The following bug report has been submitted:
Platform: Linux-5.5.8-1.el8.elrepo.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Am trying to do a buld rigid body fitting of my molecule into cryoEM map
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
> open /home/shabir/Downloads/J226_J564.cxs format session
Opened cryosparc_P28_J226_010_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.67, shown at level 0.139, step 1, values float32
Opened cryosparc_P27_J564_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.186, step 1, values float32
Log from Mon Oct 4 17:51:53 2021
> set selectionWidth 4
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 /home/shabir/Downloads/cryosparc_P23_J212_008_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P23_J212_008_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.67, shown at level 0.119, step 2, values float32
> volume #1 level 0.2672
> volume #1 level 0.3433
> close session
> open /home/shabir/Downloads/cryosparc_P28_J226_010_volume_map.mrc
Opened cryosparc_P28_J226_010_volume_map.mrc as #1, grid size 400,400,400,
pixel 0.67, shown at level 0.0992, step 2, values float32
> volume #1 level 0.1389
> open /home/shabir/Downloads/cryosparc_P27_J564_006_volume_map.mrc
Opened cryosparc_P27_J564_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.186, step 1, values float32
> ui tool show "Fit in Map"
> volume #1 step 1
Fit map cryosparc_P28_J226_010_volume_map.mrc in map
cryosparc_P27_J564_006_volume_map.mrc using 418378 points
correlation = 0.6717, correlation about mean = 0.07583, overlap = 9024
steps = 324, shift = 38.8, angle = 43.8 degrees
Position of cryosparc_P28_J226_010_volume_map.mrc (#1) relative to
cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.76205677 0.30454119 0.57142291 -103.79407097
-0.12008147 0.93365288 -0.33745036 59.20484367
-0.63627818 0.18853903 0.74806625 61.30844148
Axis 0.38004467 0.87260383 -0.30680386
Axis point 19.73690400 0.00000000 185.47461191
Rotation angle (degrees) 43.78942622
Shift along axis -6.59367736
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2
2 models selected
> ~select #2
Nothing selected
> select #2
2 models selected
Correlation = 0.6717, Correlation about mean = 0.07583, Overlap = 9024
> ~select #2
Nothing selected
> select #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.64079,0.58214,0.50049,55.892,0.22389,0.76529,-0.60349,72.665,-0.73434,-0.27465,-0.62073,301.77
> view matrix models
> #2,-0.14076,0.91005,-0.38986,71.283,0.89966,0.28195,0.33335,-59.247,0.41328,-0.30382,-0.85842,208.24
> ui mousemode right "move picked models"
> view matrix models
> #2,-0.14076,0.91005,-0.38986,68.702,0.89966,0.28195,0.33335,-42.189,0.41328,-0.30382,-0.85842,180.61
> view matrix models
> #2,-0.14076,0.91005,-0.38986,66.551,0.89966,0.28195,0.33335,-36.378,0.41328,-0.30382,-0.85842,184.34
> view matrix models
> #2,-0.14076,0.91005,-0.38986,71.993,0.89966,0.28195,0.33335,-38.228,0.41328,-0.30382,-0.85842,182.57
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.24582,0.88304,-0.39977,87.537,0.8654,0.38571,0.31986,-44.192,0.43664,-0.26734,-0.85899,176.13
> view matrix models
> #2,-0.34504,0.85537,-0.38639,99.758,0.82537,0.47252,0.309,-47.996,0.44689,-0.2123,-0.86903,170.22
> view matrix models
> #2,-0.11294,0.91359,-0.39064,68.675,0.93304,0.23268,0.2744,-29.516,0.34158,-0.33349,-0.87869,196
> view matrix models
> #2,-0.33138,0.66794,-0.66636,151.83,0.84825,0.52015,0.099546,-30.855,0.4131,-0.53226,-0.73895,193.29
> view matrix models
> #2,-0.44953,0.67997,-0.57928,153.06,0.87143,0.47635,-0.11709,-2.9479,0.19632,-0.55744,-0.80667,227.64
> view matrix models
> #2,-0.29926,0.93174,-0.20566,65.058,0.93504,0.32931,0.13137,-23.304,0.19013,-0.15299,-0.96977,203.63
> view matrix models
> #2,-0.30852,0.9272,-0.21239,67.357,0.87751,0.36361,0.31267,-42.253,0.36714,-0.089912,-0.92581,172.3
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right rotate
> ui mousemode right translate
> ~select #2
Nothing selected
Fit map cryosparc_P28_J226_010_volume_map.mrc in map
cryosparc_P27_J564_006_volume_map.mrc using 418378 points
correlation = 0.972, correlation about mean = 0.7063, overlap = 2.206e+04
steps = 160, shift = 4.97, angle = 23.4 degrees
Position of cryosparc_P28_J226_010_volume_map.mrc (#1) relative to
cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.56888246 0.82241884 0.00001346 74.82684904
0.82241884 0.56888246 -0.00000868 -77.63386013
-0.00001480 0.00000613 -1.00000000 240.16215476
Axis 0.46430373 0.88567604 -0.00001287
Axis point 57.76375873 0.00000000 120.08010514
Rotation angle (degrees) 179.99908591
Shift along axis -34.01915574
> save /home/shabir/Downloads/J226_J564.cxs
——— End of log from Mon Oct 4 17:51:53 2021 ———
opened ChimeraX session
> open /home/shabir/TOPOs/pdb3rae-in-bits.X.pdb
pdb3rae-in-bits.X.pdb title:
Quinolone(levofloxacin)-DNA cleavage complex of type IV topoisomerase from S.
