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Opened 10 months ago
Closed 9 months ago
#16631 closed defect (fixed)
Safesave: file missing
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-51-generic-x86_64-with-glibc2.38
ChimeraX Version: 1.8rc202406072045 (2024-06-07 20:45:50 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202406072045 (2024-06-07)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/azinas/Downloads/fold_clpx/fold_clpx_model_0.cif
Chain information for fold_clpx_model_0.cif #1
---
Chain | Description
A B C D E F | .
> open /home/azinas/Downloads/fold_clpx/fold_clpx_model_1.cif
Chain information for fold_clpx_model_1.cif #2
---
Chain | Description
A B C D E F | .
> open /home/azinas/Downloads/fold_clpx/fold_clpx_model_2.cif
Chain information for fold_clpx_model_2.cif #3
---
Chain | Description
A B C D E F | .
> open /home/azinas/Downloads/fold_clpx/fold_clpx_model_3.cif
Chain information for fold_clpx_model_3.cif #4
---
Chain | Description
A B C D E F | .
> open /home/azinas/Downloads/fold_clpx/fold_clpx_model_4.cif
Chain information for fold_clpx_model_4.cif #5
---
Chain | Description
A B C D E F | .
> hide atoms
> show cartoons
> ui tool show Matchmaker
> matchmaker #2-5 to #1/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain A (#1) with fold_clpx_model_1.cif,
chain A (#2), sequence alignment score = 2467.7
RMSD between 343 pruned atom pairs is 0.439 angstroms; (across all 500 pairs:
9.457)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with fold_clpx_model_2.cif,
chain D (#3), sequence alignment score = 2489.9
RMSD between 339 pruned atom pairs is 0.558 angstroms; (across all 500 pairs:
12.135)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with fold_clpx_model_3.cif,
chain A (#4), sequence alignment score = 2444.9
RMSD between 331 pruned atom pairs is 0.565 angstroms; (across all 500 pairs:
9.304)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with fold_clpx_model_4.cif,
chain A (#5), sequence alignment score = 2503.1
RMSD between 347 pruned atom pairs is 0.588 angstroms; (across all 500 pairs:
10.677)
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> open /home/azinas/Downloads/cryosparc_P27_J106_004_volume_map.mrc
Opened cryosparc_P27_J106_004_volume_map.mrc as #6, grid size 400,400,400,
pixel 1.2, shown at level 0.172, step 2, values float32
> view
> select add #1
23316 atoms, 23664 bonds, 3006 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,272.73,0,1,0,238.7,0,0,1,135.07
> view matrix models #1,1,0,0,270.82,0,1,0,238.86,0,0,1,158.35
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.94979,0.19597,-0.24393,264.92,0.022438,0.73492,0.67778,250.72,0.31209,-0.64922,0.69362,165.46
> view matrix models
> #1,0.96732,0.24451,-0.067112,266.26,-0.093253,0.58921,0.80258,254.08,0.23578,-0.77009,0.59276,165.95
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.96732,0.24451,-0.067112,245.21,-0.093253,0.58921,0.80258,244.04,0.23578,-0.77009,0.59276,154.35
> view matrix models
> #1,0.96732,0.24451,-0.067112,229.22,-0.093253,0.58921,0.80258,235.59,0.23578,-0.77009,0.59276,162.86
> open
> /home/azinas/Downloads/fold_fl_clpxadpatp/fold_fl_clpxadpatp_model_0.cif
Chain information for fold_fl_clpxadpatp_model_0.cif #7
---
Chain | Description
A B C D E F | .
> open
> /home/azinas/Downloads/fold_fl_clpxadpatp/fold_fl_clpxadpatp_model_1.cif
Chain information for fold_fl_clpxadpatp_model_1.cif #8
---
Chain | Description
A B C D E F | .
> open
> /home/azinas/Downloads/fold_fl_clpxadpatp/fold_fl_clpxadpatp_model_2.cif
Chain information for fold_fl_clpxadpatp_model_2.cif #9
---
Chain | Description
A B C D E F | .
> open
> /home/azinas/Downloads/fold_fl_clpxadpatp/fold_fl_clpxadpatp_model_3.cif
Chain information for fold_fl_clpxadpatp_model_3.cif #10
---
Chain | Description
A B C D E F | .
> open
> /home/azinas/Downloads/fold_fl_clpxadpatp/fold_fl_clpxadpatp_model_4.cif
Chain information for fold_fl_clpxadpatp_model_4.cif #11
---
Chain | Description
A B C D E F | .
