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Opened 4 years ago
Closed 4 years ago
#5488 closed defect (duplicate)
wrapped C/C++ object of type QScreen has been deleted
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5ckr format mmcif fromDatabase pdb
5ckr title:
Crystal Structure of MraY in complex with Muraymycin D2 [more info...]
Chain information for 5ckr #1
---
Chain | Description
A | Phospho-N-acetylmuramoyl-pentapeptide-transferase
Non-standard residues in 5ckr #1
---
57M — Muraymycin D2 (N-({(1S)-2-{[(2S)-1-{[3-({(1S,2S)-2-[(5-amino-5-deoxy-
beta-D-
ribofuranosyl)oxy]-1-carboxy-2-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]ethyl}amino)propyl]amino}-4-methyl-1-oxopentan-2-yl]amino}-1-[(4S)-2-amino-3,4,5,6-tetrahydropyrimidin-4-yl]-2-oxoethyl}carbamoyl)-L-valine)
5ckr mmCIF Assemblies
---
1| author_and_software_defined_assembly
> open 5JNQ
5jnq title:
MraY tunicamycin complex [more info...]
Chain information for 5jnq #2
---
Chain | Description
A | Phospho-N-acetylmuramoyl-pentapeptide-transferase
Non-standard residues in 5jnq #2
---
BOG — octyl beta-D-glucopyranoside
PLM — palmitic acid
TUM — Tunicamycin
5jnq mmCIF Assemblies
---
1| author_defined_assembly
> select #2
2440 atoms, 2496 bonds, 2 pseudobonds, 314 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,-142.47,0,1,0,-152.39,0,0,1,-235.77
> view matrix models
> #2,0.98741,-0.14601,0.060783,-135.57,-0.080333,-0.79407,-0.60249,276.05,0.13624,0.59003,-0.79581,131.5
> view matrix models
> #2,0.98741,-0.14601,0.060783,-135.85,-0.080333,-0.79407,-0.60249,303.57,0.13624,0.59003,-0.79581,129.76
> view matrix models
> #2,0.98741,-0.14601,0.060783,-136.19,-0.080333,-0.79407,-0.60249,312.86,0.13624,0.59003,-0.79581,110.78
> view matrix models
> #2,0.98903,0.065796,0.13222,-185.58,0.14459,-0.61381,-0.7761,294.77,0.030092,0.78671,-0.61659,53.399
> view matrix models
> #2,0.99395,0.10917,-0.012384,-154.49,0.057151,-0.61,-0.79034,312.74,-0.093833,0.78485,-0.61255,73.522
> view matrix models
> #2,0.99395,0.10917,-0.012384,-155.13,0.057151,-0.61,-0.79034,307.74,-0.093833,0.78485,-0.61255,66.595
> view matrix models
> #2,0.99395,0.10917,-0.012384,-154.75,0.057151,-0.61,-0.79034,301.89,-0.093833,0.78485,-0.61255,68.498
> view matrix models
> #2,0.98714,0.061075,-0.14773,-111.11,0.028384,-0.97642,-0.21401,207.42,-0.15731,0.20707,-0.9656,254.43
> view matrix models
> #2,0.98714,0.061075,-0.14773,-108.14,0.028384,-0.97642,-0.21401,208,-0.15731,0.20707,-0.9656,256.24
> view matrix models
> #2,0.99886,0.047731,0.00058642,-147.4,0.046911,-0.97929,-0.19694,200.76,-0.0088258,0.19674,-0.98042,236.48
> open 6OYH
6oyh title:
Crystal structure of MraY bound to carbacaprazamycin [more info...]
Chain information for 6oyh #3
---
Chain | Description
A B C D | Phospho-N-acetylmuramoyl-pentapeptide-transferase
E F G H | MraYAA nanobody
Non-standard residues in 6oyh #3
---
NK4 — (5S)-5'-O-(5-amino-5-deoxy-beta-D-
ribofuranosyl)-5'-C-[(2S,5S,6S)-5-carboxy-6-heptadecyl-1,4-dimethyl-3-oxo-1,4-diazepan-2-yl]uridine
6oyh mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
> select #3
27565 atoms, 27880 bonds, 6 pseudobonds, 1841 residues, 2 models selected
> view matrix models #3,1,0,0,-223.92,0,1,0,-100.28,0,0,1,-68.402
> view matrix models #3,1,0,0,-257.78,0,1,0,-9.3814,0,0,1,-237.92
> show sel cartoons
> style sel stick
Changed 27565 atom styles
> hide sel atoms
> view matrix models #3,1,0,0,-233.48,0,1,0,-19.002,0,0,1,-134.97
> view matrix models
> #3,0.99966,0.0034391,-0.025851,-239.48,-0.0035577,0.99998,-0.0045457,-20.008,0.025835,0.0046361,0.99966,-135.4
> view matrix models
> #3,-0.50399,0.2582,0.82421,-41.497,0.37841,-0.79179,0.47944,-246.62,0.7764,0.55353,0.30135,-165.21
> view matrix models
> #3,-0.50442,0.43058,0.74843,-22.123,-0.35098,-0.8942,0.27789,23.026,0.7889,-0.12251,0.60218,-245.35
Drag select of 1136 residues, 3 pseudobonds
> select clear
> select #3/B,C,D,E,F
18838 atoms, 19055 bonds, 4 pseudobonds, 1258 residues, 2 models selected
> select #3/B,C,D,E,F,G,H
22392 atoms, 22647 bonds, 4 pseudobonds, 1509 residues, 2 models selected
> delete atoms (#!3 & sel)
> delete bonds (#!3 & sel)
> select #3
5173 atoms, 5233 bonds, 2 pseudobonds, 332 residues, 2 models selected
> view matrix models
> #3,-0.50442,0.43058,0.74843,-4.7644,-0.35098,-0.8942,0.27789,44.758,0.7889,-0.12251,0.60218,-361.03
> view matrix models
> #3,-0.50442,0.43058,0.74843,-1.027,-0.35098,-0.8942,0.27789,57.361,0.7889,-0.12251,0.60218,-364.67
> view matrix models
> #3,-0.41231,0.51429,0.752,-29.216,-0.81035,0.17019,-0.56069,375.63,-0.41634,-0.84056,0.34658,49.397
> view matrix models
> #3,-0.37828,0.49243,0.78384,-46.254,-0.83137,0.19165,-0.52162,372.66,-0.40709,-0.84899,0.3369,48.982
> view matrix models
> #3,-0.37828,0.49243,0.78384,-46.036,-0.83137,0.19165,-0.52162,374.23,-0.40709,-0.84899,0.3369,48.408
> view matrix models
> #3,-0.37828,0.49243,0.78384,-45.51,-0.83137,0.19165,-0.52162,373.68,-0.40709,-0.84899,0.3369,53.433
