0.06143
> volume #8 level 0.234
> volume #8 level 0.1986
> transparency #8.1 50
> open /home/Medalia/BWang/Downloads/coot/placed_model-coot-0.pdb
Chain information for placed_model-coot-0.pdb #9
---
Chain | Description
A E | No description available
B F | No description available
C G | No description available
D H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
> hide #!4 models
> style #9 stick
Changed 12420 atom styles
> style #9 sphere
Changed 12420 atom styles
> volume #8 level 0.2384
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.1551, steps = 92
shifted from previous position = 0.991
rotated from previous position = 4.11 degrees
atoms outside contour = 8686, contour level = 0.2384
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99831745 -0.04739730 -0.03340308 13.59400727
0.04876165 0.99795670 0.04128825 -13.95517744
0.03137787 -0.04284757 0.99858876 1.40882125
Axis -0.58731568 -0.45220773 0.67124396
Axis point 304.12811469 266.99670371 0.00000000
Rotation angle (degrees) 4.10746657
Shift along axis -0.72767181
> ui mousemode right "translate selected models"
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> view matrix models
> #9,0.99832,-0.047397,-0.033403,13.874,0.048762,0.99796,0.041288,-12.871,0.031378,-0.042848,0.99859,2.6334
> view matrix models
> #9,0.99832,-0.047397,-0.033403,16.395,0.048762,0.99796,0.041288,-14.299,0.031378,-0.042848,0.99859,5.6639
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.06891, steps = 132
shifted from previous position = 1.86
rotated from previous position = 3.29 degrees
atoms outside contour = 10241, contour level = 0.2384
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99883200 0.00687400 -0.04782657 8.19797652
-0.00535685 0.99948060 0.03177803 -2.90491128
0.04802017 -0.03148472 0.99835003 1.14715533
Axis -0.54776808 -0.82990049 -0.10590233
Axis point -13.99923523 0.00000000 146.54054174
Rotation angle (degrees) 3.31043941
Shift along axis -2.20128903
> style sel stick
Changed 12420 atom styles
> view matrix models
> #9,0.99883,0.006874,-0.047827,5.5284,-0.0053569,0.99948,0.031778,-3.4622,0.04802,-0.031485,0.99835,0.24878
> show sel cartoons
> transparency #8.1 0
> view matrix models
> #9,0.99883,0.006874,-0.047827,5.145,-0.0053569,0.99948,0.031778,-1.0302,0.04802,-0.031485,0.99835,0.3718
> view matrix models
> #9,0.99883,0.006874,-0.047827,2.8351,-0.0053569,0.99948,0.031778,-2.1791,0.04802,-0.031485,0.99835,1.1955
> view matrix models
> #9,0.99883,0.006874,-0.047827,4.1075,-0.0053569,0.99948,0.031778,-2.4898,0.04802,-0.031485,0.99835,-0.32614
> volume #8 level 0.5266
> view matrix models
> #9,0.99883,0.006874,-0.047827,2.885,-0.0053569,0.99948,0.031778,-1.6251,0.04802,-0.031485,0.99835,1.1197
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 260
shifted from previous position = 4.35
rotated from previous position = 3.96 degrees
atoms outside contour = 11514, contour level = 0.52657
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99713401 -0.05938685 -0.04687185 17.90796855
0.06164403 0.99692997 0.04827687 -16.88140489
0.04386094 -0.05102788 0.99773362 4.58185001
Axis -0.54880130 -0.50142889 0.66886934
Axis point 275.15172790 303.99337671 0.00000000
Rotation angle (degrees) 5.19088956
Shift along axis 1.70156676
> view matrix models
> #9,0.99713,-0.059387,-0.046872,16.376,0.061644,0.99693,0.048277,-14.312,0.043861,-0.051028,0.99773,6.4494
> view matrix models
> #9,0.99713,-0.059387,-0.046872,16.147,0.061644,0.99693,0.048277,-16.099,0.043861,-0.051028,0.99773,8.2684
> view matrix models
> #9,0.99641,-0.078959,-0.030429,16.773,0.080199,0.9959,0.041957,-18.055,0.026991,-0.044246,0.99866,9.883
> view matrix models
> #9,0.99641,-0.078959,-0.030429,17.657,0.080199,0.9959,0.041957,-17.827,0.026991,-0.044246,0.99866,7.783
> style sel sphere
Changed 12420 atom styles
> style sel ball
Changed 12420 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 5939 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 5939 atom styles
> color sel bychain
[Repeated 1 time(s)]
> rainbow sel
> color sel bychain
> color sel byhetero
> style sel sphere
Changed 12420 atom styles
> color sel bychain
> style sel stick
Changed 12420 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> view matrix models
> #9,0.99641,-0.078959,-0.030429,16.61,0.080199,0.9959,0.041957,-18.356,0.026991,-0.044246,0.99866,9.5438
> view matrix models
> #9,0.99641,-0.078959,-0.030429,16.52,0.080199,0.9959,0.041957,-17.82,0.026991,-0.044246,0.99866,9.0246
> view matrix models
> #9,0.99641,-0.078959,-0.030429,16.933,0.080199,0.9959,0.041957,-18.512,0.026991,-0.044246,0.99866,9.3547
> view matrix models
> #9,0.99632,-0.080934,-0.028314,16.922,0.082024,0.99584,0.039739,-18.439,0.02498,-0.041915,0.99881,9.2831
> view matrix models
> #9,0.99632,-0.080934,-0.028314,16.582,0.082024,0.99584,0.039739,-18.518,0.02498,-0.041915,0.99881,9.7637
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.0546, steps = 84
shifted from previous position = 2.43
rotated from previous position = 0.81 degrees
atoms outside contour = 11820, contour level = 0.52657
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99570866 -0.08278126 -0.04137054 21.42724475
0.08461442 0.99540978 0.04471869 -18.88301591
0.03747877 -0.04802733 0.99814263 8.50036420
Axis -0.44809361 -0.38095303 0.80875640
Axis point 217.79568031 271.73033819 0.00000000
Rotation angle (degrees) 5.94015023
Shift along axis 4.46685457
> view matrix models
> #9,0.99571,-0.082781,-0.041371,21.886,0.084614,0.99541,0.044719,-18.128,0.037479,-0.048027,0.99814,8.0506
> view matrix models
> #9,0.99571,-0.082781,-0.041371,18.909,0.084614,0.99541,0.044719,-16.724,0.037479,-0.048027,0.99814,7.1408
> volume #8 level 0.301
> view matrix models
> #9,0.99571,-0.082781,-0.041371,18.525,0.084614,0.99541,0.044719,-15.851,0.037479,-0.048027,0.99814,5.0066
> view matrix models
> #9,0.99571,-0.082781,-0.041371,19.4,0.084614,0.99541,0.044719,-16.905,0.037479,-0.048027,0.99814,5.2523
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 216
shifted from previous position = 3.41
rotated from previous position = 1.38 degrees
atoms outside contour = 10462, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99713069 -0.05945788 -0.04685246 17.91975617
0.06171399 0.99692570 0.04827553 -16.89290342
0.04383806 -0.05102846 0.99773459 4.58633316
Axis -0.54857659 -0.50099394 0.66937941
Axis point 275.04001396 303.82418499 0.00000000
Rotation angle (degrees) 5.19298223
Shift along axis 1.70288054
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 48
shifted from previous position = 0.00611
rotated from previous position = 0.0106 degrees
atoms outside contour = 10461, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99713282 -0.05954843 -0.04669179 17.91296979
0.06179579 0.99692120 0.04826381 -16.90419780