> close #2-5
> ui tool show Matchmaker
> matchmaker #7-11 to #1/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_0.cif, chain A (#7), sequence alignment score =
2453.3
RMSD between 326 pruned atom pairs is 0.694 angstroms; (across all 500 pairs:
9.559)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_1.cif, chain A (#8), sequence alignment score =
2437.7
RMSD between 298 pruned atom pairs is 0.835 angstroms; (across all 500 pairs:
11.894)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_2.cif, chain E (#9), sequence alignment score =
2445.5
RMSD between 317 pruned atom pairs is 0.650 angstroms; (across all 500 pairs:
14.307)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_3.cif, chain B (#10), sequence alignment score =
2425.7
RMSD between 326 pruned atom pairs is 0.644 angstroms; (across all 500 pairs:
13.968)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_4.cif, chain A (#11), sequence alignment score =
2468.9
RMSD between 326 pruned atom pairs is 0.666 angstroms; (across all 500 pairs:
8.974)
> matchmaker #7-11 to #1/A pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_0.cif, chain A (#7), sequence alignment score =
2453.3
RMSD between 326 pruned atom pairs is 0.694 angstroms; (across all 500 pairs:
9.559)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_1.cif, chain A (#8), sequence alignment score =
2437.7
RMSD between 298 pruned atom pairs is 0.835 angstroms; (across all 500 pairs:
11.894)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_2.cif, chain E (#9), sequence alignment score =
2445.5
RMSD between 317 pruned atom pairs is 0.650 angstroms; (across all 500 pairs:
14.307)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_3.cif, chain B (#10), sequence alignment score =
2425.7
RMSD between 326 pruned atom pairs is 0.644 angstroms; (across all 500 pairs:
13.968)
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_4.cif, chain A (#11), sequence alignment score =
2468.9
RMSD between 326 pruned atom pairs is 0.666 angstroms; (across all 500 pairs:
8.974)
> show sel cartoons
> hide sel atoms
[Repeated 1 time(s)]
> select subtract #1
Nothing selected
> hide #1 models
> show #7-11 cartoons
> hide #7-11 atoms
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #7 models
> fitmap #8 inMap #6
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc (#6) using 29342 atoms
average map value = 0.1967, steps = 136
shifted from previous position = 10.7
rotated from previous position = 7.83 degrees
atoms outside contour = 13840, contour level = 0.17233
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc (#6) coordinates:
Matrix rotation and translation
-0.47224067 -0.87760932 -0.08240526 240.07877478
-0.78164679 0.46014061 -0.42106878 240.37763784
0.40745189 -0.13443400 -0.90327762 162.62215327
Axis 0.49796590 -0.85102078 0.16671413
Axis point 175.48640439 0.00000000 128.08316484
Rotation angle (degrees) 163.27337192
Shift along axis -57.90391059
> volume #6 level 0.3068
> vop flip
> volume flip
Missing or invalid "volumes" argument: empty atom specifier
> vop flip #6
Opened cryosparc_P27_J106_004_volume_map.mrc z flip as #2, grid size
400,400,400, pixel 1.2, shown at step 1, values float32
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.2203, steps = 344
shifted from previous position = 66.8
rotated from previous position = 14.1 degrees
atoms outside contour = 19605, contour level = 0.3068
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.33908772 -0.90283625 -0.26439785 235.45854516
-0.84086541 0.41689666 -0.34517030 240.62336067
0.42185884 0.10528000 -0.90052831 229.43174879
Axis 0.54717976 -0.83362310 0.07527843
Axis point 166.53608532 0.00000000 159.84377596
Rotation angle (degrees) 155.69393113
Shift along axis -54.47977999
> select add #8
29342 atoms, 29798 bonds, 3804 residues, 1 model selected
> view matrix models
> #8,-0.33909,-0.90284,-0.2644,237.91,-0.84087,0.4169,-0.34517,242.83,0.42186,0.10528,-0.90053,282.51
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.2204, steps = 200
shifted from previous position = 6.05
rotated from previous position = 22.1 degrees
atoms outside contour = 21036, contour level = 0.3068
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.50601398 -0.86183641 0.03446515 242.27489418
-0.75824733 0.42543686 -0.49402881 239.49378775
