Opened 21 months ago

Closed 21 months ago

#14520 closed defect (duplicate)

sel down: array length mismatch

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.92.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/smissour/Downloads/cryosparc_P8_J1981_003_volume_map_sharp.mrc

Opened cryosparc_P8_J1981_003_volume_map_sharp.mrc as #1, grid size
392,392,392, pixel 0.839, shown at level 0.0463, step 2, values float32  

> surface dust #1 size 8.39

> volume #1 step 1

> volume #1 level 0.1261

> volume #1 level 0.206

> transparency 50

> close #1

> open /home/smissour/Downloads/cryosparc_P8_J1981_004_volume_map_sharp.mrc

Opened cryosparc_P8_J1981_004_volume_map_sharp.mrc as #1, grid size
392,392,392, pixel 0.839, shown at level 0.0522, step 2, values float32  

> surface dust #1 size 8.39

> volume #1 level 0.1844

> volume #1 level 0.1712

> volume #1 step 1

> open /home/smissour/Downloads/cryosparc_P8_J1986_map_sharp.mrc

Opened cryosparc_P8_J1986_map_sharp.mrc as #2, grid size 392,392,392, pixel
0.839, shown at level 0.123, step 2, values float32  

> volume #2 step 1

> surface dust #2 size 8.39

> volume #2 level 0.2074

> volume #2 level 0.2915

> volume #2 level 0.2747

> open "/home/smissour/Downloads/cryosparc_P8_J1986_map_sharp (1).mrc"

Opened cryosparc_P8_J1986_map_sharp (1).mrc as #3, grid size 392,392,392,
pixel 0.839, shown at level 0.0407, step 2, values float32  

> close #2

> surface dust #3 size 8.39

> volume #3 step 1

> volume #3 level 0.1354

> open /home/smissour/Desktop/DNAP-Thermus-philo/J1927/imodfit_fitted-
> coot-2.pdb

Summary of feedback from opening /home/smissour/Desktop/DNAP-Thermus-
philo/J1927/imodfit_fitted-coot-2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 63 63 ARG A
19 LYS A 22 1 4  
End residue of secondary structure not found: HELIX 76 76 GLY A 198 VAL A 204
1 7  
Start residue of secondary structure not found: SHEET 15 1515 VAL A 9 VAL A 11
0  
  
Chain information for imodfit_fitted-coot-2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> fitmap #2 inMap #3

Fit molecule imodfit_fitted-coot-2.pdb (#2) to map
cryosparc_P8_J1986_map_sharp (1).mrc (#3) using 10266 atoms  
average map value = 0.108, steps = 140  
shifted from previous position = 2.02  
rotated from previous position = 12 degrees  
atoms outside contour = 6842, contour level = 0.13543  
  
Position of imodfit_fitted-coot-2.pdb (#2) relative to
cryosparc_P8_J1986_map_sharp (1).mrc (#3) coordinates:  
Matrix rotation and translation  
0.98795632 0.10352632 -0.11499831 3.34303472  
-0.11856800 0.98403102 -0.13275759 42.74329803  
0.09941800 0.14479382 0.98445458 -38.47681900  
Axis 0.66858503 -0.51650087 -0.53499618  
Axis point 0.00000000 294.06921898 289.48346709  
Rotation angle (degrees) 11.97976756  
Shift along axis 0.74310351  
  

> ui tool show "Model Panel"

> select #2

10266 atoms, 10626 bonds, 2 pseudobonds, 1180 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.84558,-0.3776,0.37737,306.58,-0.52064,0.42702,-0.73932,294.96,0.11802,-0.82163,-0.55768,380

> view matrix models
> #2,-0.16992,-0.68085,-0.71244,417.83,-0.3713,0.71391,-0.59369,202.58,0.91283,0.16365,-0.37411,56.319

> view matrix models
> #2,-0.75401,0.29988,-0.58441,331.12,-0.10754,-0.93406,-0.34055,392.24,-0.648,-0.19393,0.73654,196.54