> select clear
> set bgColor white
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> show sel atoms
> open /Users/karen/Box/EYS/YES_1011_header3.pdb
Chain information for YES_1011_header3.pdb #4
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E | No description available
G | No description available
> select #4
18268 atoms, 18491 bonds, 1157 residues, 1 model selected
> select #3
5173 atoms, 5233 bonds, 2 pseudobonds, 332 residues, 2 models selected
> select #2
2440 atoms, 2496 bonds, 2 pseudobonds, 314 residues, 2 models selected
> select #1
2638 atoms, 2700 bonds, 1 pseudobond, 339 residues, 2 models selected
Drag select of 448 atoms, 962 residues, 5 pseudobonds, 428 bonds
> view matrix models
> #1,1,0,0,33.578,0,1,0,41.358,0,0,1,87.229,#2,0.99886,0.047731,0.00058642,-113.82,0.046911,-0.97929,-0.19694,242.12,-0.0088258,0.19674,-0.98042,323.71,#3,-0.37828,0.49243,0.78384,-11.932,-0.83137,0.19165,-0.52162,415.03,-0.40709,-0.84899,0.3369,140.66
> view matrix models
> #1,-0.17741,0.91155,-0.37096,55.471,-0.071111,-0.38782,-0.91899,69.986,-0.98157,-0.13666,0.13362,122.12,#2,-0.13117,-0.97412,0.18407,176.9,-0.081112,0.19559,0.97732,-214.72,-0.98804,0.11326,-0.10467,270.96,#3,-0.53971,0.40228,-0.73952,384.35,0.72344,0.67086,-0.16304,-120.8,0.43053,-0.62299,-0.65309,122.86
> view matrix models
> #1,-0.11759,-0.82764,-0.54881,80.465,-0.030191,-0.54941,0.83501,59.854,-0.9926,0.11476,0.039617,119.4,#2,-0.15144,0.69691,0.70099,-198.15,-0.0633,0.70087,-0.71047,151.47,-0.98644,-0.15196,-0.062023,298.11,#3,0.95597,0.24941,0.15465,-252.78,0.12826,-0.82907,0.54423,-99.456,0.26395,-0.50043,-0.82456,209.57
> view matrix models
> #1,-0.22235,-0.36667,-0.90339,79.209,-0.044746,-0.92177,0.38514,68.527,-0.97394,0.12606,0.18854,117.74,#2,-0.23132,0.17073,0.95778,-175.27,-0.091336,0.97632,-0.19609,-18.855,-0.96858,-0.13284,-0.21025,331.2,#3,0.75671,0.5872,-0.28737,-95.958,0.62647,-0.52568,0.5755,-253.3,0.18687,-0.61551,-0.76565,219.25
> view matrix models
> #1,-0.22235,-0.36667,-0.90339,113.86,-0.044746,-0.92177,0.38514,104.28,-0.97394,0.12606,0.18854,126.54,#2,-0.23132,0.17073,0.95778,-140.62,-0.091336,0.97632,-0.19609,16.899,-0.96858,-0.13284,-0.21025,339.99,#3,0.75671,0.5872,-0.28737,-61.306,0.62647,-0.52568,0.5755,-217.55,0.18687,-0.61551,-0.76565,228.04
> view matrix models
> #1,-0.30451,-0.3413,-0.88926,115.66,0.028831,-0.93648,0.34955,102.7,-0.95207,0.080801,0.295,125.89,#2,-0.31232,0.14474,0.93889,-118.27,-0.018219,0.98723,-0.15825,-6.8929,-0.9498,-0.066531,-0.3057,352.22,#3,0.76095,0.53961,-0.36025,-45.533,0.62536,-0.46204,0.62885,-229.87,0.17289,-0.7038,-0.68904,215.18
> view matrix models
> #1,-0.3238,-0.40287,-0.85607,116.82,0.060832,-0.9118,0.40609,101.14,-0.94417,0.079416,0.31975,125.54,#2,-0.33477,0.21065,0.91845,-118.78,0.014405,0.97572,-0.21854,5.1519,-0.94219,-0.059929,-0.32968,356.27,#3,0.80592,0.49013,-0.33206,-64.729,0.56972,-0.48956,0.66011,-220.65,0.16097,-0.72118,-0.67378,215.27
> view matrix models
> #1,-0.15531,-0.38209,-0.91098,112.3,0.22961,-0.91088,0.3429,96.933,-0.96081,-0.15592,0.2292,129.8,#2,-0.16502,0.18754,0.9683,-156.95,0.18359,0.97044,-0.15666,-38.693,-0.96905,0.15192,-0.19457,294.32,#3,0.74726,0.6237,-0.22934,-72.089,0.53083,-0.35262,0.77064,-235.57,0.39978,-0.69761,-0.59458,127.51
> view matrix models
> #1,-0.15531,-0.38209,-0.91098,110.79,0.22961,-0.91088,0.3429,95.693,-0.96081,-0.15592,0.2292,133.14,#2,-0.16502,0.18754,0.9683,-158.46,0.18359,0.97044,-0.15666,-39.932,-0.96905,0.15192,-0.19457,297.66,#3,0.74726,0.6237,-0.22934,-73.598,0.53083,-0.35262,0.77064,-236.81,0.39978,-0.69761,-0.59458,130.85
> select clear
> select #4
18268 atoms, 18491 bonds, 1157 residues, 1 model selected
> hide sel atoms
> sel#4/A
Unknown command: sel#4/A
> show sel cartoons
> hide sel cartoons
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> open /Users/karen/Box/EYS/P199J278_yflip.mrc
Opened P199J278_yflip.mrc as #5, grid size 256,256,256, pixel 0.832, shown at
level 0.0845, step 1, values float32
> surface dust #5 size 8.32
> volume #5 level 0.197
> ui tool show "Fit in Map"
Fit molecule 5ckr (#1) to map P199J278_yflip.mrc (#5) using 2638 atoms
average map value = 0.1148, steps = 104
shifted from previous position = 2.88
rotated from previous position = 16.4 degrees
atoms outside contour = 2017, contour level = 0.19704
Position of 5ckr (#1) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
-0.01268458 -0.19474862 -0.98077116 105.13703317
0.07227981 -0.97846273 0.19335543 103.93306915
-0.99730373 -0.06843732 0.02648778 136.41311305
Axis -0.69938847 0.04416733 0.71337578
Axis point 112.64303041 56.01406679 0.00000000
Rotation angle (degrees) 169.21300639
Shift along axis 28.37262803
Fit molecule 5jnq (#2) to map P199J278_yflip.mrc (#5) using 2440 atoms
average map value = 0.1099, steps = 92
shifted from previous position = 2.54