0.41110928 -0.27611860 -0.86876216 285.72164875
Axis 0.48716907 -0.84204114 0.23158803
Axis point 170.93030176 0.00000000 192.66089185
Rotation angle (degrees) 167.07652451
Shift along axis -17.46507411
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.038333,0.99912,0.017152,239.35,-0.80014,0.040972,-0.59842,241.47,-0.59859,0.0092156,0.801,263.98
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.038333,0.99912,0.017152,226.51,-0.80014,0.040972,-0.59842,241.35,-0.59859,0.0092156,0.801,316.74
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.2068, steps = 396
shifted from previous position = 41.4
rotated from previous position = 36.6 degrees
atoms outside contour = 21632, contour level = 0.3068
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.21003029 0.80739714 -0.55135934 233.59043262
-0.86513655 -0.10922142 -0.48949917 238.38380838
-0.45544048 0.57981077 0.67556897 276.39956061
Axis 0.53802869 -0.04826206 -0.84154376
Axis point 328.70826009 -46.61769062 0.00000000
Rotation angle (degrees) 96.41972700
Shift along axis -118.42886456
> view matrix models
> #8,0.21003,0.8074,-0.55136,237.68,-0.86514,-0.10922,-0.4895,245.83,-0.45544,0.57981,0.67557,316.52
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.22802,0.75294,-0.61733,235.18,-0.72156,-0.55637,-0.41206,247.97,-0.65372,0.35148,0.67016,315.97
> view matrix models
> #8,-0.29466,0.92835,-0.22658,230.93,-0.89637,-0.35069,-0.27119,244.79,-0.33122,0.12319,0.93548,317.12
> view matrix models
> #8,-0.29344,0.92764,-0.23102,230.98,-0.8987,-0.35008,-0.26419,244.71,-0.32595,0.1301,0.93639,317.12
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.29344,0.92764,-0.23102,243.16,-0.8987,-0.35008,-0.26419,236.92,-0.32595,0.1301,0.93639,319.56
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.015709,0.96607,-0.25781,245.27,-0.95256,-0.092842,-0.28986,235.75,-0.30396,0.24102,0.92169,319.41
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.1947, steps = 124
shifted from previous position = 18.8
rotated from previous position = 2.06 degrees
atoms outside contour = 22977, contour level = 0.3068
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.01448315 0.97258357 -0.23210221 240.94123678
-0.95980963 -0.07858955 -0.26942373 240.43988198
-0.28027790 0.21887183 0.93463330 301.69976507
Axis 0.24491752 0.02416379 -0.96924276
Axis point 275.77835887 -17.38861074 0.00000000
Rotation angle (degrees) 94.54371576
Shift along axis -227.59964439
> view matrix models
> #8,-0.23365,0.94378,-0.23386,239.45,-0.9662,-0.25231,-0.052943,239.34,-0.10897,0.21358,0.97083,302.7
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.23365,0.94378,-0.23386,239.51,-0.9662,-0.25231,-0.052943,245.08,-0.10897,0.21358,0.97083,320.23
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.203, steps = 252
shifted from previous position = 31.4
rotated from previous position = 24.2 degrees
atoms outside contour = 22183, contour level = 0.3068
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.04253042 0.86372428 -0.50216683 242.22459334
-0.99905843 0.04107680 -0.01396220 239.27199733
0.00856792 0.50228783 0.86465804 289.63666800
Axis 0.25821142 -0.25545286 -0.93170312
Axis point 250.51383165 -82.98675146 0.00000000
Rotation angle (degrees) 91.48225657
Shift along axis -268.43294683
> view matrix models
> #8,0.04253,0.86372,-0.50217,115.23,-0.99906,0.041077,-0.013962,291.28,0.0085679,0.50229,0.86466,245.31
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.77866,0.58729,-0.22084,119.48,-0.62578,0.70129,-0.34147,294.11,-0.045669,0.40409,0.91358,244.9
> view matrix models
> #8,0.21911,0.85565,-0.46889,116.3,-0.97569,0.19479,-0.10048,291.55,0.0053597,0.47951,0.87752,245.28
> view matrix models
> #8,-0.19839,0.83,-0.52128,113.73,-0.98011,-0.16507,0.11019,291.22,0.0054139,0.53278,0.84624,245.32
> view matrix models
> #8,0.40965,0.81329,-0.41322,117.42,-0.91223,0.36334,-0.18924,292.08,-0.0037657,0.45448,0.89075,245.2
> view matrix models
> #8,0.41993,0.8302,-0.36664,117.06,-0.90735,0.37553,-0.1889,292.07,-0.019143,0.412,0.91098,245.09
> view matrix models
> #8,-0.26386,-0.96385,0.036895,115.65,-0.91478,0.26219,0.30731,288.51,-0.30587,0.047337,-0.95089,259.1
> view matrix models
> #8,0.14431,-0.94304,-0.29974,121.24,-0.97382,-0.18912,0.12615,291.23,-0.17565,0.27369,-0.94564,259.16