0.04367400 -0.05101078 0.99774269 4.60618953
Axis -0.54860536 -0.49937405 0.67056522
Axis point 274.89584049 303.26801692 0.00000000
Rotation angle (degrees) 5.19116748
Shift along axis 1.70311684
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.00642
rotated from previous position = 0.0128 degrees
atoms outside contour = 10459, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99712294 -0.05975255 -0.04664200 17.94551277
0.06199354 0.99691311 0.04817725 -16.92440526
0.04361931 -0.05093014 0.99774921 4.60252331
Axis -0.54730002 -0.49844941 0.67231754
Axis point 274.34003128 302.77222792 0.00000000
Rotation angle (degrees) 5.19479463
Shift along axis 1.70873748
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 48
shifted from previous position = 0.0116
rotated from previous position = 0.0088 degrees
atoms outside contour = 10456, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99712692 -0.05970029 -0.04662391 17.93102928
0.06194672 0.99690899 0.04832256 -16.93787160
0.04359492 -0.05107192 0.99774302 4.64228585
Axis -0.54867459 -0.49802344 0.67151236
Axis point 274.75591758 302.88531295 0.00000000
Rotation angle (degrees) 5.19679612
Shift along axis 1.71450933
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 56
shifted from previous position = 0.0183
rotated from previous position = 0.0254 degrees
atoms outside contour = 10462, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709627 -0.06012794 -0.04672970 18.04195365
0.06238050 0.99688105 0.04834085 -17.01384760
0.04367731 -0.05111550 0.99773719 4.63884561
Axis -0.54688206 -0.49712234 0.67363892
Axis point 274.18845143 302.42612419 0.00000000
Rotation angle (degrees) 5.21713137
Shift along axis 1.71604988
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 48
shifted from previous position = 0.00109
rotated from previous position = 0.00428 degrees
atoms outside contour = 10460, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709161 -0.06015030 -0.04680019 18.05769640
0.06240600 0.99687996 0.04833046 -17.01563387
0.04374708 -0.05111051 0.99773439 4.62774242
Axis -0.54651625 -0.49763749 0.67355543
Axis point 274.10386001 302.54592984 0.00000000
Rotation angle (degrees) 5.21982383
Shift along axis 1.71583379
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.00264
rotated from previous position = 0.00719 degrees
atoms outside contour = 10462, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99708828 -0.06021683 -0.04678556 18.06775206
0.06246702 0.99688138 0.04822220 -17.00970278
0.04373586 -0.05100435 0.99774031 4.61278207
Axis -0.54546961 -0.49761567 0.67441942
Axis point 273.69519918 302.38968189 0.00000000
Rotation angle (degrees) 5.21855892
Shift along axis 1.71983467
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 44
shifted from previous position = 0.0154
rotated from previous position = 0.0099 degrees
atoms outside contour = 10460, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709116 -0.06024664 -0.04668574 18.06035367
0.06249770 0.99687285 0.04835860 -17.03638861
0.04362630 -0.05113569 0.99773839 4.63838957
Axis -0.54669214 -0.49623833 0.67444438
Axis point 274.13590504 302.04551802 0.00000000
Rotation angle (degrees) 5.22094541
Shift along axis 1.70899143
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07817, steps = 48
shifted from previous position = 0.029
rotated from previous position = 0.036 degrees
atoms outside contour = 10458, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99713222 -0.05962418 -0.04660793 17.91360816
0.06187189 0.99691132 0.04837028 -16.93247647
0.04357994 -0.05111528 0.99774146 4.65662228
Axis -0.54937973 -0.49803599 0.67092628
Axis point 274.98538769 303.02587628 0.00000000
Rotation angle (degrees) 5.19487672
Shift along axis 1.71585968
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.0136
rotated from previous position = 0.0283 degrees
atoms outside contour = 10465, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709847 -0.06004849 -0.04678474 18.03106435
0.06229659 0.99689435 0.04817459 -16.97331380
0.04374663 -0.05094934 0.99774265 4.59883103
Axis -0.54574363 -0.49843583 0.67359158
Axis point 273.80609687 302.65414985 0.00000000
Rotation angle (degrees) 5.21052276
Shift along axis 1.71750298
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 60
shifted from previous position = 0.013
rotated from previous position = 0.008 degrees
atoms outside contour = 10463, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709085 -0.06018218 -0.04677550 18.06014216
0.06243119 0.99688438 0.04820666 -17.00267672
0.04372858 -0.05098667 0.99774154 4.59786483
Axis -0.54550975 -0.49772359 0.67430731
Axis point 273.79132003 302.36562059 0.00000000
Rotation angle (degrees) 5.21642195
Shift along axis 1.71102358
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 60
shifted from previous position = 0.0146
rotated from previous position = 0.0169 degrees
atoms outside contour = 10459, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99711143 -0.05993866 -0.04664923 17.98728055
0.06218637 0.99689402 0.04832349 -16.97793025
0.04360789 -0.05108485 0.99774180 4.64515795
Axis -0.54769901 -0.49727959 0.67285868
Axis point 274.40075713 302.55746649 0.00000000
Rotation angle (degrees) 5.20680595
Shift along axis 1.71669730
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.0031
rotated from previous position = 0.0117 degrees
atoms outside contour = 10462, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709893 -0.06005612 -0.04676512 18.02988595
0.06230426 0.99689271 0.04819848 -16.97873292
0.04372520 -0.05097232 0.99774242 4.60808718
Axis -0.54595527 -0.49816747 0.67361860
Axis point 273.86203290 302.61364596 0.00000000
Rotation angle (degrees) 5.21096647
Shift along axis 1.71883444
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.015
rotated from previous position = 0.00883 degrees
atoms outside contour = 10463, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99709060 -0.06020217 -0.04675513 18.06064104
0.06244740 0.99688637 0.04814442 -16.99493303
0.04371116 -0.05092409 0.99774549 4.58874686
Axis -0.54501048 -0.49768666 0.67473815
Axis point 273.58203556 302.26912298 0.00000000
Rotation angle (degrees) 5.21462559
Shift along axis 1.71111536
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 44
shifted from previous position = 0.0025
rotated from previous position = 0.0134 degrees
atoms outside contour = 10461, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99710130 -0.06011823 -0.04663481 18.02487784
0.06236544 0.99688254 0.04832972 -17.00913618
0.04358393 -0.05109803 0.99774217 4.63997136
Axis -0.54710342 -0.49643068 0.67396916
Axis point 274.22909290 302.15937644 -0.00000000
Rotation angle (degrees) 5.21351082
Shift along axis 1.70958235
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.0206