> fitmap #2 inMap #3

Fit molecule imodfit_fitted-coot-2.pdb (#2) to map
cryosparc_P8_J1986_map_sharp (1).mrc (#3) using 10266 atoms  
average map value = 0.1866, steps = 376  
shifted from previous position = 12.9  
rotated from previous position = 36.4 degrees  
atoms outside contour = 4375, contour level = 0.13543  
  
Position of imodfit_fitted-coot-2.pdb (#2) relative to
cryosparc_P8_J1986_map_sharp (1).mrc (#3) coordinates:  
Matrix rotation and translation  
-0.98247367 0.12200726 -0.14092456 329.32985234  
-0.12453326 -0.99217267 0.00921330 347.82765967  
-0.13869740 0.02660162 0.98997748 23.24020242  
Axis 0.07035162 -0.00901088 -0.99748156  
Axis point 176.29845012 163.56226966 0.00000000  
Rotation angle (degrees) 172.90115376  
Shift along axis -3.14701628  
  

> save /home/smissour/Desktop/DNAP-Thermus-philo/J1927/imodfit_fitted-
> coot-2.pdb

> open /home/smissour/Downloads/cryosparc_P8_J1985_006_volume_map_sharp.mrc

Opened cryosparc_P8_J1985_006_volume_map_sharp.mrc as #4, grid size
392,392,392, pixel 0.839, shown at level 0.0725, step 2, values float32  

> surface dust #3 size 8.39

> surface dust #4 size 8.39

> volume #4 step 1

> volume #4 level 0.08622

> volume #4 level 0.1468

> select #4

2 models selected  

> view matrix models
> #4,0.30599,-0.56504,-0.76622,307.53,-0.48199,-0.786,0.38714,320.45,-0.82101,0.25085,-0.51286,293.31

> view matrix models
> #4,0.30599,-0.56504,-0.76622,319.9,-0.48199,-0.786,0.38714,320.4,-0.82101,0.25085,-0.51286,343.5

> view matrix models
> #4,0.91553,-0.024525,-0.4015,92.233,0.053057,-0.98206,0.18097,290.07,-0.39873,-0.18699,-0.8978,402.27

> view matrix models
> #4,0.91553,-0.024525,-0.4015,89.435,0.053057,-0.98206,0.18097,288.49,-0.39873,-0.18699,-0.8978,406.78

> hide #!2 models

> fitmap #4 inMap #3

Fit map cryosparc_P8_J1985_006_volume_map_sharp.mrc in map
cryosparc_P8_J1986_map_sharp (1).mrc using 245973 points  
correlation = 0.8465, correlation about mean = 0.639, overlap = 1.867e+04  
steps = 340, shift = 4.92, angle = 19.9 degrees  
  
Position of cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) relative to
cryosparc_P8_J1986_map_sharp (1).mrc (#3) coordinates:  
Matrix rotation and translation  
0.99368213 0.01007429 -0.11177801 19.36669450  
0.04892102 -0.93524450 0.35060583 252.32162025  
-0.10100767 -0.35385904 -0.92982860 391.36172094  
Axis -0.99836673 -0.01526372 0.05505354  
Axis point 0.00000000 161.74503981 173.18485985  
Rotation angle (degrees) 159.34079780  
Shift along axis -1.64058096  
  

> volume #4 level 0.1413

> show #!2 models

> select #2

10266 atoms, 10626 bonds, 2 pseudobonds, 1180 residues, 2 models selected  

> fitmap #2 inMap #4

Fit molecule imodfit_fitted-coot-2.pdb (#2) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 10266 atoms  
average map value = 0.2658, steps = 76  
shifted from previous position = 3.9  
rotated from previous position = 4.16 degrees  
atoms outside contour = 3105, contour level = 0.14126  
  