> view matrix models
> #8,0.19327,-0.92349,-0.33138,121.78,-0.96684,-0.23672,0.095804,291.7,-0.16692,0.30187,-0.93862,259.06
> hide #!2 models
> view matrix models
> #8,-0.26724,-0.96279,0.040314,115.6,-0.91327,0.2664,0.30818,288.5,-0.30745,0.045541,-0.95047,259.09
> view matrix models
> #8,0.75309,0.6579,0.0031025,117.25,0.2321,-0.26127,-0.93695,308.8,-0.61561,0.70633,-0.34946,249.55
> view matrix models
> #8,0.87693,0.42697,-0.22067,120.81,0.018637,-0.489,-0.87208,307.58,-0.48026,0.76064,-0.43678,251.03
> select subtract #8
Nothing selected
> ui mousemode right "translate selected models"
> show #1 models
> hide #1 models
> show #!2 models
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> select add #8
29342 atoms, 29798 bonds, 3804 residues, 1 model selected
> view matrix models
> #8,0.69577,0.55256,0.45888,113.62,-0.4787,0.83304,-0.27728,294.18,-0.53549,-0.026739,0.84412,243.48
> view matrix models
> #8,0.9042,0.42615,-0.028648,119.49,-0.41448,0.85929,-0.29969,294.74,-0.1031,0.28286,0.9536,244.62
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.9042,0.42615,-0.028648,241.62,-0.41448,0.85929,-0.29969,235.18,-0.1031,0.28286,0.9536,256.05
> view matrix models
> #8,0.9042,0.42615,-0.028648,242.14,-0.41448,0.85929,-0.29969,247.66,-0.1031,0.28286,0.9536,310.36
> view matrix models
> #8,0.9042,0.42615,-0.028648,238.42,-0.41448,0.85929,-0.29969,235.32,-0.1031,0.28286,0.9536,309.93
> volume #2 level 0.4293
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.2035, steps = 172
shifted from previous position = 18.6
rotated from previous position = 20.8 degrees
atoms outside contour = 27393, contour level = 0.42926
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.86115968 0.44317215 -0.24900289 242.30976543
-0.46066987 0.88746589 -0.01369517 237.01158959
0.21491227 0.12650184 0.96840590 291.48910614
Axis 0.13670096 -0.45234666 -0.88130321
Axis point 323.26094267 -547.58196723 0.00000000
Rotation angle (degrees) 30.84966345
Shift along axis -330.97770672
> view matrix models
> #8,0.86116,0.44317,-0.249,243.5,-0.46067,0.88747,-0.013695,233.65,0.21491,0.1265,0.96841,292.27
> select subtract #8
Nothing selected
> hide #8 models
> show #1 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #1
23316 atoms, 23664 bonds, 3006 residues, 1 model selected
> view matrix models
> #1,0.24289,0.60853,-0.75544,214.01,0.61411,-0.6993,-0.36586,243.47,-0.75091,-0.37506,-0.54356,141.39
> view matrix models
> #1,0.26274,0.58174,-0.76977,214.3,0.64391,-0.69987,-0.30913,244.2,-0.71857,-0.41445,-0.55847,141.9
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.26274,0.58174,-0.76977,169.94,0.64391,-0.69987,-0.30913,250.66,-0.71857,-0.41445,-0.55847,259.53
> view matrix models
> #1,0.26274,0.58174,-0.76977,238.24,0.64391,-0.69987,-0.30913,250.87,-0.71857,-0.41445,-0.55847,257.49
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.88827,0.44097,-0.12855,249.28,0.28693,-0.75125,-0.59439,247.5,-0.35868,0.49109,-0.79384,241.93
> view matrix models
> #1,0.89628,0.41618,-0.15319,249.39,0.25414,-0.76509,-0.59165,247.66,-0.36344,0.49135,-0.79151,241.94
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.89628,0.41618,-0.15319,245.46,0.25414,-0.76509,-0.59165,244.99,-0.36344,0.49135,-0.79151,306.92
> view matrix models
> #1,0.89628,0.41618,-0.15319,243.69,0.25414,-0.76509,-0.59165,235.55,-0.36344,0.49135,-0.79151,307.13
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.95048,0.30973,-0.025607,246.91,0.21266,-0.70824,-0.67318,233.65,-0.22664,0.6344,-0.73903,305.9
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.95048,0.30973,-0.025607,253.26,0.21266,-0.70824,-0.67318,234.68,-0.22664,0.6344,-0.73903,327.57
> view matrix models
> #1,0.95048,0.30973,-0.025607,242.89,0.21266,-0.70824,-0.67318,235.85,-0.22664,0.6344,-0.73903,328.93
> view matrix models
> #1,0.95048,0.30973,-0.025607,241.49,0.21266,-0.70824,-0.67318,238.11,-0.22664,0.6344,-0.73903,319.44
> view matrix models
> #1,0.95048,0.30973,-0.025607,241.82,0.21266,-0.70824,-0.67318,242.62,-0.22664,0.6344,-0.73903,321.41
> fitmap #1 inMap #2
Fit molecule fold_clpx_model_0.cif (#1) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 23316 atoms
average map value = 0.2256, steps = 332
shifted from previous position = 57.4
rotated from previous position = 9.2 degrees