rotated from previous position = 0.0242 degrees
atoms outside contour = 10460, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99711804 -0.05977175 -0.04672207 17.96217044
0.06201443 0.99691446 0.04812246 -16.91797876
0.04370154 -0.05088121 0.99774810 4.59459977
Axis -0.54657278 -0.49920452 0.67234890
Axis point 274.06086353 303.00003814 0.00000000
Rotation angle (degrees) 5.19626695
Shift along axis 1.71707214
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 60
shifted from previous position = 0.0133
rotated from previous position = 0.00565 degrees
atoms outside contour = 10458, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99711276 -0.05984105 -0.04674599 17.98217839
0.06208765 0.99690690 0.04818463 -16.94167518
0.04371798 -0.05094786 0.99774398 4.59109304
Axis -0.54672134 -0.49891401 0.67244374
Axis point 274.22737989 302.87680791 0.00000000
Rotation angle (degrees) 5.20162878
Shift along axis 1.70845016
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07818, steps = 44
shifted from previous position = 0.00647
rotated from previous position = 0.0161 degrees
atoms outside contour = 10462, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99713321 -0.05962893 -0.04658071 17.91159965
0.06187090 0.99691621 0.04827068 -16.91757887
0.04355873 -0.05101428 0.99774755 4.62558575
Axis -0.54867112 -0.49813091 0.67143548
Axis point 274.79882345 302.86469875 -0.00000000
Rotation angle (degrees) 5.19108727
Shift along axis 1.70537385
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.07819, steps = 48
shifted from previous position = 0.00376
rotated from previous position = 0.0114 degrees
atoms outside contour = 10461, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99712188 -0.05978046 -0.04662890 17.94881088
0.06201942 0.99691301 0.04814613 -16.92375707
0.04360675 -0.05089946 0.99775132 4.59920228
Axis -0.54699025 -0.49833638 0.67265334
Axis point 274.20778525 302.68626849 0.00000000
Rotation angle (degrees) 5.19449466
Shift along axis 1.70956805
> view matrix models
> #9,0.9959,-0.05359,-0.072933,21.599,0.052577,0.99849,-0.015735,-4.6689,0.073666,0.011836,0.99721,-11.098
> view matrix models
> #9,0.9959,-0.05359,-0.072933,22.468,0.052577,0.99849,-0.015735,-2.5585,0.073666,0.011836,0.99721,-11.08
> view matrix models
> #9,0.9959,-0.05359,-0.072933,23.041,0.052577,0.99849,-0.015735,-3.4213,0.073666,0.011836,0.99721,-14.301
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) using 12420 atoms
average map value = 0.4273, steps = 76
shifted from previous position = 2.21
rotated from previous position = 2.01 degrees
atoms outside contour = 4577, contour level = 0.30105
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J245_010_volume_map_sharp.mrc (#8) coordinates:
Matrix rotation and translation
0.99715150 -0.05992941 -0.04579684 17.97608166
0.05824198 0.99760418 -0.03733335 -2.32475525
0.04792448 0.03455971 0.99825291 -14.15344481
Axis 0.43028316 -0.56092623 0.70726103
Axis point 61.77549729 303.99219906 0.00000000
Rotation angle (degrees) 4.79216470
Shift along axis -0.97135851
> ~select #9
Nothing selected
> transparency #8.1 50
> volume #8 level 0.2301
> volume #8 level 0.07553
> volume #8 level 0.1465
> volume #8 level 0.205
> show #!1 models
> volume #1 level 0.1615
> volume #1 level 0.1971
> transparency #1.1#8.1 0
> transparency #1.1#8.1 50
> volume #1 level 0.1437
> volume #1 level 0.1793
> open /home/Medalia/BWang/Downloads/cryosparc_P30_J98_mask(1).mrc
Opened cryosparc_P30_J98_mask(1).mrc as #10, grid size 512,512,512, pixel
0.65, shown at level 5e-05, step 2, values float32
> hide #9 models
> show #!1 models
> hide #!10 models
> surface undust #1
> volume #1 level 0.2269
> ui tool show "Map Eraser"
> volume erase #1 center 197.09,196.83,246.97 radius 28.608
Opened cryosparc_P30_J226_014_volume_map_sharp.mrc copy as #12, grid size
256,256,256, pixel 1.3, shown at step 1, values float32
> volume erase #12 center 193.05,171.91,228.49 radius 28.454
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J209_class_03_00064_volume(1).mrc
Opened cryosparc_P30_J209_class_03_00064_volume(1).mrc as #13, grid size
120,120,120, pixel 2.77, shown at level 0.0698, step 1, values float32
> volume #13 level 0.0934
Can only have one displayed volume when erasing
[Repeated 1 time(s)]
> hide #!12 models
> volume erase #13 center 196.59,182.36,239.62 radius 28.288
Opened cryosparc_P30_J209_class_03_00064_volume(1).mrc copy as #14, grid size
120,120,120, pixel 2.77, shown at step 1, values float32
> volume erase #14 center 110.45,162.86,144.36 radius 28.288
> volume erase #14 center 131.38,181.97,147.06 radius 5.1584
> volume erase #14 center 133.35,183.17,145.07 radius 5.1584
> volume erase #14 center 215.77,178.07,167.19 radius 16.806
> volume erase #14 center 201.98,176.29,142.42 radius 7.3216
> volume erase #14 center 221.14,171.18,144.37 radius 7.3216
> volume erase #14 center 195.54,156.66,187.43 radius 7.3216
> volume erase #14 center 189.79,163.64,208.68 radius 7.3216
> volume erase #14 center 195.53,126.8,147.5 radius 4.3264
> volume erase #14 center 141.5,131.22,199.77 radius 4.3264
> save /home/Medalia/BWang/Downloads/J209_class03_mask_1.mrc models #14
> open /home/Medalia/BWang/Downloads/cryosparc_P30_J219_mask(2).mrc
Opened cryosparc_P30_J219_mask(2).mrc as #15, grid size 120,120,120, pixel
2.77, shown at level 1, step 1, values float32
> volume #15 level 0.9576
> volume #15 level 1
> open /home/Medalia/BWang/Downloads/cryosparc_P30_J247_mask.mrc
Opened cryosparc_P30_J247_mask.mrc as #16, grid size 120,120,120, pixel 2.77,
shown at level 0.933, step 1, values float32
> volume #16 level 0.7649
> volume #16 level 0.8379
> volume #16 level 0.497
> open /home/Medalia/BWang/Downloads/cryosparc_P30_J248_mask.mrc
Opened cryosparc_P30_J248_mask.mrc as #17, grid size 120,120,120, pixel 2.77,
shown at level 1, step 1, values float32
> volume #15 level 1
> volume #16 level 0.7939
> volume #17 level 1
> volume #17 level 0.9394
> volume #17 level 1
> volume #16 level 1
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J237_008_volume_map_sharp(1).mrc
Opened cryosparc_P30_J237_008_volume_map_sharp(1).mrc as #18, grid size
256,256,256, pixel 1.3, shown at level 0.072, step 1, values float32
> volume #18 level 0.09751
> surface dust #18 size 7.8
> hide #!16 models
> hide #!14 models
> hide #11 models
> volume #18 level 0.123
> show #9 models
> transparency #18.1 50
> volume #18 level 0.169
> transparency #18.1 0
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.99715,-0.059929,-0.045797,17.071,0.058242,0.9976,-0.037333,-5.6465,0.047924,0.03456,0.99825,-14.804
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J237_008_volume_map_sharp(1).mrc (#18) using 12420 atoms
average map value = 0.2588, steps = 76