Pneumoniae [more info...]
Chain information for pdb3rae-in-bits.X.pdb #3
---
Chain | Description
A B | topoisomerase IV subunit A
C D | topoisomerase IV subunit B
E | 5'-D(*CP*ap*TP*GP*ap*ap*T)-3'
F | 5'-D(P*ap*GP*TP*CP*ap*TP*TP*CP*ap*TP*G)-3'
G | 5'-D(*CP*GP*TP*GP*CP*ap*T)-3'
H | 5'-D(P*GP*ap*CP*TP*ap*TP*GP*CP*ap*CP*G)-3'
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
Non-standard residues in pdb3rae-in-bits.X.pdb #3
---
LFX —
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic
acid (levofloxacin)
MG — magnesium ion
pdb3rae-in-bits.X.pdb title:
Quinolone(levofloxacin)-DNA cleavage complex of type IV topoisomerase from S.
Pneumoniae [more info...]
Chain information for pdb3rae-in-bits.X.pdb
---
Chain | Description
3.2/A 3.2/B | topoisomerase IV subunit A
3.2/C 3.2/D | topoisomerase IV subunit B
3.2/E | 5'-D(*CP*ap*TP*GP*ap*ap*T)-3'
3.2/F | 5'-D(P*ap*GP*TP*CP*ap*TP*TP*CP*ap*TP*G)-3'
3.2/G | 5'-D(*CP*GP*TP*GP*CP*ap*T)-3'
3.2/H | 5'-D(P*GP*ap*CP*TP*ap*TP*GP*CP*ap*CP*G)-3'
3.2/I | No description available
3.2/J | No description available
3.2/K | No description available
3.2/L | No description available
3.2/M | No description available
3.2/N | No description available
3.2/P | No description available
Non-standard residues in pdb3rae-in-bits.X.pdb #3.2
---
LFX —
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic
acid (levofloxacin)
MG — magnesium ion
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> close #3.3
> volume #2 level 0.1
> hide #!1 models
> volume #2 level 0.1534
> select #3/A,B,C,D,E,F,G,H,I,J,K,L,M,N,P
21504 atoms, 21704 bonds, 15 pseudobonds, 1479 residues, 3 models selected
> fitmap #3/A,B,C,D,E,F,G,H,I,J,K,L,M,N,P inMap #2
Fit molecule pdb3rae-in-bits.X.pdb (#3.2) to map
cryosparc_P27_J564_006_volume_map.mrc (#2) using 21504 atoms
average map value = 0.1698, steps = 92
shifted from previous position = 2.02
rotated from previous position = 5.65 degrees
atoms outside contour = 9725, contour level = 0.15343
Position of pdb3rae-in-bits.X.pdb (#3.2) relative to
cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.32627213 0.90139565 0.28466188 1.68988369
0.91786821 0.37409536 -0.13255415 -28.76195849
-0.22597442 0.21803337 -0.94941930 204.58035577
Axis 0.56580799 0.82410835 0.02658483
Axis point 30.47500689 0.00000000 101.64766304
Rotation angle (degrees) 161.95213554
Shift along axis -17.30808574
> isolde start
> set selectionWidth 4
Done loading forcefield
> clipper associate #2 toModel #3
Opened cryosparc_P27_J564_006_volume_map.mrc as #3.1.1.1, grid size
256,256,256, pixel 0.85, shown at step 1, values float32
> clipper associate #1 toModel #3
Opened cryosparc_P28_J226_010_volume_map.mrc as #3.1.1.2, grid size
400,400,400, pixel 0.67, shown at step 1, values float32
> close session
> lighting simple
> set bgColor white
> set silhouettes true
> open /home/shabir/TOPOs/pdb3rae-in-bits.X.pdb
pdb3rae-in-bits.X.pdb title:
Quinolone(levofloxacin)-DNA cleavage complex of type IV topoisomerase from S.