atoms outside contour = 20923, contour level = 0.42926
Position of fold_clpx_model_0.cif (#1) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.94742082 0.29696633 0.11918363 232.05957048
0.28894735 -0.63392085 -0.71739371 242.06379683
-0.13748879 0.71411155 -0.68639746 264.82863584
Axis 0.98428784 0.17648524 -0.00551377
Axis point 0.00000000 41.89476786 175.66030308
Rotation angle (degrees) 133.34965026
Shift along axis 269.67389772
> view matrix models
> #1,0.94742,0.29697,0.11918,240.18,0.28895,-0.63392,-0.71739,238.48,-0.13749,0.71411,-0.6864,319.27
> molmap #1 8
Opened fold_clpx_model_0.cif map 8 as #3, grid size 78,76,74, pixel 2.67,
shown at level 0.0761, step 1, values float32
> close #3
> select 1-60
Expected an objects specifier or a keyword
> select #1 1-60
Expected a keyword
> select #1:1-60
2718 atoms, 2748 bonds, 366 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> molmap #1 8
Opened fold_clpx_model_0.cif map 8 as #3, grid size 63,61,64, pixel 2.67,
shown at level 0.0804, step 1, values float32
> select add #2
2 models selected
> view matrix models #2,1,0,0,78.096,0,1,0,99.086,0,0,1,10.379
> volume #2 level 0.2549
> close #3
> select #1:1-160
4872 atoms, 4992 bonds, 600 residues, 1 model selected
> select #1:1-130
3378 atoms, 3480 bonds, 420 residues, 1 model selected
> select #1:1-130
3378 atoms, 3480 bonds, 420 residues, 1 model selected
> select #1:1-180
5904 atoms, 6042 bonds, 720 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select add #1
14694 atoms, 14862 bonds, 1920 residues, 1 model selected
> view matrix models
> #1,0.94742,0.29697,0.11918,311.25,0.28895,-0.63392,-0.71739,329.61,-0.13749,0.71411,-0.6864,331.02
> select subtract #1
Nothing selected
> fitmap #1 inMap #2
Fit molecule fold_clpx_model_0.cif (#1) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 14694 atoms
average map value = 0.2194, steps = 148
shifted from previous position = 13
rotated from previous position = 12.2 degrees
atoms outside contour = 8876, contour level = 0.25494
Position of fold_clpx_model_0.cif (#1) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.97587685 0.21669889 0.02656917 243.81648218
0.14128889 -0.53407721 -0.83354600 238.79108625
-0.16643851 0.81719219 -0.55181075 316.44568310
Axis 0.99221308 0.11601158 -0.04532686
Axis point 0.00000000 16.71737109 220.18012670
Rotation angle (degrees) 123.71109815
Shift along axis 255.27694239
> molmap #1 8
Opened fold_clpx_model_0.cif map 8 as #3, grid size 63,56,60, pixel 2.67,
shown at level 0.0773, step 1, values float32
> hide #!2 models
> show #!2 models
> hide #1 models
> fitmap #2 inMap #3
Fit map cryosparc_P27_J106_004_volume_map.mrc z flip in map
fold_clpx_model_0.cif map 8 using 348758 points
correlation = 0.4434, correlation about mean = -0.05249, overlap = 7542
steps = 120, shift = 6.02, angle = 4.16 degrees
Position of cryosparc_P27_J106_004_volume_map.mrc z flip (#2) relative to
fold_clpx_model_0.cif map 8 (#3) coordinates:
Matrix rotation and translation
0.97083141 0.14031023 -0.19442083 -208.19694637
0.23970849 -0.58533328 0.77454815 -161.22395224
-0.00512396 -0.79855998 -0.60189347 381.47858981
Axis -0.99088978 -0.11923677 0.06261027
Axis point 0.00000000 23.03729964 216.90980069
Rotation angle (degrees) 127.45929577
Shift along axis 249.40852679
> select add #3
2 models selected
> view matrix models
> #3,0.97588,0.2167,0.026569,239.02,0.14129,-0.53408,-0.83355,233.46,-0.16644,0.81719,-0.55181,313.16
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.24119,-0.57144,-0.7844,236.77,0.87848,0.47204,-0.073761,238.63,0.41242,-0.67129,0.61585,286.38
> view matrix models
> #3,0.21614,-0.49752,-0.84009,238.08,0.96065,0.26211,0.091933,234.85,0.17446,-0.82691,0.5346,285.5
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.21614,-0.49752,-0.84009,202.76,0.96065,0.26211,0.091933,221.18,0.17446,-0.82691,0.5346,284.94
> show #1 models
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select add #1
14694 atoms, 14862 bonds, 1920 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.70489,-0.15753,-0.69161,323.99,0.57006,0.70602,0.42019,341.11,0.4221,-0.69045,0.58747,299
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.70489,-0.15753,-0.69161,183.62,0.57006,0.70602,0.42019,280.77,0.4221,-0.69045,0.58747,300.57
> select #1:A
Nothing selected