rotated from previous position = 9.46 degrees
atoms outside contour = 1896, contour level = 0.19704
Position of 5jnq (#2) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
-0.04662594 0.22631934 0.97293657 -185.10319081
0.08291079 0.97151187 -0.22201461 -4.08418162
-0.99546563 0.07031530 -0.06406197 281.04614444
Axis 0.14652015 0.98659279 -0.07187852
Axis point 38.85011535 0.00000000 224.31126512
Rotation angle (degrees) 93.99032498
Shift along axis -51.35195296
Fit molecule 6oyh (#3) to map P199J278_yflip.mrc (#5) using 5173 atoms
average map value = 0.1465, steps = 96
shifted from previous position = 2
rotated from previous position = 11.3 degrees
atoms outside contour = 3595, contour level = 0.19704
Position of 6oyh (#3) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
0.65006207 0.70355409 -0.28710789 -33.09567334
0.67407240 -0.35949310 0.64528375 -249.82780678
0.35077871 -0.61300599 -0.70793922 168.99914160
Axis -0.89174013 -0.45206526 -0.02089345
Axis point 0.00000000 -76.72694558 128.18707985
Rotation angle (degrees) 135.12803413
Shift along axis 138.92023887
Fit molecule YES_1011_header3.pdb (#4) to map P199J278_yflip.mrc (#5) using
18268 atoms
average map value = 0.1497, steps = 44
shifted from previous position = 0.00311
rotated from previous position = 0.0207 degrees
atoms outside contour = 13082, contour level = 0.19704
Position of YES_1011_header3.pdb (#4) relative to P199J278_yflip.mrc (#5)
coordinates:
Matrix rotation and translation
0.99999996 -0.00015229 0.00023905 -0.01018872
0.00015223 0.99999996 0.00022505 -0.03973284
-0.00023908 -0.00022502 0.99999995 0.04999791
Axis -0.62180678 0.66056856 0.42072022
Axis point 207.13768026 0.00000000 39.73256637
Rotation angle (degrees) 0.02073573
Shift along axis 0.00112429
> select #2
2440 atoms, 2496 bonds, 2 pseudobonds, 314 residues, 2 models selected
> view matrix models
> #2,-0.046626,0.22632,0.97294,-184.76,0.082911,0.97151,-0.22201,-4.0584,-0.99547,0.070315,-0.064062,277.91
> view matrix models
> #2,-0.046626,0.22632,0.97294,-184.5,0.082911,0.97151,-0.22201,-2.5501,-0.99547,0.070315,-0.064062,277.85
> view matrix models
> #2,-0.046626,0.22632,0.97294,-184.37,0.082911,0.97151,-0.22201,-2.467,-0.99547,0.070315,-0.064062,277.49
> view matrix models
> #2,-0.055571,0.11482,0.99183,-172,0.092575,0.98968,-0.10939,-36.55,-0.99415,0.08574,-0.065627,275.49
Fit molecule 5jnq (#2) to map P199J278_yflip.mrc (#5) using 2440 atoms
average map value = 0.1739, steps = 76
shifted from previous position = 1.36
rotated from previous position = 5.54 degrees
atoms outside contour = 1528, contour level = 0.19704
Position of 5jnq (#2) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
-0.01812439 0.18379049 0.98279833 -185.84984248
0.03963185 0.98231934 -0.18297004 -6.98756268
-0.99904996 0.03563389 -0.02508790 271.60659682
Axis 0.10935266 0.99138375 -0.07211275
Axis point 38.68262360 0.00000000 223.96439423
Rotation angle (degrees) 91.74472433
Shift along axis -46.83682998
> hide #!5 models
> select #1
2638 atoms, 2700 bonds, 1 pseudobond, 339 residues, 2 models selected
> view matrix models
> #1,-0.012685,-0.19475,-0.98077,106.1,0.07228,-0.97846,0.19336,103.59,-0.9973,-0.068437,0.026488,135.31
> view matrix models
> #1,-0.012685,-0.19475,-0.98077,106.2,0.07228,-0.97846,0.19336,104.18,-0.9973,-0.068437,0.026488,135.73
> view matrix models
> #1,-0.012685,-0.19475,-0.98077,105.85,0.07228,-0.97846,0.19336,103.64,-0.9973,-0.068437,0.026488,131.94
Fit molecule 5ckr (#1) to map P199J278_yflip.mrc (#5) using 2638 atoms
average map value = 0.1933, steps = 60
shifted from previous position = 1.23
rotated from previous position = 4.05 degrees
atoms outside contour = 1518, contour level = 0.19704
Position of 5ckr (#1) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
-0.02286810 -0.25347290 -0.96707215 106.31400598
0.03801507 -0.96684600 0.25251469 104.63501352
-0.99901547 -0.03098878 0.03174572 130.56604133
Axis -0.69507897 0.07831696 0.71465493
Axis point 109.26365144 54.21193394 0.00000000
Rotation angle (degrees) 168.23276990
Shift along axis 27.60773155
> view matrix models
> #1,-0.022868,-0.25347,-0.96707,106.31,0.038015,-0.96685,0.25251,104.62,-0.99902,-0.030989,0.031746,130.8
> undo
> select clear
> open 4ODL
4odl title:
Structure of SlyD from Thermus thermophilus in complex with S2 peptide [more
info...]
Chain information for 4odl #6
---
Chain | Description
A B | Peptidyl-prolyl cis-trans isomerase SlyD
C D E F | 30S ribosomal protein S2
Non-standard residues in 4odl #6
---
CL — chloride ion
NH2 — amino group
4odl mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select #6
2791 atoms, 2859 bonds, 366 residues, 1 model selected
> view matrix models #6,1,0,0,31.865,0,1,0,130.38,0,0,1,82.225
> hide sel atoms
> show sel cartoons
> view matrix models #6,1,0,0,34.359,0,1,0,141.08,0,0,1,85.873
> view matrix models
> #6,-0.22039,-0.96376,-0.15029,71.821,0.7913,-0.086559,-0.60527,73.938,0.57033,-0.25232,0.7817,50.771