Pneumoniae [more info...]
Chain information for pdb3rae-in-bits.X.pdb #1
---
Chain | Description
A B | topoisomerase IV subunit A
C D | topoisomerase IV subunit B
E | 5'-D(*CP*ap*TP*GP*ap*ap*T)-3'
F | 5'-D(P*ap*GP*TP*CP*ap*TP*TP*CP*ap*TP*G)-3'
G | 5'-D(*CP*GP*TP*GP*CP*ap*T)-3'
H | 5'-D(P*GP*ap*CP*TP*ap*TP*GP*CP*ap*CP*G)-3'
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
Non-standard residues in pdb3rae-in-bits.X.pdb #1
---
LFX —
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic
acid (levofloxacin)
MG — magnesium ion
pdb3rae-in-bits.X.pdb title:
Quinolone(levofloxacin)-DNA cleavage complex of type IV topoisomerase from S.
Pneumoniae [more info...]
Chain information for pdb3rae-in-bits.X.pdb
---
Chain | Description
1.2/A 1.2/B | topoisomerase IV subunit A
1.2/C 1.2/D | topoisomerase IV subunit B
1.2/E | 5'-D(*CP*ap*TP*GP*ap*ap*T)-3'
1.2/F | 5'-D(P*ap*GP*TP*CP*ap*TP*TP*CP*ap*TP*G)-3'
1.2/G | 5'-D(*CP*GP*TP*GP*CP*ap*T)-3'
1.2/H | 5'-D(P*GP*ap*CP*TP*ap*TP*GP*CP*ap*CP*G)-3'
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/P | No description available
Non-standard residues in pdb3rae-in-bits.X.pdb #1.2
---
LFX —
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic
acid (levofloxacin)
MG — magnesium ion
> close session
> open /home/shabir/TOPOs/pdb3rae.in-bits.pdb
Summary of feedback from opening /home/shabir/TOPOs/pdb3rae.in-bits.pdb
---
warnings | Start residue of secondary structure not found: HELIX 2 2 LYS A 38
ASP A 51 1 14
Start residue of secondary structure not found: HELIX 3 3 SER A 62 PHE A 73 1
12
Start residue of secondary structure not found: HELIX 4 4 GLY A 77 MET A 88 1
12
Start residue of secondary structure not found: HELIX 5 5 SER A 124 GLN A 132
1 9
Start residue of secondary structure not found: HELIX 6 6 ASP A 133 LYS A 137
5 5
30 messages similar to the above omitted
Cannot find LINK/SSBOND residue TYR (118 )
Cannot find LINK/SSBOND residue GLN (322 )
Cannot find LINK/SSBOND residue THR (319 )
Cannot find LINK/SSBOND residue PHE (316 )
pdb3rae.in-bits.pdb title:
Quinolone(levofloxacin)-DNA cleavage complex of type IV topoisomerase from S.
Pneumoniae [more info...]
Chain information for pdb3rae.in-bits.pdb #1
---
Chain | Description
A B | topoisomerase IV subunit A
C D | topoisomerase IV subunit B
E | 5'-D(*CP*ap*TP*GP*ap*ap*T)-3'
F | 5'-D(P*ap*GP*TP*CP*ap*TP*TP*CP*ap*TP*G)-3'
G | 5'-D(*CP*GP*TP*GP*CP*ap*T)-3'
H | 5'-D(P*GP*ap*CP*TP*ap*TP*GP*CP*ap*CP*G)-3'
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
P | No description available
Non-standard residues in pdb3rae.in-bits.pdb #1
---
LFX —
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic
acid (levofloxacin)
MG — magnesium ion
pdb3rae.in-bits.pdb title:
Quinolone(levofloxacin)-DNA cleavage complex of type IV topoisomerase from S.
Pneumoniae [more info...]