> select #1:/A
Expected an objects specifier or a keyword
> select #1/A
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> view matrix models
> #1,0.70489,-0.15753,-0.69161,185.57,0.57006,0.70602,0.42019,284.22,0.4221,-0.69045,0.58747,300.11
> ui mousemode right "translate selected atoms"
> select #1/B
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> select #1/C
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> select #1/D
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> select #1/E
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> select ~sel & ##selected
12245 atoms, 12385 bonds, 1600 residues, 1 model selected
> select #1/F
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> fitmap #1 inMap #2
Fit molecule fold_clpx_model_0.cif (#1) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 14694 atoms
average map value = 0.2204, steps = 92
shifted from previous position = 6.18
rotated from previous position = 9.43 degrees
atoms outside contour = 8695, contour level = 0.25494
Position of fold_clpx_model_0.cif (#1) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.72963665 -0.26912291 -0.62865187 103.85794398
0.61938894 0.64968339 0.44075936 184.73271805
0.28980625 -0.71097421 0.64072457 302.14708021
Axis -0.66948709 -0.53388724 0.51647987
Axis point 0.00000000 455.29314710 -42.59286480
Rotation angle (degrees) 59.33468381
Shift along axis -12.10510702
> select #1/A
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> close #3
> molmap #1 8
Opened fold_clpx_model_0.cif map 8 as #3, grid size 71,64,65, pixel 2.67,
shown at level 0.0704, step 1, values float32
> hide #1 models
> select add #1
14694 atoms, 14862 bonds, 1920 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #1 models
> hide #!3 models
> select #1/B
2449 atoms, 2477 bonds, 320 residues, 1 model selected
> show #!2 models
> select add #1
14694 atoms, 14862 bonds, 1920 residues, 1 model selected
> select subtract #1
Nothing selected
> molmap #1 8
Opened fold_clpx_model_0.cif map 8 as #3, grid size 73,64,65, pixel 2.67,
shown at level 0.0698, step 1, values float32
> hide #!2 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> hide #1 models
> show #1 models
> show #!6 models
> hide #!6 models
> show #7 models
> hide #7 models
> show #7 models
> ui tool show Matchmaker
> matchmaker #7/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_0.cif, chain A (#7), sequence alignment score =
2199.5
RMSD between 286 pruned atom pairs is 0.627 angstroms; (across all 320 pairs:
3.653)
> matchmaker #7/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain B (#1) with
fold_fl_clpxadpatp_model_0.cif, chain B (#7), sequence alignment score =
2199.5
RMSD between 286 pruned atom pairs is 0.605 angstroms; (across all 320 pairs:
3.605)
> split #7
Split fold_fl_clpxadpatp_model_0.cif (#7) into 12 models
Chain information for fold_fl_clpxadpatp_model_0.cif A #7.1
---
Chain | Description
A | No description available
Chain information for fold_fl_clpxadpatp_model_0.cif B #7.2
---
Chain | Description
B | No description available
Chain information for fold_fl_clpxadpatp_model_0.cif C #7.3
---
Chain | Description
C | No description available
Chain information for fold_fl_clpxadpatp_model_0.cif D #7.4
---
Chain | Description
D | No description available
Chain information for fold_fl_clpxadpatp_model_0.cif E #7.5
---
Chain | Description
E | No description available
Chain information for fold_fl_clpxadpatp_model_0.cif F #7.6
---
Chain | Description
F | No description available
> matchmaker #7.1/A to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain A (#1) with
fold_fl_clpxadpatp_model_0.cif A, chain A (#7.1), sequence alignment score =
2199.5
RMSD between 286 pruned atom pairs is 0.627 angstroms; (across all 320 pairs:
3.653)
> matchmaker #7.2/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain B (#1) with
fold_fl_clpxadpatp_model_0.cif B, chain B (#7.2), sequence alignment score =
2199.5
RMSD between 286 pruned atom pairs is 0.605 angstroms; (across all 320 pairs:
3.605)
> matchmaker #7.2/B to #1/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain B (#1) with
fold_fl_clpxadpatp_model_0.cif B, chain B (#7.2), sequence alignment score =
2199.5
RMSD between 286 pruned atom pairs is 0.605 angstroms; (across all 320 pairs:
3.605)