> view matrix models
> #6,0.32966,-0.8023,0.49763,37.612,0.62733,-0.20776,-0.75053,81.126,0.70554,0.5596,0.43482,74.173
> view matrix models
> #6,0.32966,-0.8023,0.49763,38.577,0.62733,-0.20776,-0.75053,80.026,0.70554,0.5596,0.43482,105.1
> view matrix models
> #6,0.49916,-0.41135,0.76265,37.711,0.64319,-0.41389,-0.64421,71.123,0.58065,0.81209,0.057983,125.39
> view matrix models
> #6,0.49916,-0.41135,0.76265,35.069,0.64319,-0.41389,-0.64421,55.645,0.58065,0.81209,0.057983,144.89
> select #6/B,C,E
1367 atoms, 1398 bonds, 181 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #6
1424 atoms, 1461 bonds, 185 residues, 1 model selected
> view matrix models
> #6,0.49916,-0.41135,0.76265,28.629,0.64319,-0.41389,-0.64421,69.048,0.58065,0.81209,0.057983,144.91
> view matrix models
> #6,-0.1207,0.31736,0.94059,80.461,0.79886,-0.53142,0.28182,9.5946,0.58928,0.78542,-0.18939,155.9
> view matrix models
> #6,-0.1207,0.31736,0.94059,80.234,0.79886,-0.53142,0.28182,9.5907,0.58928,0.78542,-0.18939,153.28
> view matrix models
> #6,-0.1207,0.31736,0.94059,78.164,0.79886,-0.53142,0.28182,14.691,0.58928,0.78542,-0.18939,157.66
> show #!5 models
> view matrix models
> #6,0.33218,-0.089517,0.93896,39.495,0.75286,-0.57453,-0.32112,45.469,0.5682,0.81358,-0.12346,156.52
> view matrix models
> #6,0.33218,-0.089517,0.93896,30.461,0.75286,-0.57453,-0.32112,34.75,0.5682,0.81358,-0.12346,157.98
> view matrix models
> #6,0.57021,-0.29587,0.76637,19.224,0.58925,-0.50272,-0.63251,61.169,0.57241,0.81224,-0.11232,157.16
> view matrix models
> #6,0.57021,-0.29587,0.76637,17.134,0.58925,-0.50272,-0.63251,65.555,0.57241,0.81224,-0.11232,156.42
> view matrix models
> #6,0.43506,-0.040156,0.8995,28.056,0.7205,-0.5836,-0.37454,42.881,0.53999,0.81105,-0.22497,163.55
Fit molecule 4odl (#6) to map P199J278_yflip.mrc (#5) using 1424 atoms
average map value = 0.1024, steps = 108
shifted from previous position = 3.15
rotated from previous position = 7.84 degrees
atoms outside contour = 1147, contour level = 0.19704
Position of 4odl (#6) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
0.50340000 0.05866176 0.86205988 31.10709293
0.74250084 -0.53962227 -0.39686308 43.87007105
0.44190603 0.83986106 -0.31520226 176.67964724
Axis 0.83883753 0.28497934 0.46383011
Axis point 0.00000000 -15.01596098 82.23513298
Rotation angle (degrees) 132.50948609
Shift along axis 120.54520082
> hide #!5 models
> hide #4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> select clear
> select #6/D
132 atoms, 138 bonds, 16 residues, 1 model selected
> hbonds sel reveal true
17 hydrogen bonds found
> style sel stick
Changed 132 atom styles
> color sel byhetero
> hide sel cartoons
> show sel cartoons
> select #6/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> ui tool show H-Bonds
> select #6/D
132 atoms, 138 bonds, 1 pseudobond, 16 residues, 2 models selected
> hbonds sel color #43d2c9 intraMol false intraRes false reveal true
16 hydrogen bonds found
> hbonds sel color #43d2c9 intraMol false intraRes false reveal true
16 hydrogen bonds found
> style sel stick
Changed 132 atom styles
> select clear
Drag select of 7 atoms, 59 residues, 6 bonds, 4 pseudobonds
> show sel atoms
> style sel stick
Changed 458 atom styles
> color sel byhetero
Drag select of 218 atoms, 139 residues, 180 bonds, 2 pseudobonds
> hide sel atoms
> select #6/D:32
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/D:30
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/D:30
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> show sel atoms
> select #6/D:29
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/D:30
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/D:30
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #6/A:94
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/A:92
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #6 cartoons
> show #4 models
> select #4
18268 atoms, 18491 bonds, 1157 residues, 1 model selected
> show sel cartoons
> select #6
1424 atoms, 1461 bonds, 5 pseudobonds, 185 residues, 2 models selected
> show sel cartoons
> show #!5 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #6 models
> hide #7 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #7 models
> hide #7 models
> interfaces #4 & ~solvent
8 buried areas: A B 1910, E G 1759, A E 1624, C G 852, D G 737, C B 735, D B
666, B G 327
> show sel atoms
> style sel stick
Changed 404 atom styles
> hide
> show sel atoms
> hide HC
> color sel byhetero
> show #!5 models
> hide #!5 models
> hbonds sel color #43d2c9 dashes 6 intraMol false intraRes false reveal true
> retainCurrent true
8 hydrogen bonds found
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> view matrix models
> #4,1,-0.00015229,0.00023905,2.0779,0.00015223,1,0.00022505,2.52,-0.00023908,-0.00022502,1,1.0217
> undo
> hide #!5 models
> hide #4 models
> show #!3 models
> show #!2 models
> show #!1 models