Chain information for pdb3rae.in-bits.pdb
---
Chain | Description
1.2/A 1.2/B | topoisomerase IV subunit A
1.2/C 1.2/D | topoisomerase IV subunit B
1.2/E | 5'-D(*CP*ap*TP*GP*ap*ap*T)-3'
1.2/F | 5'-D(P*ap*GP*TP*CP*ap*TP*TP*CP*ap*TP*G)-3'
1.2/G | 5'-D(*CP*GP*TP*GP*CP*ap*T)-3'
1.2/H | 5'-D(P*GP*ap*CP*TP*ap*TP*GP*CP*ap*CP*G)-3'
1.2/I | No description available
1.2/J | No description available
1.2/K | No description available
1.2/L | No description available
1.2/M | No description available
1.2/N | No description available
1.2/P | No description available
Non-standard residues in pdb3rae.in-bits.pdb #1.2
---
LFX —
(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic
acid (levofloxacin)
MG — magnesium ion
> open /home/shabir/Downloads/cryosparc_P27_J564_006_volume_map.mrc
Opened cryosparc_P27_J564_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.186, step 1, values float32
> hide #1.3 models
> ui mousemode right "translate selected models"
> select #1.2
11218 atoms, 11418 bonds, 15 pseudobonds, 1479 residues, 7 models selected
> view matrix models #1.2,1,0,0,119.32,0,1,0,42.733,0,0,1,159.13
> view matrix models #1.2,1,0,0,156.93,0,1,0,51.24,0,0,1,127.34
> view matrix models #1.2,1,0,0,163.2,0,1,0,54.499,0,0,1,137.14
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.44907,-0.5691,0.68881,184.96,-0.40748,0.55564,0.72473,76.163,-0.79517,-0.60612,0.017623,117.38
> view matrix models
> #1.2,0.5647,-0.81778,-0.11116,193.45,-0.013825,-0.14405,0.98947,150.15,-0.82518,-0.55722,-0.092651,110.38
> ui mousemode right "translate selected models"
> view matrix models
> #1.2,0.5647,-0.81778,-0.11116,194.15,-0.013825,-0.14405,0.98947,135.83,-0.82518,-0.55722,-0.092651,97.581
> view matrix models
> #1.2,0.5647,-0.81778,-0.11116,192.73,-0.013825,-0.14405,0.98947,131.96,-0.82518,-0.55722,-0.092651,99.561
> view matrix models
> #1.2,0.5647,-0.81778,-0.11116,189.58,-0.013825,-0.14405,0.98947,133.05,-0.82518,-0.55722,-0.092651,97.408
> view matrix models
> #1.2,0.5647,-0.81778,-0.11116,188.92,-0.013825,-0.14405,0.98947,131.33,-0.82518,-0.55722,-0.092651,95.955
> view matrix models
> #1.2,0.5647,-0.81778,-0.11116,189.17,-0.013825,-0.14405,0.98947,131.3,-0.82518,-0.55722,-0.092651,96.246
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.57145,-0.81348,-0.10814,189.3,0.15595,-0.021727,0.98753,132.1,-0.80569,-0.58118,0.11445,102.76
> view matrix models
> #1.2,0.45577,-0.88836,0.055602,191.17,0.14176,0.13411,0.98077,120.56,-0.87874,-0.43912,0.18706,90.439
> ui mousemode right "translate selected models"
> view matrix models
> #1.2,0.45577,-0.88836,0.055602,192.63,0.14176,0.13411,0.98077,126.68,-0.87874,-0.43912,0.18706,90.821
> view matrix models
> #1.2,0.45577,-0.88836,0.055602,190.28,0.14176,0.13411,0.98077,123.2,-0.87874,-0.43912,0.18706,91.606
> view matrix models
> #1.2,0.45577,-0.88836,0.055602,190.35,0.14176,0.13411,0.98077,122.96,-0.87874,-0.43912,0.18706,92.975
> view matrix models
> #1.2,0.45577,-0.88836,0.055602,190.4,0.14176,0.13411,0.98077,127.04,-0.87874,-0.43912,0.18706,91.564
> ui mousemode right "rotate selected models"
> view matrix models
> #1.2,0.51916,-0.85463,-0.0087743,190.35,0.12676,0.066843,0.98968,130.99,-0.84522,-0.51491,0.14304,97.743
> ui tool show "Fit in Map"
Fit molecule pdb3rae.in-bits.pdb (#1.2) to map
cryosparc_P27_J564_006_volume_map.mrc (#2) using 11218 atoms
average map value = 0.1773, steps = 104
shifted from previous position = 3.07
rotated from previous position = 8.06 degrees
atoms outside contour = 6018, contour level = 0.18648
Position of pdb3rae.in-bits.pdb (#1.2) relative to
cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.55799187 -0.82970983 0.01505560 191.40030404
0.00229235 0.01968370 0.99980363 127.16822845
-0.82984325 -0.55784778 0.01288533 101.85419083
Axis -0.79567762 0.43159022 0.42500236
Axis point 0.00000000 179.24027220 25.19117138
Rotation angle (degrees) 101.81308249
Shift along axis -54.12010435
> view initial #1
> view matrix models
Missing "models" keyword's argument
> select #1/A,B,C,D,E,F,G,H,I,J,K,L,M,N,P
11218 atoms, 11418 bonds, 15 pseudobonds, 1479 residues, 3 models selected