> matchmaker #7.3/C to #1/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain C (#1) with
fold_fl_clpxadpatp_model_0.cif C, chain C (#7.3), sequence alignment score =
2186.9
RMSD between 284 pruned atom pairs is 0.614 angstroms; (across all 320 pairs:
3.682)
> matchmaker #7.5/E to #1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain E (#1) with
fold_fl_clpxadpatp_model_0.cif E, chain E (#7.5), sequence alignment score =
2199.5
RMSD between 286 pruned atom pairs is 0.611 angstroms; (across all 320 pairs:
3.599)
> matchmaker #7.6/F to #1/F pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain F (#1) with
fold_fl_clpxadpatp_model_0.cif F, chain F (#7.6), sequence alignment score =
2199.5
RMSD between 289 pruned atom pairs is 0.616 angstroms; (across all 320 pairs:
3.579)
> matchmaker #7.4/D to #1/D pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_clpx_model_0.cif, chain D (#1) with
fold_fl_clpxadpatp_model_0.cif D, chain D (#7.4), sequence alignment score =
2196.5
RMSD between 284 pruned atom pairs is 0.667 angstroms; (across all 320 pairs:
3.697)
> hide #1 models
> show #!2 models
> volume #2 level 0.363
> flip #7 180
Unknown command: flip #7 180
> turn #7 180
Expected an axis vector or a keyword
> turn #7 Z 180
Expected an axis vector or a keyword
> turn #7 z180
Expected an axis vector or a keyword
> turn #7 z 180
Expected an axis vector or a keyword
> turn z 180
[Repeated 2 time(s)]
> undo
> turn z 180
> turn sel z 180
Expected an axis vector or a keyword
> turn z 180 models #7
> hide #!2 models
> show #!6 models
> show #!2 models
> hide #!6 models
> select add #7
29342 atoms, 29798 bonds, 3804 residues, 13 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.30424,-0.95126,0.050367,740.29,-0.95126,0.3006,-0.068863,519.12,0.050367,-0.068863,-0.99635,622.45
> view matrix models
> #7,-0.30424,-0.95126,0.050367,716.9,-0.95126,0.3006,-0.068863,557.39,0.050367,-0.068863,-0.99635,611.7
> view matrix models
> #7,-0.30424,-0.95126,0.050367,724.73,-0.95126,0.3006,-0.068863,549.7,0.050367,-0.068863,-0.99635,639.55
> view matrix models
> #7,-0.30424,-0.95126,0.050367,712.67,-0.95126,0.3006,-0.068863,550.45,0.050367,-0.068863,-0.99635,632.99
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 12 atomic models, 1 maps.
> view matrix models
> #7,-0.30424,-0.95126,0.050367,712.57,-0.95126,0.3006,-0.068863,560.91,0.050367,-0.068863,-0.99635,634.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.14937,-0.97298,0.17604,536.96,-0.97503,-0.17452,-0.1373,747.29,0.16432,-0.15113,-0.97476,619.04
> view matrix models
> #7,0.14572,-0.95115,0.27217,503.35,-0.96798,-0.19391,-0.15939,757.75,0.20438,-0.24023,-0.94896,628.63
> view matrix models
> #7,-0.034738,-0.97114,0.23596,578.26,-0.9877,-0.0026475,-0.15631,699.27,0.15242,-0.23849,-0.95911,647.58
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.034738,-0.97114,0.23596,585.33,-0.9877,-0.0026475,-0.15631,698.71,0.15242,-0.23849,-0.95911,649.26
> view matrix models
> #7,-0.034738,-0.97114,0.23596,581.51,-0.9877,-0.0026475,-0.15631,697.74,0.15242,-0.23849,-0.95911,649.22
> hide #!7 models
> show #8 models
> ui tool show Matchmaker
> matchmaker #8-11 to #7.1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_fl_clpxadpatp_model_0.cif A, chain A (#7.1) with
fold_fl_clpxadpatp_model_1.cif, chain A (#8), sequence alignment score =
3135.5
RMSD between 383 pruned atom pairs is 0.719 angstroms; (across all 633 pairs:
14.102)
Matchmaker fold_fl_clpxadpatp_model_0.cif A, chain A (#7.1) with
fold_fl_clpxadpatp_model_2.cif, chain E (#9), sequence alignment score =
3155.9
RMSD between 415 pruned atom pairs is 0.669 angstroms; (across all 633 pairs:
9.599)
Matchmaker fold_fl_clpxadpatp_model_0.cif A, chain A (#7.1) with
fold_fl_clpxadpatp_model_3.cif, chain E (#10), sequence alignment score =
3138.5
RMSD between 425 pruned atom pairs is 0.640 angstroms; (across all 633 pairs:
8.180)
Matchmaker fold_fl_clpxadpatp_model_0.cif A, chain A (#7.1) with
fold_fl_clpxadpatp_model_4.cif, chain A (#11), sequence alignment score =
3109.7
RMSD between 405 pruned atom pairs is 0.561 angstroms; (across all 633 pairs:
9.294)
> matchmaker #8-11 to #7.2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_fl_clpxadpatp_model_0.cif B, chain B (#7.2) with
fold_fl_clpxadpatp_model_1.cif, chain A (#8), sequence alignment score =