shifted from previous position = 2.97
rotated from previous position = 5.03 degrees
atoms outside contour = 3209, contour level = 0.16895
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J237_008_volume_map_sharp(1).mrc (#18) coordinates:
Matrix rotation and translation
0.99999652 0.00124734 0.00232295 -0.68496046
-0.00125801 0.99998864 0.00459831 -0.53938529
-0.00231719 -0.00460121 0.99998673 0.84739691
Axis -0.86757479 0.43759541 -0.23627153
Axis point 0.00000000 191.89876223 132.81169245
Rotation angle (degrees) 0.30377551
Shift along axis 0.15800614
> transparency #18.1 50
> ~select #9
Nothing selected
> volume #18 level 0.2212
> volume #18 level 0.2358
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J238_008_volume_map_sharp.mrc
Opened cryosparc_P30_J238_008_volume_map_sharp.mrc as #19, grid size
256,256,256, pixel 1.3, shown at level 0.0724, step 1, values float32
> surface dust #19 size 7.8
> volume #19 level 0.1014
> volume #19 level 0.1773
> transparency #18.1#19.1 0
> transparency #18.1#19.1 50
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J239_008_volume_map_sharp.mrc
Opened cryosparc_P30_J239_008_volume_map_sharp.mrc as #20, grid size
256,256,256, pixel 1.3, shown at level 0.0711, step 1, values float32
> volume #20 level 0.1347
> surface dust #20 size 7.8
> transparency #18.1#19.1#20.1 0
> transparency #18.1#19.1#20.1 50
> volume #20 level 0.1506
> volume #20 level 0.1251
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J243_010_volume_map_sharp.mrc
Opened cryosparc_P30_J243_010_volume_map_sharp.mrc as #21, grid size
256,256,256, pixel 1.3, shown at level 0.178, step 1, values float32
> volume #21 level 0.5049
> surface dust #21 size 7.8
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J243_010_volume_map_sharp.mrc (#21) using 12420 atoms
average map value = 0.8973, steps = 80
shifted from previous position = 0.923
rotated from previous position = 5.02 degrees
atoms outside contour = 3536, contour level = 0.50487
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J243_010_volume_map_sharp.mrc (#21) coordinates:
Matrix rotation and translation
0.99679300 -0.05925777 -0.05377945 19.06358841
0.05792819 0.99798330 -0.02595501 -4.03221447
0.05520902 0.02275643 0.99821546 -13.01793247
Axis 0.29119061 -0.65151872 0.70052222
Axis point 91.38089833 321.38544794 0.00000000
Rotation angle (degrees) 4.79793084
Shift along axis -0.94114995
> volume #21 level 0.403
> volume #21 level 0.1789
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J192_009_volume_map_sharp(1).mrc
Opened cryosparc_P30_J192_009_volume_map_sharp(1).mrc as #22, grid size
256,256,256, pixel 1.3, shown at level 0.121, step 1, values float32
> volume #22 level 0.2182
> surface dust #22 size 7.8
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> view matrix models
> #9,0.94099,-0.30921,0.13758,38.195,0.05928,0.55081,0.83252,-75.622,-0.3332,-0.77524,0.53664,267.94
> view matrix models
> #9,0.94099,-0.30921,0.13758,39,0.05928,0.55081,0.83252,-74.856,-0.3332,-0.77524,0.53664,267.72
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J192_009_volume_map_sharp(1).mrc (#22) using 12420 atoms
average map value = 0.4267, steps = 112
shifted from previous position = 7.03
rotated from previous position = 15.9 degrees
atoms outside contour = 3386, contour level = 0.2182
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J192_009_volume_map_sharp(1).mrc (#22) coordinates:
Matrix rotation and translation
0.99658533 -0.06327979 0.05304107 3.67182341
-0.00185512 0.62506051 0.78057409 -64.75441078
-0.08254845 -0.77800708 0.62280874 206.29933701
Axis -0.99547026 0.08660141 0.03923212
Axis point 0.00000000 182.55402711 170.51532830
Rotation angle (degrees) 51.52103385
Shift along axis -1.16945481
> volume #22 level 0.1603
> transparency #22.1 50
> volume #22 level 0.1965
> volume #22 level 0.1386
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J193_010_volume_map_sharp.mrc
Opened cryosparc_P30_J193_010_volume_map_sharp.mrc as #23, grid size
256,256,256, pixel 1.3, shown at level 0.067, step 1, values float32
> surface dust #23 size 7.8
> volume #23 level 0.1136
> vop flip #23
Opened cryosparc_P30_J193_010_volume_map_sharp.mrc z flip as #24, grid size
256,256,256, pixel 1.3, shown at step 1, values float32
> volume #24 level 0.2103
> view matrix models
> #9,0.99659,-0.06328,0.053041,2.6388,-0.0018551,0.62506,0.78057,-65.565,-0.082548,-0.77801,0.62281,197.92
> view matrix models
> #9,0.99659,-0.06328,0.053041,2.5735,-0.0018551,0.62506,0.78057,-61.935,-0.082548,-0.77801,0.62281,198.15
> view matrix models
> #9,0.61431,-0.21361,0.7596,-26.171,-0.55912,-0.79711,0.22803,368.25,0.55678,-0.56479,-0.60911,261.21
> view matrix models
> #9,0.61431,-0.21361,0.7596,-24.171,-0.55912,-0.79711,0.22803,369.9,0.55678,-0.56479,-0.60911,236.23
> view matrix models
> #9,0.61431,-0.21361,0.7596,-24.194,-0.55912,-0.79711,0.22803,369.87,0.55678,-0.56479,-0.60911,236.1
> view matrix models
> #9,0.64183,-0.2413,0.72789,-18.806,-0.53162,-0.82409,0.19558,375.27,0.55265,-0.51249,-0.65721,236.14
> view matrix models
> #9,0.64183,-0.2413,0.72789,-23.283,-0.53162,-0.82409,0.19558,372.9,0.55265,-0.51249,-0.65721,206.07
> view matrix models
> #9,0.60437,-0.25097,0.75614,-19.993,-0.68555,-0.64737,0.33308,346.33,0.40591,-0.71967,-0.5633,250.31
> view matrix models
> #9,0.99675,0.057104,-0.05689,-1.5245,0.079191,-0.56204,0.82331,116.24,0.01504,-0.82514,-0.56473,335.95
> view matrix models
> #9,0.99675,0.057104,-0.05689,-2.5283,0.079191,-0.56204,0.82331,111.72,0.01504,-0.82514,-0.56473,299.55
> view matrix models
> #9,0.99675,0.057104,-0.05689,-1.41,0.079191,-0.56204,0.82331,112.55,0.01504,-0.82514,-0.56473,388.61
> view matrix models
> #9,0.98449,0.16178,0.067895,-38.234,0.040971,-0.58827,0.80763,126.26,0.1706,-0.79232,-0.58577,359.77
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J193_010_volume_map_sharp.mrc z flip (#24) using 12420 atoms
average map value = 0.129, steps = 112
shifted from previous position = 5.52
rotated from previous position = 14.9 degrees
atoms outside contour = 8951, contour level = 0.21033
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J193_010_volume_map_sharp.mrc z flip (#24) coordinates:
Matrix rotation and translation
0.99506656 -0.09204053 0.03702817 10.22003280
-0.08263241 -0.56235685 0.82275553 136.64771050
-0.05490381 -0.82175624 -0.56718802 402.24643052
Axis -0.99842483 0.05581424 0.00571191
Axis point 0.00000000 174.46293742 165.18887042
Rotation angle (degrees) 124.55792713
Shift along axis -0.27945353
> view matrix models
> #9,0.98845,-0.14655,0.038599,20.303,-0.13136,-0.70147,0.70049,189.42,-0.075583,-0.69747,-0.71261,409.63
> view matrix models
> #9,0.98845,-0.14655,0.038599,20.699,-0.13136,-0.70147,0.70049,192.57,-0.075583,-0.69747,-0.71261,411.14