> view initial #1
> view matrix models
Missing "models" keyword's argument
> log thumbnail
> fitmap #1/A,B,C,D,E,F,G,H,I,J,K,L,M,N,P
Missing required "in_map" argument
> fitmap #1/A,B,C,D,E,F,G,H,I,J,K,L,M,N,P inMap #2
Fit molecule pdb3rae.in-bits.pdb (#1.2) to map
cryosparc_P27_J564_006_volume_map.mrc (#2) using 11218 atoms
average map value = 0.1773, steps = 48
shifted from previous position = 0.0188
rotated from previous position = 0.0214 degrees
atoms outside contour = 6012, contour level = 0.18648
Position of pdb3rae.in-bits.pdb (#1.2) relative to
cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999994 0.00035673 -0.00004735 -0.04359589
-0.00035672 0.99999993 0.00010310 0.04377522
0.00004739 -0.00010308 0.99999999 0.00991406
Axis -0.27539031 -0.12654786 -0.95296685
Axis point 121.63351822 124.53472342 0.00000000
Rotation angle (degrees) 0.02144754
Shift along axis -0.00298155
> isolde start
> isolde start
> clipper associate #2 toModel #1
Opened cryosparc_P27_J564_006_volume_map.mrc as #1.1.1.1, grid size
256,256,256, pixel 0.85, shown at step 1, values float32
> set silhoettes false
Expected a keyword
> set silhouettes false
> addh
Summary of feedback from adding hydrogens to pdb3rae.in-bits.pdb #1.2
---
warnings | Not adding hydrogens to /A ASN 3 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A ILE 4 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 5 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A MET 7 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 10 CB because it is missing heavy-atom bond
partners
214 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /B MET 85 SD; /J MET 85 SD; /D ARG 613 NE
notes | Termini for pdb3rae.in-bits.pdb (#1.2) chain A determined from SEQRES
records
Termini for pdb3rae.in-bits.pdb (#1.2) chain B determined from SEQRES records
Termini for pdb3rae.in-bits.pdb (#1.2) chain C determined from SEQRES records
Termini for pdb3rae.in-bits.pdb (#1.2) chain D determined from SEQRES records
Termini for pdb3rae.in-bits.pdb (#1.2) chain E determined from SEQRES records
3 messages similar to the above omitted
No usable SEQRES records for pdb3rae.in-bits.pdb (#1.2) chain I; guessing
termini instead
No usable SEQRES records for pdb3rae.in-bits.pdb (#1.2) chain J; guessing
termini instead
No usable SEQRES records for pdb3rae.in-bits.pdb (#1.2) chain K; guessing
termini instead
No usable SEQRES records for pdb3rae.in-bits.pdb (#1.2) chain L; guessing
termini instead
No usable SEQRES records for pdb3rae.in-bits.pdb (#1.2) chain M; guessing
termini instead
2 messages similar to the above omitted
Chain-initial residues that are actual N termini: /E DC 9, /F DA 1, /G DC 9,
/H DG 1, /I ASP 32, /J PHE 55, /K LYS 136, /L ARG 235, /M ASN 328, /N ASP 386,
/P ASP 431, /I ASP 32, /J PHE 55, /K LYS 136, /L ARG 235, /M ASN 328, /N ASP
386, /P ASP 431
Chain-initial residues that are not actual N termini: /A ASN 3, /B ASN 3, /C
GLY 414, /C TYR 557, /C LEU 577, /D LYS 415, /D TYR 557, /D LEU 577
Chain-final residues that are actual C termini: /E DT 15, /F DG 11, /G DT 15,
/H DG 11, /I THR 54, /J GLU 135, /K GLY 234, /L PHE 327, /M LEU 385, /N THR
430, /P ASP 484
Chain-final residues that are not actual C termini: /A PRO 31, /B ASP 484, /C
LYS 544, /C LYS 569, /C THR 640, /D MET 545, /D GLN 570, /D THR 640, /I THR
54, /J GLU 135, /K GLY 234, /L PHE 327, /M LEU 385, /N THR 430, /P ASP 484
Missing OXT added to C-terminal residue /I THR 54
Missing OXT added to C-terminal residue /J GLU 135
Missing OXT added to C-terminal residue /K GLY 234
Missing OXT added to C-terminal residue /L PHE 327
Missing OXT added to C-terminal residue /M LEU 385
2 messages similar to the above omitted
1485 hydrogen bonds
Adding 'H' to /A ASN 3
Adding 'H' to /B ASN 3
Adding 'H' to /C GLY 414
Adding 'H' to /C TYR 557
Adding 'H' to /C LEU 577
3 messages similar to the above omitted
/A PRO 31 is not terminus, removing H atom from 'C'
/B ASP 484 is not terminus, removing H atom from 'C'
/C THR 640 is not terminus, removing H atom from 'C'
/D THR 640 is not terminus, removing H atom from 'C'
10279 hydrogens added
> hide HC
> select #1