Position of imodfit_fitted-coot-2.pdb (#2) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.97793466 0.03789749 -0.20544492 351.34985708  
0.12288678 0.89963202 -0.41900013 65.31025259  
0.16894577 -0.43500120 -0.88443841 352.97494518  
Axis -0.04164242 -0.97434294 0.22118262  
Axis point 156.71330633 0.00000000 201.38299173  
Rotation angle (degrees) 168.92319447  
Shift along axis -0.19371940  
  

> transparency #4.1 50

> select /D:20

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /E:36

41 atoms, 44 bonds, 2 residues, 1 model selected  

> select up

1187 atoms, 1329 bonds, 58 residues, 1 model selected  

> select up

10266 atoms, 10626 bonds, 1180 residues, 1 model selected  

> select down

1187 atoms, 1329 bonds, 58 residues, 1 model selected  

> select clear

> select /D:29

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select add /E:36

41 atoms, 44 bonds, 2 residues, 1 model selected  

> select up

1187 atoms, 1329 bonds, 58 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open /home/smissour/Desktop/DNAP-Thermus-philo/DNAP-Thermus-
> philo_oSM0070-oSM0071.pdb.pdb

Chain information for DNAP-Thermus-philo_oSM0070-oSM0071.pdb.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #5

1187 atoms, 1329 bonds, 58 residues, 1 model selected  

> view matrix models
> #5,-0.65255,0.42142,-0.62975,257.7,-0.65409,-0.73285,0.18735,347.16,-0.38256,0.53417,0.75386,22.802

> view matrix models
> #5,0.72343,-0.03095,-0.68971,155.05,-0.63317,-0.42799,-0.64492,398.68,-0.27523,0.90326,-0.32921,114.43

> fitmap #5 inMap #4

Fit molecule DNAP-Thermus-philo_oSM0070-oSM0071.pdb.pdb (#5) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1187 atoms  
average map value = 0.194, steps = 188  
shifted from previous position = 8.22  
rotated from previous position = 11.5 degrees  
atoms outside contour = 410, contour level = 0.14126  
  
Position of DNAP-Thermus-philo_oSM0070-oSM0071.pdb.pdb (#5) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.62569869 -0.00040055 -0.78006474 177.61751618  
0.77442334 0.12036847 0.62111185 -45.45253848  
0.09364642 -0.99272921 0.07562459 291.02603172  
Axis -0.81014666 -0.43860216 0.38896084  
Axis point 0.00000000 95.81067306 216.46869088  
Rotation angle (degrees) 95.11494631  
Shift along axis -10.76292435  
  

> select #2/A:109

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

82 atoms, 83 bonds, 11 residues, 1 model selected  

> select up

1221 atoms, 1252 bonds, 156 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> open /home/smissour/Desktop/DNAP-Thermus-philo/udglike-apo.pdb

Chain information for udglike-apo.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select #6

1293 atoms, 1326 bonds, 165 residues, 1 model selected  

> view matrix models #6,1,0,0,-32.514,0,1,0,15.874,0,0,1,4.3839

> view matrix models #6,1,0,0,-38.668,0,1,0,38.696,0,0,1,7.5916

> view matrix models #6,1,0,0,-11.216,0,1,0,48.279,0,0,1,19.173

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1825, steps = 288  
shifted from previous position = 21  
rotated from previous position = 56.9 degrees  
atoms outside contour = 537, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.63455833 -0.15879265 0.75638656 -34.98095852  
0.11517193 -0.94831080 -0.29570606 309.26233618  
0.76424549 0.27475724 -0.58347005 120.66435109  
Axis 0.90136588 -0.01241757 0.43288030  
Axis point 0.00000000 144.17801370 96.60994214  
Rotation angle (degrees) 161.55200308  
Shift along axis 16.86229222  
  

> view matrix models
> #6,0.54628,-0.19805,0.81385,-48.297,0.19128,0.97547,0.10899,8.3492,-0.81547,0.09613,0.57076,180.33

> view matrix models
> #6,-0.11951,-0.70956,0.69444,135.08,0.89251,0.22962,0.38821,-28.492,-0.43491,0.66619,0.60585,41.728