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> show sel atoms
> select :TUM
45 atoms, 48 bonds, 1 residue, 1 model selected
> show sel atoms
> select :57M
64 atoms, 67 bonds, 1 residue, 1 model selected
> show sel atoms
> view matrix models
> #1,-0.022868,-0.25347,-0.96707,106.03,0.038015,-0.96685,0.25251,104.58,-0.99902,-0.030989,0.031746,130.57
> undo
> view matrix models
> #1,-0.022868,-0.25347,-0.96707,106.33,0.038015,-0.96685,0.25251,104.64,-0.99902,-0.030989,0.031746,130.57
> select clear
> color #!1-3 byhetero
> hide #!1 models
> hide #!2 models
> show #4 models
> hide #4 models
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show #!3 cartoons
> show #!3 cartoons
> show #4 models
> select #4
18268 atoms, 18491 bonds, 8 pseudobonds, 1157 residues, 2 models selected
> hide sel cartoons
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> color sel teal
> select clear
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> show sel cartoons
> color sel peru
> select clear
> hide #4 models
> select #3/A:401@C34
1 atom, 1 residue, 1 model selected
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> hbonds sel color #43d2c9 intraMol false intraRes false reveal true
21 hydrogen bonds found
> show #7 models
> interfaces sel & ~solvent
0 buried areas:
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> show #4 models
Drag select of 31 residues, 218 atoms, 188 bonds
> hide sel atoms
> hide #!1 models
> hide #!2 models
> show #!2 models
> select #1
2638 atoms, 2700 bonds, 1 pseudobond, 339 residues, 2 models selected
> ~select #1
Nothing selected
> hide #!3 models
> show #!3 models
> hide #!2 models
> color #4#!3 byhetero
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel orchid
> color sel medium violet red
> color sel purple
> color sel dark magenta
> color sel purple
> color sel byhetero
> lighting soft
> graphics silhouettes true
> select clear
> graphics silhouettes false
> set bgColor black
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #4/B:23
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 19 atom styles
> select clear
> hide HC
> select clear
> select #4/B:22
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:26
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #4/B:25
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> view matrix models
> #4,1,-0.00015229,0.00023905,-1.3538,0.00015223,1,0.00022505,2.1554,-0.00023908,-0.00022502,1,0.31892
> undo
> hide HC
> style sel stick
Changed 19 atom styles
> select clear
> style #!3-4 stick
Changed 23441 atom styles
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel atoms
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
Fit molecule YES_1011_header3.pdb (#4) to map P199J278_yflip.mrc (#5) using
18268 atoms
average map value = 0.1497, steps = 48
shifted from previous position = 0.0177
rotated from previous position = 0.00944 degrees
atoms outside contour = 13097, contour level = 0.19704
Position of YES_1011_header3.pdb (#4) relative to P199J278_yflip.mrc (#5)
coordinates:
Matrix rotation and translation
0.99999997 -0.00017977 0.00013402 0.00594909
0.00017972 0.99999992 0.00034907 -0.05716333
-0.00013408 -0.00034905 0.99999993 0.06945661
Axis -0.84136307 0.32310914 0.43325359
Axis point 0.00000000 190.74026497 169.92391522
Rotation angle (degrees) 0.02377069
Shift along axis 0.00661699
Fit molecule 6oyh (#3) to map P199J278_yflip.mrc (#5) using 5173 atoms
average map value = 0.1465, steps = 40
shifted from previous position = 0.0208
rotated from previous position = 0.0266 degrees
atoms outside contour = 3593, contour level = 0.19704
Position of 6oyh (#3) relative to P199J278_yflip.mrc (#5) coordinates:
Matrix rotation and translation
0.65017310 0.70344984 -0.28711193 -33.13012163
0.67415469 -0.35983891 0.64500497 -249.77694460
0.35041460 -0.61292273 -0.70819159 169.18213979
Axis -0.89179292 -0.45196687 -0.02076845
Axis point 0.00000000 -76.67860216 128.24404698
Rotation angle (degrees) 135.14781812
Shift along axis 138.92246123
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> mlp sel
Map values for surface "YES_1011_header3.pdb_A SES surface": minimum -27.97,
mean 2.047, maximum 25.03
To also show corresponding color key, enter the above mlp command and add key
true
> hide sel surfaces
> select #4/B:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain #4/B
Alignment identifier is 4/B
> select #4/B:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #4/B:21-24
63 atoms, 63 bonds, 4 residues, 1 model selected
> show sel atoms
> select #4/B:25
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #4/B:25-27
56 atoms, 56 bonds, 3 residues, 1 model selected
> show sel atoms
> select #4/B:26
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #4/B:26-27
37 atoms, 37 bonds, 2 residues, 1 model selected
> hide sel atoms
> hide sel atoms
> select #4/B:24