21504 atoms, 21704 bonds, 15 pseudobonds, 1479 residues, 14 models selected
> clipper isolate #1 maskRadius 16
> hide
> show #HC
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show ~HC
> isolde restrain distances "#1/A,I"
> isolde restrain distances "#1/I,J"
> isolde restrain distances "#1/J,K"
> isolde restrain distances "#1/K,L"
> isolde restrain distances "#1/L,M"
> isolde restrain distances "#1/M,N"
> isolde restrain distances "#1/N,P"
> isolde restrain distances "#1/B,D"
> isolde restrain distances "#1/E,F"
> isolde restrain distances "#1/G,H"
> select #1/; isolde sim start
Expected an objects specifier or a keyword
> hide sideonly
> select #1
21504 atoms, 21704 bonds, 15 pseudobonds, 1479 residues, 15 models selected
> isolde sim start sel
Loading residue template for LFX from internal database
ISOLDE: stopped sim
> close
> open /home/shabir/TOPOs/TOPO-full_15Jan2021_real_space_refined-coot-8.pdb
Chain information for TOPO-full_15Jan2021_real_space_refined-coot-8.pdb #1
---
Chain | Description
A D | No description available
B | No description available
C | No description available
E | No description available
F | No description available
Chain information for TOPO-full_15Jan2021_real_space_refined-coot-8.pdb
---
Chain | Description
1.2/A 1.2/D | No description available
1.2/B | No description available
1.2/C | No description available
1.2/E | No description available
1.2/F | No description available
> close
> open /home/shabir/TOPOs/TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
Chain information for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb #1
---
Chain | Description
A D | No description available
B | No description available
C | No description available
E | No description available
F | No description available
Chain information for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
---
Chain | Description
1.2/A 1.2/D | No description available
1.2/B | No description available
1.2/C | No description available
1.2/E | No description available
1.2/F | No description available
> hide #1.3 models
> hide #!1 models
> show #!1 models
> open /home/shabir/Downloads/cryosparc_P27_J564_006_volume_map.mrc
Opened cryosparc_P27_J564_006_volume_map.mrc as #2, grid size 256,256,256,
pixel 0.85, shown at level 0.186, step 1, values float32
> select #1
12216 atoms, 12494 bonds, 1474 residues, 8 models selected
> select #1
12216 atoms, 12494 bonds, 1474 residues, 8 models selected
> select #1.2
12216 atoms, 12494 bonds, 1474 residues, 5 models selected
> select #1
12216 atoms, 12494 bonds, 1474 residues, 8 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.013862,0.9858,0.16736,-23.153,0.96676,0.055951,-0.2495,31.281,-0.25532,0.15834,-0.9538,198.49
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.013862,0.9858,0.16736,-25.286,0.96676,0.055951,-0.2495,15.557,-0.25532,0.15834,-0.9538,209.79
> view matrix models
> #1,-0.013862,0.9858,0.16736,-30.425,0.96676,0.055951,-0.2495,14.077,-0.25532,0.15834,-0.9538,208.44
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.29498,0.89745,0.32797,-3.3832,0.92708,0.35191,-0.12913,-29.53,-0.2313,0.26596,-0.93582,190.74
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.29498,0.89745,0.32797,-2.375,0.92708,0.35191,-0.12913,-29.894,-0.2313,0.26596,-0.93582,196.66
> select #1
12216 atoms, 12494 bonds, 1474 residues, 8 models selected
> view matrix models
> #1,-0.29498,0.89745,0.32797,-3.0945,0.92708,0.35191,-0.12913,-28.964,-0.2313,0.26596,-0.93582,201.25
> view matrix models
> #1,-0.29498,0.89745,0.32797,-3.0483,0.92708,0.35191,-0.12913,-28.634,-0.2313,0.26596,-0.93582,201.27
> ~select #1.1
12216 atoms, 12494 bonds, 1474 residues, 7 models selected
> view matrix models
> #1,-0.29498,0.89745,0.32797,-3.1877,0.92708,0.35191,-0.12913,-29.691,-0.2313,0.26596,-0.93582,200.33
> view matrix models
> #1,-0.29498,0.89745,0.32797,-2.9431,0.92708,0.35191,-0.12913,-26.577,-0.2313,0.26596,-0.93582,197.1
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.33356,0.89075,0.3087,4.0989,0.91508,0.38465,-0.12112,-30.027,-0.22663,0.24209,-0.94341,200.24
> view matrix models