> view matrix models
> #6,0.27664,-0.93267,-0.2315,249.67,-0.64391,-0.0010776,-0.7651,394.15,0.71334,0.36072,-0.60085,103.91

> view matrix models
> #6,0.64363,-0.7542,-0.13009,157.69,-0.20414,-0.0053503,-0.97893,364.86,0.73761,0.65662,-0.1574,-7.5695

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1781, steps = 244  
shifted from previous position = 24.6  
rotated from previous position = 37.3 degrees  
atoms outside contour = 576, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.70737485 -0.58284087 0.39989669 67.66427550  
-0.31911719 0.24147872 0.91643454 20.45993629  
-0.63070204 -0.77587664 -0.01517856 379.98157151  
Axis -0.84662125 0.51558294 0.13193441  
Axis point 0.00000000 247.66542459 184.57421074  
Rotation angle (degrees) 91.90041945  
Shift along axis 3.39542378  
  

> view matrix models
> #6,0.25285,-0.93626,-0.24388,252.71,0.43172,0.33477,-0.83758,202.82,0.86584,0.10649,0.48885,-38.734

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1557, steps = 180  
shifted from previous position = 20.8  
rotated from previous position = 11.9 degrees  
atoms outside contour = 638, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.18654091 -0.83766618 -0.51333991 305.99259488  
-0.71678591 -0.47337860 0.51198698 235.92112107  
-0.67187830 0.27244829 -0.68873179 338.30522851  
Axis -0.76861631 0.50870780 0.38787284  
Axis point 0.00000000 236.15550338 234.74573422  
Rotation angle (degrees) 171.03537555  
Shift along axis 16.04342275  
  

> view matrix models
> #6,0.25324,-0.8676,-0.42795,279.1,0.44393,0.49727,-0.74542,165.42,0.85953,-0.0012102,0.51108,-31.336

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1557, steps = 128  
shifted from previous position = 10.9  
rotated from previous position = 0.0474 degrees  
atoms outside contour = 639, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.18640150 -0.83749920 -0.51366290 306.03789392  
-0.71626821 -0.47369862 0.51241533 235.82913775  
-0.67246884 0.27240542 -0.68817219 338.30799633  
Axis -0.76856398 0.50853117 0.38820801  
Axis point 0.00000000 236.13200884 234.81055519  
Rotation angle (degrees) 171.01697770  
Shift along axis 16.05064131  
  

> view matrix models
> #6,0.25318,-0.86743,-0.42833,284.07,0.44323,0.49756,-0.74564,170.01,0.85991,-0.001074,0.51044,-33.249

> view matrix models
> #6,-0.21252,-0.97511,-0.063147,309.88,0.85617,-0.15467,-0.493,164.79,0.47097,-0.15884,0.86773,-10.09

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.208, steps = 428  
shifted from previous position = 23.5  
rotated from previous position = 60.6 degrees  
atoms outside contour = 456, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.89518537 -0.35814144 0.26528826 286.12492266  
-0.35661100 0.93259316 0.05566513 64.63343030  
-0.26734201 -0.04477410 -0.96256093 372.71016294  
Axis -0.18530549 0.98267691 0.00282359  
Axis point 175.34139792 0.00000000 166.00831997  
Rotation angle (degrees) 164.27563151  
Shift along axis 11.54563896  
  

> view matrix models
> #6,-0.86324,-0.34148,0.37177,259.06,0.19599,-0.90542,-0.37656,342.72,0.46519,-0.2522,0.84852,2.2079

> view matrix models
> #6,-0.748,-0.61609,-0.24684,364.1,0.42122,-0.72808,0.54081,152.89,-0.5129,0.30055,0.80411,85.16