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J193_010_volume_map_sharp.mrc z flip (#24) using 12420 atoms
average map value = 0.2457, steps = 72
shifted from previous position = 3.9
rotated from previous position = 9.75 degrees
atoms outside contour = 5232, contour level = 0.21033
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J193_010_volume_map_sharp.mrc z flip (#24) coordinates:
Matrix rotation and translation
0.99501056 -0.07022552 0.07086864 2.09359022
-0.09857451 -0.80159238 0.58968867 218.64210371
0.01539657 -0.59373230 -0.80451532 392.56232760
Axis -0.99861735 0.04680953 -0.02392200
Axis point 0.00000000 173.86830505 160.32075994
Rotation angle (degrees) 143.66326707
Shift along axis -1.24703722
> volume #24 level 0.1547
> surface dust #23 size 12.37
> surface dust #24 size 7.8
> transparency #24.1 50
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J198_009_volume_map_sharp.mrc
Opened cryosparc_P30_J198_009_volume_map_sharp.mrc as #25, grid size
256,256,256, pixel 1.3, shown at level 0.156, step 1, values float32
> surface dust #25 size 7.8
> hide #!24 models
> volume #25 level 0.3116
> view matrix models
> #9,0.69641,-0.56045,0.44822,72.38,0.65264,0.23489,-0.72034,136.39,0.29843,0.79418,0.52935,-117.63
> view matrix models
> #9,0.95523,0.0044656,0.29584,-41.93,0.25831,0.475,-0.84122,184.66,-0.14428,0.87998,0.45258,-42.409
> view matrix models
> #9,0.95523,0.0044656,0.29584,-28.672,0.25831,0.475,-0.84122,186.57,-0.14428,0.87998,0.45258,-47.181
> view matrix models
> #9,0.95523,0.0044656,0.29584,-29.954,0.25831,0.475,-0.84122,176.5,-0.14428,0.87998,0.45258,-25.524
> view matrix models
> #9,0.94894,0.23259,0.21309,-53.316,0.065459,0.51562,-0.85431,205.15,-0.30858,0.82464,0.47407,8.3802
> view matrix models
> #9,0.96298,0.096759,-0.25162,46.421,-0.2597,0.58343,-0.76952,235.48,0.072348,0.80638,0.58696,-73.66
> view matrix models
> #9,0.99054,-0.09132,-0.10238,47.905,0.050536,0.93667,-0.34654,49.995,0.12754,0.33809,0.93243,-63.178
> view matrix models
> #9,0.99054,-0.09132,-0.10238,46.06,0.050536,0.93667,-0.34654,58.604,0.12754,0.33809,0.93243,-67.962
> view matrix models
> #9,0.99054,-0.09132,-0.10238,31.174,0.050536,0.93667,-0.34654,64.164,0.12754,0.33809,0.93243,-69.78
> vop flip #25
Opened cryosparc_P30_J198_009_volume_map_sharp.mrc z flip as #26, grid size
256,256,256, pixel 1.3, shown at step 1, values float32
> view matrix models
> #9,0.99054,-0.09132,-0.10238,18.688,0.050536,0.93667,-0.34654,74.046,0.12754,0.33809,0.93243,-75.41
> view matrix models
> #9,0.99054,-0.09132,-0.10238,22.755,0.050536,0.93667,-0.34654,55.652,0.12754,0.33809,0.93243,-73.437
> view matrix models
> #9,0.99054,-0.09132,-0.10238,13.442,0.050536,0.93667,-0.34654,59.038,0.12754,0.33809,0.93243,-76.045
> volume #26 level 0.7344
> view matrix models
> #9,0.99054,-0.09132,-0.10238,-8.0228,0.050536,0.93667,-0.34654,4.5243,0.12754,0.33809,0.93243,-59.724
> view matrix models
> #9,0.99054,-0.09132,-0.10238,-15.184,0.050536,0.93667,-0.34654,47.243,0.12754,0.33809,0.93243,-59.325
> view matrix models
> #9,-0.43611,0.5949,-0.67521,213.73,-0.7636,-0.64165,-0.072137,407.92,-0.47616,0.48413,0.73409,54.4
> view matrix models
> #9,-0.60819,0.79372,-0.010412,96.687,-0.69525,-0.52632,0.4895,280.85,0.38305,0.30495,0.87194,-87.809
> view matrix models
> #9,-0.91244,0.32102,0.25375,184.27,-0.2811,-0.94237,0.18142,331.8,0.29737,0.094203,0.9501,-50.677
> view matrix models
> #9,-0.96562,0.25994,0.0013869,246.81,-0.25548,-0.95001,0.17948,328.99,0.047972,0.17296,0.98376,-26.566
> view matrix models
> #9,-0.96562,0.25994,0.0013869,276.72,-0.25548,-0.95001,0.17948,338.59,0.047972,0.17296,0.98376,-14.457
> view matrix models
> #9,-0.96562,0.25994,0.0013869,273.24,-0.25548,-0.95001,0.17948,333.55,0.047972,0.17296,0.98376,-37.308
> view matrix models
> #9,-0.96562,0.25994,0.0013869,272.28,-0.25548,-0.95001,0.17948,334.66,0.047972,0.17296,0.98376,-38.432
> volume #26 level 0.5675
> view matrix models
> #9,-0.96562,0.25994,0.0013869,272.57,-0.25548,-0.95001,0.17948,340.98,0.047972,0.17296,0.98376,-41.067
> view matrix models
> #9,-0.96562,0.25994,0.0013869,269.34,-0.25548,-0.95001,0.17948,279.56,0.047972,0.17296,0.98376,3.6278
> view matrix models
> #9,-0.96562,0.25994,0.0013869,294.27,-0.25548,-0.95001,0.17948,305.16,0.047972,0.17296,0.98376,-31.798
> view matrix models
> #9,-0.96562,0.25994,0.0013869,290.46,-0.25548,-0.95001,0.17948,314.04,0.047972,0.17296,0.98376,-25.918
> view matrix models
> #9,-0.53261,-0.13534,0.83547,140.02,0.64251,0.5779,0.50321,-154.27,-0.55092,0.80481,-0.22084,176.48
> view matrix models
> #9,-0.53261,-0.13534,0.83547,149.06,0.64251,0.5779,0.50321,-125.13,-0.55092,0.80481,-0.22084,164.36
> view matrix models
> #9,-0.53261,-0.13534,0.83547,149.32,0.64251,0.5779,0.50321,-122.34,-0.55092,0.80481,-0.22084,158.45
> view matrix models
> #9,-0.56386,-0.12006,0.8171,155.29,0.72983,0.39065,0.56103,-115.79,-0.38655,0.91268,-0.13265,96.753
> view matrix models
> #9,-0.93671,0.14762,0.31746,260.02,0.33949,0.6046,0.72056,-111.49,-0.085571,0.78273,-0.61645,148.99
> view matrix models
> #9,-0.88019,0.22461,0.41811,220.06,0.46719,0.56536,0.67978,-120.01,-0.083698,0.79367,-0.60256,144.45
> view matrix models
> #9,-0.88019,0.22461,0.41811,215.55,0.46719,0.56536,0.67978,-120.02,-0.083698,0.79367,-0.60256,144.84
> view matrix models
> #9,-0.88821,0.23966,0.39198,218.7,0.45441,0.58411,0.67255,-119.86,-0.067776,0.77549,-0.62771,149.43
> view matrix models
> #9,-0.97322,0.027869,0.2282,297.11,0.19857,0.60208,0.77335,-95.812,-0.11584,0.79795,-0.59149,147.78
> view matrix models
> #9,-0.96791,0.01989,0.2505,293.73,0.22634,0.50207,0.83468,-94.214,-0.10917,0.8646,-0.49046,118.13
> view matrix models
> #9,-0.97537,0.21544,0.0474,296.67,0.1751,0.62542,0.76038,-93.516,0.13417,0.74995,-0.64774,122.24
> view matrix models
> #9,-0.97537,0.21544,0.0474,282.44,0.1751,0.62542,0.76038,-92.547,0.13417,0.74995,-0.64774,123.69
> view matrix models
> #9,-0.97537,0.21544,0.0474,282.7,0.1751,0.62542,0.76038,-94.539,0.13417,0.74995,-0.64774,121.93
> view matrix models
> #9,-0.9611,0.2333,0.14781,260.08,0.19911,0.9562,-0.21458,11.725,-0.1914,-0.17681,-0.96546,389.09
> view matrix models
> #9,-0.9611,0.2333,0.14781,269.06,0.19911,0.9562,-0.21458,13.108,-0.1914,-0.17681,-0.96546,381.32
> view matrix models
> #9,-0.9611,0.2333,0.14781,268.37,0.19911,0.9562,-0.21458,12.343,-0.1914,-0.17681,-0.96546,380.93
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J198_009_volume_map_sharp.mrc z flip (#26) using 12420 atoms
average map value = 0.602, steps = 120
shifted from previous position = 7.48
rotated from previous position = 15.7 degrees
atoms outside contour = 6159, contour level = 0.56752
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J198_009_volume_map_sharp.mrc z flip (#26) coordinates:
Matrix rotation and translation
-0.99103782 0.10552788 -0.08190174 326.60999878
0.12453012 0.95171050 -0.28060534 34.53598544
0.04833506 -0.28828974 -0.95632251 361.99325200
Axis -0.05828585 -0.98784056 0.14413118
Axis point 156.23812510 0.00000000 188.96988059
Rotation angle (degrees) 176.22032430
Shift along axis -0.97827353
> volume #26 level 0.345
> volume #26 level 0.256
> surface dust #25 size 7.8
> surface dust #26 size 7.8
> transparency #26.1 50
> volume #26 level 0.1948
> surface dust #26 size 35.07
[Repeated 1 time(s)]
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J202_009_volume_map_sharp.mrc
Opened cryosparc_P30_J202_009_volume_map_sharp.mrc as #27, grid size
256,256,256, pixel 1.3, shown at level 0.172, step 1, values float32
> volume #27 level 0.2739
> surface dust #27 size 7.8
> volume #27 level 0.3569
> view matrix models
> #9,-0.99104,0.10553,-0.081902,330.09,0.12453,0.95171,-0.28061,38.578,0.048335,-0.28829,-0.95632,361.53
> view matrix models
> #9,-0.34033,-0.92049,0.19203,343.63,-0.50875,0.352,0.78566,67.703,-0.79079,0.16969,-0.5881,366.96
> view matrix models
> #9,0.10656,-0.98196,-0.15622,335.96,-0.21256,-0.17598,0.96117,75.772,-0.97132,-0.069214,-0.22747,377.18
> view matrix models
> #9,0.10656,-0.98196,-0.15622,335.43,-0.21256,-0.17598,0.96117,75.91,-0.97132,-0.069214,-0.22747,376.4
> view matrix models
> #9,0.90827,-0.23416,0.34672,-15.328,-0.4015,-0.25478,0.87971,135.83,-0.11766,-0.93822,-0.32543,391.71
> view matrix models
> #9,0.90827,-0.23416,0.34672,-17.198,-0.4015,-0.25478,0.87971,135,-0.11766,-0.93822,-0.32543,389.61
> view matrix models
> #9,0.27223,0.59239,-0.75827,141.87,-0.84551,-0.22893,-0.48239,439.83,-0.45935,0.77244,0.43855,29.703
> view matrix models
> #9,0.70268,0.47949,-0.52567,46.794,-0.6065,0.017348,-0.79489,410.05,-0.37203,0.87737,0.303,19.937
> view matrix models
> #9,0.90044,-0.40828,0.15002,47.196,0.43255,0.80413,-0.40776,31.623,0.045847,0.43206,0.90068,-79.084
> view matrix models
> #9,0.90044,-0.40828,0.15002,46.925,0.43255,0.80413,-0.40776,34.336,0.045847,0.43206,0.90068,-64.783
> view matrix models
> #9,0.90044,-0.40828,0.15002,69.279,0.43255,0.80413,-0.40776,38.53,0.045847,0.43206,0.90068,-67.454
> view matrix models
> #9,0.95589,-0.28521,0.07021,52.472,0.28669,0.8539,-0.43436,59.902,0.063934,0.43533,0.898,-70.68
> view matrix models
> #9,0.94862,-0.14971,0.27875,-4.7033,0.24753,0.89989,-0.35907,46.073,-0.19708,0.40962,0.89071,-19.945
> view matrix models
> #9,0.94862,-0.14971,0.27875,-15.668,0.24753,0.89989,-0.35907,42.827,-0.19708,0.40962,0.89071,-14.465
> view matrix models
> #9,0.94862,-0.14971,0.27875,-14.468,0.24753,0.89989,-0.35907,34.641,-0.19708,0.40962,0.89071,-14.231
> view matrix models
> #9,0.94862,-0.14971,0.27875,-12.69,0.24753,0.89989,-0.35907,31.309,-0.19708,0.40962,0.89071,-12.346
> view matrix models
> #9,0.94862,-0.14971,0.27875,-7.0298,0.24753,0.89989,-0.35907,34.501,-0.19708,0.40962,0.89071,-14.352
> view matrix models
> #9,0.99229,-0.014197,0.12316,-10.961,0.063549,0.91122,-0.40698,72.55,-0.10644,0.41166,0.9051,-32.816
> view matrix models
> #9,0.99471,-0.055285,0.086544,1.7945,0.086324,0.90661,-0.41304,70.428,-0.055627,0.41832,0.90659,-42.979
> view matrix models
> #9,0.99471,-0.055285,0.086544,0.47648,0.086324,0.90661,-0.41304,65.413,-0.055627,0.41832,0.90659,-40.647
> view matrix models
> #9,0.99589,-0.047704,0.076945,0.6275,0.075378,0.90767,-0.41287,67.1,-0.050145,0.41698,0.90753,-41.527
> view matrix models
> #9,0.99731,-0.0083561,0.072762,-5.5467,0.052015,0.78022,-0.62334,128.53,-0.051561,0.62545,0.77855,-54.485
> view matrix models
> #9,0.99731,-0.0083561,0.072762,-6.0346,0.052015,0.78022,-0.62334,129.04,-0.051561,0.62545,0.77855,-57.582
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J202_009_volume_map_sharp.mrc (#27) using 12420 atoms
average map value = 0.7232, steps = 84
shifted from previous position = 3.48
rotated from previous position = 7.04 degrees
atoms outside contour = 2767, contour level = 0.35694
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J202_009_volume_map_sharp.mrc (#27) coordinates:
Matrix rotation and translation
0.99762112 0.00237738 0.06889442 -9.90857441
0.03418905 0.85076680 -0.52443011 106.00943278
-0.05985986 0.52553799 0.84866166 -51.65931680
Axis 0.99211656 0.12166013 0.03005890
Axis point 0.00000000 144.64133696 160.63145137
Rotation angle (degrees) 31.94842128
Shift along axis 1.51383800
> view matrix models
> #9,0.99762,0.0023774,0.068894,-9.7575,0.034189,0.85077,-0.52443,106.71,-0.05986,0.52554,0.84866,-51.194
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J202_009_volume_map_sharp.mrc (#27) using 12420 atoms
average map value = 0.7232, steps = 64
shifted from previous position = 0.851
rotated from previous position = 0.0182 degrees
atoms outside contour = 2762, contour level = 0.35694
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J202_009_volume_map_sharp.mrc (#27) coordinates:
Matrix rotation and translation
0.99762086 0.00238275 0.06889798 -9.91153078
0.03416739 0.85093332 -0.52416130 105.92611419
-0.05987653 0.52526831 0.84882742 -51.61450855
Axis 0.99210702 0.12174051 0.03004848
Axis point 0.00000000 144.57605670 160.61975547
Rotation angle (degrees) 31.93044141
Shift along axis 1.51126276
> volume #27 level 0.2897
> open
> /home/Medalia/BWang/Downloads/cryosparc_P30_J249_015_volume_map_sharp.mrc
Opened cryosparc_P30_J249_015_volume_map_sharp.mrc as #28, grid size
256,256,256, pixel 1.3, shown at level 0.11, step 1, values float32
> surface dust #28 size 7.8
> volume #28 level 0.1954
> view matrix models
> #9,0.99762,0.0023827,0.068898,-10.772,0.034167,0.85093,-0.52416,112.57,-0.059877,0.52527,0.84883,-59.26
> view matrix models
> #9,0.99762,0.0023827,0.068898,-11.158,0.034167,0.85093,-0.52416,105.61,-0.059877,0.52527,0.84883,-48.62
> view matrix models
> #9,0.99762,0.0023827,0.068898,-11.115,0.034167,0.85093,-0.52416,105.5,-0.059877,0.52527,0.84883,-48.553
> view matrix models
> #9,0.99762,0.0023827,0.068898,-8.6045,0.034167,0.85093,-0.52416,104.34,-0.059877,0.52527,0.84883,-52.041
> view matrix models
> #9,0.86425,0.097363,0.49356,-73.956,0.40001,0.46196,-0.79157,152.57,-0.30508,0.88154,0.3603,13.127
> view matrix models
> #9,0.86425,0.097363,0.49356,-63.456,0.40001,0.46196,-0.79157,156.38,-0.30508,0.88154,0.3603,14.622
> vop flip #28
Opened cryosparc_P30_J249_015_volume_map_sharp.mrc z flip as #29, grid size
256,256,256, pixel 1.3, shown at step 1, values float32
> view matrix models
> #9,0.86425,0.097363,0.49356,-65.597,0.40001,0.46196,-0.79157,138.64,-0.30508,0.88154,0.3603,4.4071
> view matrix models
> #9,0.86425,0.097363,0.49356,-67.474,0.40001,0.46196,-0.79157,145.58,-0.30508,0.88154,0.3603,1.8617
> view matrix models
> #9,0.84815,-0.083449,0.52314,-39.133,0.3079,0.88124,-0.35862,15.478,-0.43109,0.46524,0.77312,22.861