> #1,-0.29718,0.90031,0.318,-2.0816,0.92745,0.35135,-0.128,-26.659,-0.22697,0.25689,-0.93941,198.07
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.29718,0.90031,0.318,-2.6103,0.92745,0.35135,-0.128,-28.331,-0.22697,0.25689,-0.93941,195.84
> select #1
12216 atoms, 12494 bonds, 1474 residues, 8 models selected
> ~select #1.1
12216 atoms, 12494 bonds, 1474 residues, 7 models selected
> select #1.2
12216 atoms, 12494 bonds, 1474 residues, 5 models selected
> select #1.3
1 model selected
> select #1.3
1 model selected
> ui mousemode right zoom
> ui mousemode right select
> select clear
> select clear
> select clear
> volume #2 level 0.1
> hide
> cartoon
> color bychain
> color byhetero
> select #1/A,B,C,D,E,F
12216 atoms, 12494 bonds, 1474 residues, 1 model selected
> view initial #1
> view matrix models
> #1,0.198,-0.674,0.699,86.9,0.821,0.511,0.260,-63.7,-0.534,0.522,0.655,53.6
> fitmap #1/A,B,C,D,E,F inMap #2
Fit molecule TOPO-full_15Jan2021_real_space_refined-on3rae.pdb (#1.2) to map
cryosparc_P27_J564_006_volume_map.mrc (#2) using 12216 atoms
average map value = 0.1117, steps = 228
shifted from previous position = 26.3
rotated from previous position = 27.4 degrees
atoms outside contour = 6428, contour level = 0.1
Position of TOPO-full_15Jan2021_real_space_refined-on3rae.pdb (#1.2) relative
to cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.92085330 0.31453495 -0.23042778 12.25155774
-0.36352863 0.90626651 -0.21570340 58.07102043
0.14098272 0.28239828 0.94888096 -57.29669642
Axis 0.54160007 -0.40384515 -0.73727774
Axis point 175.36600069 48.95965232 0.00000000
Rotation angle (degrees) 27.37695804
Shift along axis 25.42732295
> select #1
12216 atoms, 12494 bonds, 1474 residues, 8 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.58665,0.33337,0.73804,51.493,0.19791,0.94273,-0.26851,15.781,-0.78529,-0.011451,-0.61903,275.19
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.58665,0.33337,0.73804,52.374,0.19791,0.94273,-0.26851,15.541,-0.78529,-0.011451,-0.61903,267.14
> fitmap #1/A,B,C,D,E,F inMap #2
Fit molecule TOPO-full_15Jan2021_real_space_refined-on3rae.pdb (#1.2) to map
cryosparc_P27_J564_006_volume_map.mrc (#2) using 12216 atoms
average map value = 0.2075, steps = 96
shifted from previous position = 3.96
rotated from previous position = 7.24 degrees
atoms outside contour = 1504, contour level = 0.1
Position of TOPO-full_15Jan2021_real_space_refined-on3rae.pdb (#1.2) relative
to cryosparc_P27_J564_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.94293987 0.21542792 -0.25388031 28.38047610
-0.28929990 0.90755007 -0.30439849 63.57675563
0.16483316 0.36047702 0.91808842 -67.03409161
Axis 0.71195014 -0.44835929 -0.54046364
Axis point 0.00000000 187.92270692 192.92433252
Rotation angle (degrees) 27.83582569
Shift along axis 27.92974424
> clipper associate #2 toModel #1
Opened cryosparc_P27_J564_006_volume_map.mrc as #1.1.1.1, grid size
256,256,256, pixel 0.85, shown at step 1, values float32
> set silhouettes false
> addh
Summary of feedback from adding hydrogens to TOPO-
full_15Jan2021_real_space_refined-on3rae.pdb #1.2
---
warnings | Not adding hydrogens to /B DG 9 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /C DC 1 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /E DC 10 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /F DC 1 P because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-
on3rae.pdb (#1.2) chain A; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain B; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain C; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain D; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain E; guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A LYS 415, /B DG 9, /C DC
1, /D LYS 415, /E DC 10, /F DC 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 1132, /B DG 18, /C DC
10, /D ASP 1132, /E DG 18, /F DG 9
Chain-final residues that are not actual C termini:
1094 hydrogen bonds
12029 hydrogens added
> addh
Summary of feedback from adding hydrogens to TOPO-
full_15Jan2021_real_space_refined-on3rae.pdb #1.2
---