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.2021, steps = 268  
shifted from previous position = 31.3  
rotated from previous position = 46.4 degrees  
atoms outside contour = 520, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.09508749 -0.70618619 -0.70161203 367.67376667  
-0.50211814 0.64260166 -0.57874044 221.97497961  
0.85955556 0.29726115 -0.41569227 83.33481900  
Axis 0.48619757 -0.86647776 0.11326166  
Axis point 215.73611846 0.00000000 190.18286285  
Rotation angle (degrees) 115.72734303  
Shift along axis -4.13565057  
  

> view matrix models
> #6,0.29518,-0.90484,-0.30681,264.94,0.9404,0.21839,0.26069,-13.969,-0.16888,-0.36548,0.91537,112.42

> view matrix models
> #6,0.017526,-0.99979,-0.010233,272.75,-0.20767,0.0063716,-0.97818,364.13,0.97804,0.019269,-0.20752,65.796

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1853, steps = 212  
shifted from previous position = 25.7  
rotated from previous position = 40.1 degrees  
atoms outside contour = 551, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.41986633 -0.90657473 0.04283133 330.65625669  
-0.61170671 0.31753467 0.72455962 77.40052817  
-0.67046787 0.27801798 -0.68787996 340.75045855  
Axis -0.50077141 0.79992505 0.33067795  
Axis point 239.22628497 0.00000000 105.08892159  
Rotation angle (degrees) 153.52202450  
Shift along axis 9.01008441  
  

> view matrix models
> #6,-0.34843,-0.92872,0.12675,308.15,0.31649,-0.24385,-0.91672,317.12,0.88229,-0.2793,0.37889,17.796

> view matrix models
> #6,-0.11043,-0.99386,0.0071838,280.1,0.98273,-0.10811,0.15021,40.313,-0.14851,0.023647,0.98863,22.596

> view matrix models
> #6,-0.11043,-0.99386,0.0071838,276.24,0.98273,-0.10811,0.15021,40.501,-0.14851,0.023647,0.98863,21.362

> view matrix models
> #6,-0.0063909,-0.96747,-0.25291,297.44,0.43515,0.22502,-0.87179,236.44,0.90034,-0.11562,0.41955,-14.827

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1697, steps = 280  
shifted from previous position = 27.3  
rotated from previous position = 23 degrees  
atoms outside contour = 645, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.04159163 -0.75778266 -0.65118015 342.83316973  
-0.64593024 -0.51762374 0.56110587 228.86048585  
-0.76226260 0.39727964 -0.51100354 304.81603260  
Axis -0.72058145 0.48859058 0.49197726  
Axis point 0.00000000 242.43312513 260.67235108  
Rotation angle (degrees) 173.47271165  
Shift along axis 14.74241059  
  

> view matrix models
> #6,-0.25766,-0.39979,-0.87965,355.4,-0.50611,0.83135,-0.22959,182.74,0.82308,0.38604,-0.41654,68.631

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.21, steps = 448  
shifted from previous position = 36.1  
rotated from previous position = 31.3 degrees  
atoms outside contour = 497, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.33630882 -0.21008848 -0.91801918 366.76461049  
-0.35815477 -0.87302100 0.33099773 277.13969344  
-0.87098883 0.44011041 0.21836047 212.68468469  
Axis 0.57474664 -0.24773049 -0.77993327  
Axis point 270.01998022 93.19161557 0.00000000  
Rotation angle (degrees) 174.55314593  
Shift along axis -23.73908435  
  

> view matrix models
> #6,-0.55726,-0.58672,-0.58756,374.09,-0.48101,-0.34869,0.80439,180.88,-0.67683,0.73087,-0.087909,175.62

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1854, steps = 244  
shifted from previous position = 24.9  
rotated from previous position = 33.9 degrees  
atoms outside contour = 553, contour level = 0.14126  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.63936844 -0.60308327 -0.47696811 392.23106473  
0.76613083 -0.44707452 -0.46170113 173.01556180  
0.06520394 -0.66061710 0.74788603 151.31862986  
Axis -0.13385791 -0.36484760 0.92139475  
Axis point 163.21965426 211.97617573 0.00000000  
Rotation angle (degrees) 132.01140091  
Shift along axis 23.79665028  
  