> view matrix models
> #9,0.84815,-0.083449,0.52314,-39.389,0.3079,0.88124,-0.35862,8.6791,-0.43109,0.46524,0.77312,26.645
> view matrix models
> #9,0.84815,-0.083449,0.52314,-39.027,0.3079,0.88124,-0.35862,31.908,-0.43109,0.46524,0.77312,23.563
> view matrix models
> #9,0.84815,-0.083449,0.52314,-38.784,0.3079,0.88124,-0.35862,18.436,-0.43109,0.46524,0.77312,21.646
> view matrix models
> #9,0.84815,-0.083449,0.52314,-38.938,0.3079,0.88124,-0.35862,19.392,-0.43109,0.46524,0.77312,18.425
> view matrix models
> #9,0.73071,-0.056722,0.68033,-49.839,0.3745,0.86652,-0.32999,5.4795,-0.5708,0.49591,0.65442,57.618
> view matrix models
> #9,0.96216,-0.072467,0.26269,-16.217,0.17703,0.89908,-0.40039,46.125,-0.20716,0.43174,0.87789,-32.463
> view matrix models
> #9,0.94527,-0.10286,0.30965,-16.158,0.067371,0.99009,0.12322,-39.389,-0.31926,-0.095611,0.94283,64.908
> view matrix models
> #9,0.94984,-0.09208,0.29886,-16.933,0.10279,0.9945,-0.020282,-21.843,-0.29535,0.049985,0.95408,34.272
> view matrix models
> #9,0.94984,-0.09208,0.29886,-16.192,0.10279,0.9945,-0.020282,-18.887,-0.29535,0.049985,0.95408,41.287
> view matrix models
> #9,0.94984,-0.09208,0.29886,-15.845,0.10279,0.9945,-0.020282,-16.25,-0.29535,0.049985,0.95408,43.157
> view matrix models
> #9,0.95348,-0.084844,0.28926,-16.064,0.12796,0.98275,-0.13354,0.64989,-0.27294,0.16434,0.94789,21.026
> view matrix models
> #9,0.95348,-0.084844,0.28926,-15.662,0.12796,0.98275,-0.13354,5.7972,-0.27294,0.16434,0.94789,20.829
> view matrix models
> #9,0.95348,-0.084844,0.28926,-29.169,0.12796,0.98275,-0.13354,1.9065,-0.27294,0.16434,0.94789,25.066
> view matrix models
> #9,0.94843,-0.15506,0.27649,-14.261,0.16545,0.98611,-0.014476,-25.402,-0.2704,0.059473,0.96091,40.123
> view matrix models
> #9,0.94843,-0.15506,0.27649,-15.951,0.16545,0.98611,-0.014476,-24.262,-0.2704,0.059473,0.96091,37.887
> view matrix models
> #9,0.79774,-0.37816,0.4697,15.003,0.41816,0.90813,0.020939,-60.859,-0.43446,0.1797,0.88258,59.288
> view matrix models
> #9,0.70615,-0.70354,0.079879,152.26,0.67666,0.6373,-0.36876,6.4872,0.20853,0.31445,0.92609,-82.324
> view matrix models
> #9,0.79076,-0.41528,0.44971,25.886,0.46251,0.8866,0.0054571,-62.275,-0.40098,0.20368,0.89316,47.633
> view matrix models
> #9,0.99779,0.028567,0.06001,-18.611,-0.028615,0.99959,-5.0971e-05,4.551,-0.059987,-0.0016664,0.9982,5.4504
> view matrix models
> #9,0.91918,-0.026041,0.39299,-52.527,-0.072858,0.96935,0.23464,-22.928,-0.38705,-0.24431,0.8891,121.68
> view matrix models
> #9,0.93759,0.33652,0.087687,-64.843,-0.13592,0.12252,0.98312,3.2165,0.32009,-0.93367,0.16061,239.89
> view matrix models
> #9,0.93759,0.33652,0.087687,-61.727,-0.13592,0.12252,0.98312,3.8388,0.32009,-0.93367,0.16061,241.11
> volume #29 level 0.3883
> view matrix models
> #9,0.74601,0.55509,0.36789,-113.05,-0.42446,-0.029326,0.90497,92.633,0.51313,-0.83128,0.21373,181.41
> view matrix models
> #9,0.8482,0.35856,-0.38987,31.524,0.2715,0.33771,0.90124,-89.163,0.45481,-0.87028,0.1891,202.27
> view matrix models
> #9,0.93608,0.099777,-0.33734,50.965,0.35141,-0.22125,0.9097,-10.248,0.016132,-0.9701,-0.24217,368.52
> view matrix models
> #9,0.88683,0.46078,0.03492,-64.836,0.22565,-0.49776,0.83745,70.458,0.40326,-0.73479,-0.5454,313.56
> view matrix models
> #9,0.88683,0.46078,0.03492,-64.161,0.22565,-0.49776,0.83745,70.499,0.40326,-0.73479,-0.5454,307.66
> view matrix models
> #9,0.88683,0.46078,0.03492,-57.667,0.22565,-0.49776,0.83745,71.394,0.40326,-0.73479,-0.5454,309.42
> view matrix models
> #9,0.96272,0.092888,0.25407,-46.175,-0.16427,-0.54549,0.82186,149.55,0.21493,-0.83296,-0.50989,352.48
> view matrix models
> #9,0.96272,0.092888,0.25407,-48.723,-0.16427,-0.54549,0.82186,144.18,0.21493,-0.83296,-0.50989,352.15
> view matrix models
> #9,0.96318,0.11766,0.24173,-50.889,-0.14169,-0.54197,0.82837,138.57,0.22848,-0.83212,-0.50535,348.89
> view matrix models
> #9,0.98404,0.10708,0.14212,-35.745,0.012652,-0.83876,0.54435,210.32,0.1775,-0.53387,-0.82673,362.16
> view matrix models
> #9,0.98404,0.10708,0.14212,-34.592,0.012652,-0.83876,0.54435,211.65,0.1775,-0.53387,-0.82673,357.47
> view matrix models
> #9,0.98404,0.10708,0.14212,-33.367,0.012652,-0.83876,0.54435,210.96,0.1775,-0.53387,-0.82673,356.66
> view matrix models
> #9,0.98404,0.10708,0.14212,-34.932,0.012652,-0.83876,0.54435,211.96,0.1775,-0.53387,-0.82673,357.06
> view matrix models
> #9,0.98404,0.10708,0.14212,-32.041,0.012652,-0.83876,0.54435,210.14,0.1775,-0.53387,-0.82673,358.39
> view matrix models
> #9,0.98421,0.10967,0.13894,-31.965,0.014827,-0.83327,0.55267,207.42,0.17639,-0.54188,-0.82173,359.08
> view matrix models
> #9,0.98421,0.10967,0.13894,-33.924,0.014827,-0.83327,0.55267,208.76,0.17639,-0.54188,-0.82173,363.38
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) using 12420 atoms
average map value = 0.3875, steps = 96
shifted from previous position = 5.14
rotated from previous position = 10.5 degrees
atoms outside contour = 6471, contour level = 0.38831
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) coordinates:
Matrix rotation and translation
0.99637147 -0.05351868 0.06617885 -0.66932663
-0.08182493 -0.81631374 0.57178366 221.52075291
0.02342159 -0.57512401 -0.81773089 391.67618991
Axis -0.99900202 0.03724326 -0.02465586
Axis point 0.00000000 172.61347344 160.85100161
Rotation angle (degrees) 144.96849992
Shift along axis -0.73829921
> volume #29 level 0.2982
> volume #29 level 0.243
> volume #29 level 0.2197
> view matrix models
> #9,0.99637,-0.053519,0.066179,-0.034395,-0.081825,-0.81631,0.57178,221.51,0.023422,-0.57512,-0.81773,391.78
Fit molecule placed_model-coot-0.pdb (#9) to map
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) using 12420 atoms
average map value = 0.3875, steps = 44
shifted from previous position = 0.643
rotated from previous position = 0.00663 degrees
atoms outside contour = 3330, contour level = 0.21974
Position of placed_model-coot-0.pdb (#9) relative to
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) coordinates:
Matrix rotation and translation
0.99637027 -0.05354789 0.06617331 -0.66220936
-0.08184824 -0.81624827 0.57187378 221.48287918
0.02339121 -0.57521421 -0.81766831 391.68769476
Axis -0.99900165 0.03725903 -0.02464684
Axis point 0.00000000 172.60840560 160.85588620
Rotation angle (degrees) 144.96216986
Shift along axis -0.74008029
> select clear
> volume #29 level 0.15
> surface dust #29 size 7.8
> open 7z21
Summary of feedback from opening 7z21 fetched from pdb
---
notes | Fetching compressed mmCIF 7z21 from
http://files.rcsb.org/download/7z21.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
Fetching CCD CSX from http://ligand-expo.rcsb.org/reports/C/CSX/CSX.cif
7z21 title:
BAF A12T bound to the lamin A/C Ig-fold domain [more info...]