warnings | Not adding hydrogens to /B DG 9 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /C DC 1 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /E DC 10 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /F DC 1 P because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-
on3rae.pdb (#1.2) chain A; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain B; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain C; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain D; guessing termini instead
No usable SEQRES records for TOPO-full_15Jan2021_real_space_refined-on3rae.pdb
(#1.2) chain E; guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A LYS 415, /B DG 9, /C DC
1, /D LYS 415, /E DC 10, /F DC 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 1132, /B DG 18, /C DC
10, /D ASP 1132, /E DG 18, /F DG 9
Chain-final residues that are not actual C termini:
1048 hydrogen bonds
0 hydrogens added
> hide HC
> clipper isolate #1 maskRadius 16
> isolde restrain distances "#1/C,D"
> isolde restrain distances "#1/C,D"
> isolde restrain distances "#1/B,C"
> isolde restrain distances "#1/E,F"
> isolde release distances "#1/C,D"
> view matrix models #1,1,0,0,-0.10695,0,1,0,1.1641,0,0,1,-6.801
> select #1
24245 atoms, 24523 bonds, 1474 residues, 13 models selected
> isolde sim start sel
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/home/shabir/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/cmd/cmd.py", line 95, in _sim_start_cb
isolde.start_sim()
File "/home/shabir/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2780, in start_sim
sm.start_sim()
File "/home/shabir/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 674, in start_sim
sh.start_sim()
File "/home/shabir/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1601, in start_sim
self._prepare_sim()
File "/home/shabir/.local/share/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1561, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/simtk/openmm/app/simulation.py", line 105, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__
this = _openmm.new_Context(*args)
simtk.openmm.OpenMMException: No compatible CUDA device is available
Error processing trigger "frame drawn":
simtk.openmm.OpenMMException: No compatible CUDA device is available
File "/usr/libexec/UCSF-ChimeraX/lib/python3.8/site-
packages/simtk/openmm/openmm.py", line 17752, in __init__
this = _openmm.new_Context(*args)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 440.64
OpenGL renderer: GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: CentOS Linux 8
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen 9 3950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 78Gi 9.9Gi 61Gi 224Mi 7.0Gi 67Gi
Swap: 7.9Gi 0B 7.9Gi
Graphics:
09:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 SUPER] [10de:1e81] (rev a1)
Subsystem: eVga.com. Corp. Device [3842:3081]
Kernel driver in use: nvidia
Locale: ('en_GB', '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
biopython: 1.79
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: 0.16.0
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-LinuxSupport: 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-Phenix: 0.3
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-StrudelScore: 0.1.9
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
distro: 1.5.0
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
MolecularDynamicsViewer: 1.2
mrcfile: 1.3.0
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
pandas: 1.3.2
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.2.4
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
recordtype: 1.3
requests: 2.24.0
scipy: 1.5.2
Send2Trash: 1.8.0
SEQCROW: 1.2.2
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
threed-strudel: 0.9.7
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: 1.2.0
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Looks like your display driver version is too old. OpenMM uses CUDA 11, which requires driver version >=450.80.02 (https://docs.nvidia.com/deploy/cuda-compatibility/#default-to-minor-version) - yours is 440.64. The latest Linux version compatible with your card is 470.74.