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Opened 2 years ago
Last modified 2 years ago
#8900 assigned defect
glDrawBuffer: invalid operation setting contour level
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
Change History (5)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → glDrawBuffer: invalid operation setting contour level |
comment:2 by , 2 years ago
| Cc: | added |
|---|---|
| Description: | modified (diff) |
comment:3 by , 2 years ago
Greg, do you know what the expected OpenGL behavior is if ChimeraX is running on Linux (Ubuntu) and the user switches user so the ChimeraX process no longer has the console, and ChimeraX attempts to make its context current and render? I could imagine QOpenGL.makeCurrent() failing. Or maybe it succeeds but then glDrawBuffer(GL_BACK) fails on the default framebuffer as in the error in this bug report.
comment:4 by , 2 years ago
I do not know for sure, but it makes sense that the context might be reset. That is very common with WebGL and could easily have shown up in GUI toolkits, like Qt. If you look at the OpenGL extension ARB_robustness, https://registry.khronos.org/OpenGL/extensions/ARB/ARB_robustness.txt, we could be notified when a context is reset.
follow-up: 5 comment:5 by , 2 years ago
The QOpenGLContext.isValid() call that supposedly checks for a context reset has documentation that suggests that a reset will cause subsequent QOpenGLContext.makeCurrent() calls to fail. But in our bug reports it clearly has succeeded and only later glDrawBuffer(GL_BACK) gives an error. So my suspicion is the OpenGL context has not been reset.
Note:
See TracTickets
for help on using tickets.
Duplicate of #2729.
This has been reported a few dozen times, always on Linux. It appears the OpenGL connection has been dropped. In ticket #2729 the user was switched (so the console belonged to a different user) then when they switched back to the original user ChimeraX gave this error. Maybe the trouble is just that ChimeraX tries to render after a new user has the console and it does not detect that it does not have a valid window. The drawing code calls QWindow.isExposed() to check if the graphics should be drawn. This may be incorrectly claiming that the window is exposed. The drawing code in these reports does make the OpenGL context current on the graphics window. I think that would give an error if the window could not be rendered, but not certain about that.
The errors in is invalid operation in glDrawBuffer(GL_BACK). Docs say that means the framebuffer does not have a back buffer.
It may be worth testing switching users while ChimeraX is running on Ubuntu to see if this error can be produced. If it can maybe I can find a more reliable way to tell if the QOpenGLContext can render. The QOpenGLContext.isValid() call says the context can be lost on some operating systems. But it also suggests that makeCurrent() should then fail, and it has not failed in these reports. So maybe the context is not lost but the QWindow cannot be rendered since the console no longer belongs to the user. I have not seen any OpenGL documentation about the behavior in this case.