3135.5
RMSD between 381 pruned atom pairs is 0.791 angstroms; (across all 633 pairs:
13.868)
Matchmaker fold_fl_clpxadpatp_model_0.cif B, chain B (#7.2) with
fold_fl_clpxadpatp_model_2.cif, chain E (#9), sequence alignment score =
3155.9
RMSD between 409 pruned atom pairs is 0.620 angstroms; (across all 633 pairs:
8.781)
Matchmaker fold_fl_clpxadpatp_model_0.cif B, chain B (#7.2) with
fold_fl_clpxadpatp_model_3.cif, chain E (#10), sequence alignment score =
3138.5
RMSD between 423 pruned atom pairs is 0.624 angstroms; (across all 633 pairs:
7.263)
Matchmaker fold_fl_clpxadpatp_model_0.cif B, chain B (#7.2) with
fold_fl_clpxadpatp_model_4.cif, chain A (#11), sequence alignment score =
3109.7
RMSD between 403 pruned atom pairs is 0.591 angstroms; (across all 633 pairs:
9.737)
> select subtract #7
Nothing selected
> select add #8
29342 atoms, 29798 bonds, 3804 residues, 1 model selected
> fitmap #8 inMap #2
Fit molecule fold_fl_clpxadpatp_model_1.cif (#8) to map
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) using 29342 atoms
average map value = 0.203, steps = 216
shifted from previous position = 39.2
rotated from previous position = 15.7 degrees
atoms outside contour = 25017, contour level = 0.36299
Position of fold_fl_clpxadpatp_model_1.cif (#8) relative to
cryosparc_P27_J106_004_volume_map.mrc z flip (#2) coordinates:
Matrix rotation and translation
0.04243530 0.86383826 -0.50197879 242.20680464
-0.99906299 0.04096798 -0.01395646 239.24791214
0.00850894 0.50210066 0.86476731 289.63195476
Axis 0.25811525 -0.25532961 -0.93176355
Axis point 250.48070637 -82.93605932 0.00000000
Rotation angle (degrees) 91.48496959
Shift along axis -268.43830548
> view matrix models
> #8,0.053202,0.84369,-0.53419,323.86,-0.99605,0.082889,0.031713,335.15,0.071035,0.53039,0.84477,357.85
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 109,
in __exit__
os.replace(self._tmp_filename, self.name)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/azinas/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp' ->
'/home/azinas/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/lib/python3.11/site-packages/chimerax/ui/gui.py", line 964, in
resizeEvent
self.session.ui.settings.last_window_size = wh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/lib/python3.11/site-packages/chimerax/core/settings.py", line 199,
in __setattr__
ConfigFile.__setattr__(self, name, value)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
386, in __setattr__
ConfigFile.save(self)
File "/app/lib/python3.11/site-packages/chimerax/core/configfile.py", line
335, in save
with SaveTextFile(self._filename) as f:
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 127,
in __exit__
os.remove(self._tmp_filename)
FileNotFoundError: [Errno 2] No such file or directory:
'/home/azinas/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
FileNotFoundError: [Errno 2] No such file or directory:
'/home/azinas/.var/app/edu.ucsf.rbvi.ChimeraX/config/ChimeraX/ui-1.2.tmp'
File "/app/lib/python3.11/site-packages/chimerax/core/safesave.py", line 127,
in __exit__
os.remove(self._tmp_filename)
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 24.3.1 (git-c815d651b8)
OpenGL renderer: AMD Radeon Graphics (radeonsi, renoir, LLVM 17.0.6, DRM 3.57, 6.8.0-51-generic)
OpenGL vendor: AMD
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20YM
OS: Freedesktop SDK 23.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 30Gi 19Gi 1.2Gi 309Mi 10Gi 11Gi
Swap: 8.0Gi 1.1Gi 6.9Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106M [GeForce RTX 3060 Mobile / Max-Q] [10de:2520] (rev a1)
Subsystem: Lenovo Device [17aa:3801]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202406072045
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-maskChains: 1.4
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
distro: 1.9.0
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.46
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 9 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Safesave: file missing |
comment:2 by , 9 months ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Now also embed process start time.
Note:
See TracTickets
for help on using tickets.
Process IDs between Flatpak processes can conflict (usually process ID is 2).