Chain information for 7z21 #30
---
Chain | Description | UniProt
A B C D | Barrier-to-autointegration factor, N-terminally processed |
BAF_HUMAN
E F | Lamin-A/C | LMNA_HUMAN
Non-standard residues in 7z21 #30
---
CL — chloride ion
7z21 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide #!29 models
> show #!29 models
> select #30
9838 atoms, 9228 bonds, 1285 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> show sel cartoons
> select clear
> select #30/E
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> combine sel
> hide #30 models
> select #30
9838 atoms, 9228 bonds, 1285 residues, 1 model selected
> hide #31 models
> show #31 models
> hide #31 models
> show #31 models
> show #30 models
> ~select #30
Nothing selected
> hide #30 models
> hide #31 models
> show #31 models
> select #30/E
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> combine #30/E
> hide #31 models
> hide #32 models
> show #32 models
> cp #30/E
Unknown command: cp #30/E
> copy #30/E
Unknown command: copy #30/E
> select #30/E
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> hide #32 models
> show #30 models
> save /home/Medalia/BWang/Downloads/lamina.pdb models #30 selectedOnly true
> hide #30 models
> select #30
9838 atoms, 9228 bonds, 1285 residues, 1 model selected
> ~select #30
Nothing selected
> open /home/Medalia/BWang/Downloads/lamina.pdb
Summary of feedback from opening /home/Medalia/BWang/Downloads/lamina.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 SER A 4
THR A 12 1 9
Start residue of secondary structure not found: HELIX 2 2 PRO A 19 LEU A 23 1
5
Start residue of secondary structure not found: HELIX 3 3 GLY A 27 ARG A 37 1
11
Start residue of secondary structure not found: HELIX 4 4 LYS A 41 LEU A 52 1
12
Start residue of secondary structure not found: HELIX 5 5 ASP A 55 GLY A 68 1
14
31 messages similar to the above omitted
Chain information for lamina.pdb #33
---
Chain | Description
E | No description available
> select #33
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> view matrix models #33,1,0,0,93.392,0,1,0,-7.897,0,0,1,-30.254
> view matrix models #33,1,0,0,273.58,0,1,0,54.828,0,0,1,-23.078
> view matrix models #33,1,0,0,329.6,0,1,0,188.87,0,0,1,126.62
> view matrix models #33,1,0,0,273.77,0,1,0,159.27,0,0,1,111.49
> view matrix models #33,1,0,0,250.57,0,1,0,163.5,0,0,1,142.6
> view matrix models #33,1,0,0,256.84,0,1,0,174.8,0,0,1,140.89
> view matrix models
> #33,-0.79041,0.13629,-0.59722,220.04,-0.47011,-0.76001,0.44875,87.474,-0.39273,0.63546,0.6648,159.01
> view matrix models
> #33,-0.79041,0.13629,-0.59722,214.3,-0.47011,-0.76001,0.44875,92.733,-0.39273,0.63546,0.6648,155.47
> view matrix models
> #33,-0.79041,0.13629,-0.59722,212.2,-0.47011,-0.76001,0.44875,95.142,-0.39273,0.63546,0.6648,160.89
> view matrix models
> #33,-0.79041,0.13629,-0.59722,211.65,-0.47011,-0.76001,0.44875,95.372,-0.39273,0.63546,0.6648,163.08
> view matrix models
> #33,-0.79041,0.13629,-0.59722,212.08,-0.47011,-0.76001,0.44875,94.6,-0.39273,0.63546,0.6648,164.22
Fit molecule lamina.pdb (#33) to map
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) using 1986 atoms
average map value = 0.06932, steps = 140
shifted from previous position = 9.39
rotated from previous position = 29.9 degrees
atoms outside contour = 1697, contour level = 0.15
Position of lamina.pdb (#33) relative to
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) coordinates:
Matrix rotation and translation
-0.97538237 -0.05505638 -0.21353695 179.71766208
-0.04499368 -0.89827573 0.43712273 111.03504168
-0.21588145 0.43596962 0.87368512 156.20670346
Axis -0.11091502 0.22551210 0.96790606
Axis point 98.70715309 37.58482060 0.00000000
Rotation angle (degrees) 179.70216494
Shift along axis 156.29977393
> view matrix models
> #33,-0.97538,-0.055056,-0.21354,184.11,-0.044994,-0.89828,0.43712,101.25,-0.21588,0.43597,0.87369,154.48
> view matrix models
> #33,-0.97538,-0.055056,-0.21354,184.76,-0.044994,-0.89828,0.43712,99.871,-0.21588,0.43597,0.87369,154.29
> view matrix models
> #33,-0.93496,0.14775,-0.32252,196.3,-0.30127,-0.81073,0.50195,91.669,-0.18731,0.56647,0.80251,161.84
> view matrix models
> #33,-0.93496,0.14775,-0.32252,199.57,-0.30127,-0.81073,0.50195,97.134,-0.18731,0.56647,0.80251,163.9
> select clear
> select #31
9838 atoms, 9228 bonds, 1285 residues, 1 model selected
> view matrix models #31,1,0,0,0.30807,0,1,0,0.65658,0,0,1,-1.504
> ~select #31
Nothing selected
> select #33
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> view matrix models
> #33,-0.90087,0.41101,-0.13962,202.91,-0.43404,-0.85708,0.27753,98.718,-0.0055999,0.31062,0.95052,156.98
> view matrix models
> #33,-0.90087,0.41101,-0.13962,203.02,-0.43404,-0.85708,0.27753,97.091,-0.0055999,0.31062,0.95052,155.46
Fit molecule lamina.pdb (#33) to map
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) using 1986 atoms
average map value = 0.06172, steps = 84
shifted from previous position = 3.27
rotated from previous position = 15.1 degrees
atoms outside contour = 1675, contour level = 0.15
Position of lamina.pdb (#33) relative to
cryosparc_P30_J249_015_volume_map_sharp.mrc z flip (#29) coordinates:
Matrix rotation and translation
-0.89132902 0.31267504 -0.32827869 205.00067167
-0.37349710 -0.91688314 0.14080211 104.66586711
-0.25696789 0.24811214 0.93402777 145.07411647
Axis 0.15370320 -0.10214048 -0.98282381
Axis point 122.29984253 24.28433501 0.00000000
Rotation angle (degrees) 159.56882575
Shift along axis -121.76365830
> select clear
> hide #33 models
> show #33 models
> select #33
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> select #30
9838 atoms, 9228 bonds, 1285 residues, 1 model selected
> ~select #30
Nothing selected
> hide #9 models
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> show #9 models
> select #33
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> combine sel
> hide #33 models
> hide #9 models
> show #9 models
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> select #33
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> hide #34 models
> show #34 models
> hide #34 models
> show #33 models
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> select #33
1986 atoms, 1848 bonds, 275 residues, 1 model selected
> hide #33 models
> show #33 models
> select #9
12420 atoms, 13077 bonds, 1236 residues, 1 model selected
> select #9,#33
Expected an objects specifier or a keyword
> volume #29 level 0.1862
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
Traceback (most recent call last):
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73, in
draw_new_frame
view.draw(check_for_changes = False)
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 165, in
draw
self._draw_scene(camera, drawings)
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 249, in
_draw_scene
draw_highlight_outline(r, highlight_drawings, color = self._highlight_color,
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1569,
in draw_highlight_outline
r.outline.finish_rendering_outline(color=color, pixel_width=pixel_width)
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1864,
in finish_rendering_outline
r.pop_framebuffer()
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 714,
in pop_framebuffer
fb.activate()
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2250,
in activate
GL.glDrawBuffer(self._draw_buffer)
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glDrawBuffer,
cArguments = (GL_BACK,)
)
OpenGL version: 3.3.0 NVIDIA 440.82
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 5820 Tower
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 20 Intel(R) Xeon(R) W-2155 CPU @ 3.30GHz
Cache Size: 14080 KB
Memory:
total used free shared buff/cache available
Mem: 62G 10G 45G 185M 6.2G 51G
Swap: 23G 0B 23G
Graphics:
0000:65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1)
Subsystem: Dell Device [1028:12a0]
Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-Clipper: 0.17.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
line-profiler: 3.3.0
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
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