19 atoms, 18 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #4/B:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> color sel fire brick
> color sel byhetero
> select clear
> hide HC
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel atoms
> select #4/B:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel atoms
> hide HC
> set bgColor white
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select up
368 atoms, 370 bonds, 22 residues, 1 model selected
> select up
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> select up
18268 atoms, 18491 bonds, 1157 residues, 1 model selected
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> hide #!3 models
> show #!4 atoms
> hide #!4 atoms
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> show #!4 atoms
> hide #!4 atoms
> show #!4 cartoons
> hide #!4 cartoons
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> show #!3 models
> hide sel cartoons
> hide sel cartoons
> select #3
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> hide sel cartoons
> select #3/A
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> hide sel atoms
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!3 models
> show #!3 models
> show sel cartoons
> select #3
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> show sel cartoons
> hide #7 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide HC
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh.png" width
> 1166 height 1123 supersample 4 transparentBackground true
> show #!4 models
> hide #!3 models
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_EYS.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel cartoons
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_Y.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> select #4
18268 atoms, 18491 bonds, 1157 residues, 1 model selected
> ~select #4
1 model selected
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> hide sel cartoons
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_E.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!4 models
> show #!3 models
> select #3/A
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> hide sel cartoons
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_carb.png"
> width 1166 height 1123 supersample 3 transparentBackground true
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_carb.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> select #3
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> hide sel atoms
> select #3/A
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> show sel cartoons
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh.png" width
> 1166 height 1123 supersample 4 transparentBackground true
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh.png" width
> 1166 height 1123 supersample 4 transparentBackground true
> hide #!3 cartoons
> select :NK4
122 atoms, 125 bonds, 1 residue, 1 model selected
> show sel atoms
> hide HC
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_carb.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> select #3/A
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> show sel cartoons
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> select #7
21 pseudobonds, 1 model selected
> ~select #7
Nothing selected
> hide #!3 models
> show #!3 models
> select #3
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> select #3/A
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> hide sel cartoons
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel cartoons
> save "/Users/karen/Box/Glyco Team/EYS21
> Data/Figures/Figure3/6oyh_Y_carb.png" width 1166 height 1123 supersample 4
> transparentBackground true
> select #3
5173 atoms, 5233 bonds, 9 pseudobonds, 332 residues, 3 models selected
> color sel byhetero
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide #!4 models
> show #!4 models
> open "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/e_95.jvp"
Unrecognized file suffix '.jvp'
> open /Users/karen/Box/MSAs/E_95.aln
Summary of feedback from opening /Users/karen/Box/MSAs/E_95.aln
---
notes | Alignment identifier is E_95.aln
Associated YES_1011_header3.pdb chain B to ID21/1-76 with 0 mismatches
Associated YES_1011_header3.pdb chain G to ID21/1-76 with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment E_95.aln
Opened 21 sequences from E_95.aln
> color #4/B byattr seq_conservation palette cyanmaroon
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> select #4/B
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> color byattribute seq_conservation palette cyanmaroon
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
Fetching compressed palette Giant Goldfish from
http://www.colourlovers.com/api/palettes?keywords=Giant%20Goldfish&format=json&numResults=100
Found 5 ColourLover palettes with name "Giant Goldfish", using palette id
92095 by author manekineko with most views (1095482). To choose a different
one use "name by author" or id number.
> color byattribute seq_conservation palette "Giant Goldfish"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> hide #!3 models
> show #!3 models
> hide #!3 models
> select up
18268 atoms, 18491 bonds, 1157 residues, 1 model selected
> select clear
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> hide sel cartoons
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_Econs.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> show #!3 models
> select #4/A
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
Fetching compressed palette one more partygirl from
http://www.colourlovers.com/api/palettes?keywords=one%20more%20partygirl&format=json&numResults=100
> color byattribute seq_conservation palette "one more partygirl"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" atom
> seq_conservation range 1.34 to -1.42
Expected a keyword
> color byattribute seq_conservation palette "one more partygirl" range 1.34
> to -1.42
Invalid "range" argument: Need exactly 2 ','-separated numbers
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42 key true
> key #fe9746:-1.42 #e77152:-0.73 #d04c5e:-0.04 #b92669:0.65 #a20075:1.34
> ui tool show "Color Key"
> ui mousemode left "color key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> key #a20075:1.34 #b92669:0.65 #d04c5e:-0.04 #e77152:-0.73 #fe9746:-1.42
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42 key true
> key #fe9746:-1.42 #e77152:-0.73 #d04c5e:-0.04 #b92669:0.65 #a20075:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
Fetching compressed palette Peas and Queues from
http://www.colourlovers.com/api/palettes?keywords=Peas%20and%20Queues&format=json&numResults=100
> color byattribute seq_conservation palette "Peas and Queues" range full key
> true
> key #d0ec7b:-1.42 #b0ea84:-0.73 #79e38e:-0.04 #4ad890:0.65 #1fce92:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
Fetching compressed palette evil jack from
http://www.colourlovers.com/api/palettes?keywords=evil%20jack&format=json&numResults=100
> color byattribute seq_conservation palette "evil jack" range full key true
> key #350504:-1.42 #a21a00:-0.73 #f56f15:-0.04 #fcb521:0.65 #ffe870:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
Fetching compressed palette The Sun Or Bust from
http://www.colourlovers.com/api/palettes?keywords=The%20Sun%20Or%20Bust&format=json&numResults=100
> color byattribute seq_conservation palette "The Sun Or Bust" range full key
> true
> key #f1ea9b:-1.42 #f2ba49:-0.73 #e87646:-0.04 #d6456e:0.65 #a61b69:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "The Sun Or Bust" range
> 1.34,-1.42 key true
> key #a61b69:-1.42 #d6456e:-0.73 #e87646:-0.04 #f2ba49:0.65 #f1ea9b:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "The Sun Or Bust" range full key
> true
> key #f1ea9b:-1.42 #f2ba49:-0.73 #e87646:-0.04 #d6456e:0.65 #a61b69:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "The Sun Or Bust" range
> 1.34,-1.42 key true
> key #a61b69:-1.42 #d6456e:-0.73 #e87646:-0.04 #f2ba49:0.65 #f1ea9b:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "The Sun Or Bust" range full key
> true
> key #f1ea9b:-1.42 #f2ba49:-0.73 #e87646:-0.04 #d6456e:0.65 #a61b69:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "The Sun Or Bust" range full key
> true
> key #f1ea9b:-1.42 #f2ba49:-0.73 #e87646:-0.04 #d6456e:0.65 #a61b69:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range full
> key true
> key #a20075:-1.42 #b92669:-0.73 #d04c5e:-0.04 #e77152:0.65 #fe9746:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range
> 1.34,-1.42
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "one more partygirl" range full
> key true
> key #a20075:-1.42 #b92669:-0.73 #d04c5e:-0.04 #e77152:0.65 #fe9746:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> color byattribute seq_conservation palette "The Sun Or Bust" range full key
> true
> key #f1ea9b:-1.42 #f2ba49:-0.73 #e87646:-0.04 #d6456e:0.65 #a61b69:1.34
> ui tool show "Color Key"
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> key pos 0.533423,0.308344 size 0.0746657,0.0118058
> key pos 0.720392,0.220847 size 0.198935,0.0214057
> color byattribute seq_conservation palette "The Sun Or Bust" range full key
> false
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> hide #8 models
> key pos 0.811181,0.281424 size 0,0
> key pos 0.621483,0.331193 size 0.0576768,0.00314991
> key pos 0.612614,0.337053 size 0.0706266,3.35884e-05
> close #8
> ui mousemode left rotate
> hide #!3 models
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel cartoons
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_Y.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> show #!3 models
> save "/Users/karen/Box/Glyco Team/EYS21
> Data/Figures/Figure3/6oyh_Y_carb.png" width 1166 height 1123 supersample 4
> transparentBackground true
> save "/Users/karen/Box/Glyco Team/EYS21
> Data/Figures/Figure3/6oyh_Y_carb.png" width 1166 height 1123 supersample 4
> transparentBackground true
> hide #!3 models
> hide #!4 models
> show #!4 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> hide sel cartoons
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_Econs.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> show #!3 models
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel cartoons
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_carb.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!3 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> hide sel cartoons
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> show sel cartoons
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_Econs.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> show #!3 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1
2638 atoms, 2700 bonds, 1 pseudobond, 339 residues, 2 models selected
> hide sel cartoons
> select #2
2440 atoms, 2496 bonds, 2 pseudobonds, 314 residues, 2 models selected
> hide sel cartoons
> select #1
2638 atoms, 2700 bonds, 1 pseudobond, 339 residues, 2 models selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select #1/A:70@CA
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select #1/A:70@CB
1 atom, 1 residue, 1 model selected
Drag select of 5 atoms, 4 bonds
> hide sel atoms
Drag select of 4 atoms, 3 bonds
> hide sel atoms
Drag select of 5 atoms, 4 bonds
> hide sel cartoons
> hide sel atoms
Drag select of 11 atoms, 10 bonds
> hide sel atoms
> select #1/A:508@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> show #!2 models
> hide #!1 models
> select #1
2638 atoms, 2700 bonds, 1 pseudobond, 339 residues, 2 models selected
> ~select #1
Nothing selected
Drag select of 6 atoms, 4 bonds
Drag select of 5 atoms, 4 bonds
> hide sel atoms
Drag select of 4 atoms, 3 bonds
> hide sel atoms
Drag select of 4 atoms, 3 bonds
> hide sel atoms
> show #!3 models
> hide #!2 models
> show #!2 models
> show #!1 models
> show #!4 models
> hide #!4 models
Drag select of 1 atoms
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> show #!4 models
> hide #!1 models
> hide #!3 models
Drag select of 12 atoms, 13 bonds, 18 residues
> select clear
> select #4/c
2300 atoms, 2320 bonds, 154 residues, 1 model selected
> select #4/c
2300 atoms, 2320 bonds, 154 residues, 1 model selected
> show sel cartoons
> select #4/d
2300 atoms, 2320 bonds, 154 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select #4/g
1075 atoms, 1086 bonds, 64 residues, 1 model selected
> show sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select #4/c
2300 atoms, 2320 bonds, 154 residues, 1 model selected
> color sel maroon
> color sel brown
> select #4/c
2300 atoms, 2320 bonds, 154 residues, 1 model selected
> hide sel cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_EY.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!2 models
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!2 models
> show #!3 models
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_carb.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!3 models
> show #!2 models
> color #!2 byhetero
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> color #!2 byhetero
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 3 transparentBackground true
> color #!2 byhetero
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> color #!2 byhetero
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> show #!4 models
> color sel byhetero
> select #2
2440 atoms, 2496 bonds, 2 pseudobonds, 314 residues, 2 models selected
> color sel byhetero
> color sel chartreuse
> color sel lawn green
> color sel green
> color sel lawn green
> color sel lawn green
> color sel spring green
> color sel chartreuse
> color sel lime
> color sel spring green
> color sel lawn green
> color sel chartreuse
> color sel lime
> color sel green yellow
> color sel lawn green
> color sel chartreuse
> color sel lime green
> color sel lime
> color sel byhetero
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> color sel peru
> hide #!4 models
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!2 models
> show #!4 models
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_EY.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!4 models
> show #!2 models
> graphics silhouettes true
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/5jnq_tun.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!2 models
> show #!4 models
> graphics silhouettes false
> show #!3 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> hide sel cartoons
> hide #!3 models
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_E.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!3 cartoons
> graphics silhouettes true
> save "/Users/karen/Box/Glyco Team/EYS21
> Data/Figures/Figure3/6oyh_carbalone.png" width 1166 height 1123 supersample
> 4 transparentBackground true
> hide #!3 models
> show #!4 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> hide sel cartoons
> show #!3 models
> graphics silhouettes false
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_carb.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> hide #!3 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> hide sel cartoons
> select #4/b
1089 atoms, 1101 bonds, 65 residues, 1 model selected
> show sel cartoons
> color byattribute seq_conservation palette "The Sun Or Bust" range full
29943 atoms, 2327 residues, 1 surfaces, atom seq_conservation range -1.42 to
1.34
> select clear
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/6oyh_E.png"
> width 1166 height 1123 supersample 4 transparentBackground true
> show #!3 models
> select #4/a
5758 atoms, 5838 bonds, 360 residues, 1 model selected
> show sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2149, in <lambda>
dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 626, in close_request
tool_instance.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 512, in delete
ToolInstance.delete(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 154, in delete
self.session.ui.remove_tool(self)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 345, in remove_tool
self.main_window.remove_tool(tool_instance)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 725, in remove_tool
tw._destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2049, in _destroy
self.__toolkit.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2189, in destroy
sbar.destroy()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy
v.delete()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete
self.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current
return self._opengl_context.make_current()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current
qc = self._initialize_context()
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
RuntimeError: wrapped C/C++ object of type QScreen has been deleted
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context
qc.setScreen(self._screen)
See log for complete Python traceback.
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:307
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #4/A:307
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> save "/Users/karen/Box/Glyco Team/EYS21 Data/Figures/Figure3/fig3.cxs"
> includeMaps true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff049316af0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff0010430d0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff049316af0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff0010430d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff049316af0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff0010430d0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 281, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/seq-view/tool.py", line 695, in take_snapshot
'ToolInstance': ToolInstance.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/tools.py", line 96, in take_snapshot
data['shown'] = self.tool_window.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1983, in shown
return self.__toolkit.shown
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 2267, in shown
return not self.dock_widget.isHidden()
RuntimeError: wrapped C/C++ object of type QDockWidget has been deleted
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 260, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 284, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff049316af0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff0010430d0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/dialog.py", line 51, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/save_command/cmd.py", line 87, in provider_save
provider_info.bundle_info.run_provider(session, provider_info.format_name,
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 877, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 607, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x7ff049316af0> -> <chimerax.seq-view.tool.SequenceViewer object at
0x7ff0010430d0>: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x7ff049316af0> -> <chimerax.seq-
view.tool.SequenceViewer object at 0x7ff0010430d0>
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 262, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon Pro 5500 XT OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 8-Core Intel Core i7
Processor Speed: 3.8 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 40 GB
System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 11.6 (20G165)
Kernel Version: Darwin 20.6.0
Time since boot: 22 days 19:28
Graphics/Displays:
AMD Radeon Pro 5500 XT:
Chipset Model: AMD Radeon Pro 5500 XT
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0041
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XT-012
Option ROM Version: 113-D322A1XT-012
EFI Driver Version: 01.01.231
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.16.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
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: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.2
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
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: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
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: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 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: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
matplotlib-inline: 0.1.2
MolecularDynamicsViewer: 1.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
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: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → wrapped C/C++ object of type QScreen has been deleted |
comment:2 by , 4 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Fixed 6 months ago, not in 1.2.5, #4538.