> view matrix models
> #6,-0.6349,-0.52993,-0.5622,374.46,-0.72494,0.157,0.67068,165.85,-0.26715,0.83338,-0.48385,163.15

> volume #4 level 0.1964

> view matrix models
> #6,-0.45303,-0.86608,-0.21137,337.8,-0.88919,0.42192,0.17699,230.23,-0.064108,0.26813,-0.96125,288.08

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1751, steps = 208  
shifted from previous position = 24.2  
rotated from previous position = 36.6 degrees  
atoms outside contour = 850, contour level = 0.1964  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.06896860 -0.91828603 -0.38986424 318.46090539  
0.94482816 -0.06531568 0.32098853 -24.48053883  
-0.32022353 -0.39049283 0.86311776 146.42263085  
Axis -0.35653262 -0.03489787 0.93363089  
Axis point 199.03259889 154.32910577 0.00000000  
Rotation angle (degrees) 93.81956757  
Shift along axis 24.01730903  
  

> view matrix models
> #6,0.84159,-0.52769,-0.11519,106.51,-0.39461,-0.45511,-0.79822,422.78,0.36879,0.71723,-0.59125,107.53

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1736, steps = 204  
shifted from previous position = 16.3  
rotated from previous position = 28.2 degrees  
atoms outside contour = 817, contour level = 0.1964  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.82888547 -0.45400222 0.32684995 42.53995179  
-0.22253248 0.26845941 0.93723469 -1.14356769  
-0.51325256 -0.84959493 0.12149187 350.95151802  
Axis -0.89881146 0.42258857 0.11643396  
Axis point 0.00000000 227.17465088 179.50369017  
Rotation angle (degrees) 83.71821149  
Shift along axis 2.14402079  
  

> view matrix models
> #6,0.87878,-0.35346,0.32065,7.6064,0.068723,-0.57116,-0.81796,381.72,0.47226,0.74084,-0.47763,82.908

> volume #4 level 0.1137

> view matrix models
> #6,0.87878,-0.35346,0.32065,-4.1457,0.068723,-0.57116,-0.81796,378.62,0.47226,0.74084,-0.47763,74.815

> view matrix models
> #6,0.11542,-0.83953,0.53091,137.97,0.92716,0.28285,0.24571,-20.427,-0.35645,0.46388,0.81102,28.89

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.2204, steps = 396  
shifted from previous position = 44.6  
rotated from previous position = 29.5 degrees  
atoms outside contour = 405, contour level = 0.1137  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.50297578 -0.59620275 0.62574569 77.07375803  
-0.39836971 -0.80241946 -0.44432487 385.54485351  
0.76701822 -0.02579348 -0.64110667 178.15609201  
Axis 0.86471884 -0.29188019 0.40873864  
Axis point -0.00000000 193.90920376 98.80267941  
Rotation angle (degrees) 165.99513271  
Shift along axis 26.93350677  
  

> view matrix models
> #6,-0.13285,-0.82592,-0.54792,346.99,0.98563,-0.1683,0.01471,82.111,-0.10436,-0.53809,0.8364,131.22

> view matrix models
> #6,0.4258,0.76079,0.48978,-109.61,-0.50661,-0.24805,0.82573,181.82,0.74969,-0.59972,0.2798,103.05

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.2169, steps = 284  
shifted from previous position = 27.7  
rotated from previous position = 30 degrees  
atoms outside contour = 322, contour level = 0.1137  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.22236534 0.96585090 0.13298761 -36.22988278  
-0.20254637 0.17919081 -0.96273861 296.78576114  
-0.95369211 0.18714354 0.23547542 255.85986600  
Axis 0.58464985 0.55251500 -0.59406374  
Axis point 319.26083271 288.98790727 0.00000000  
Rotation angle (degrees) 100.45622310  
Shift along axis -9.20027986  
  

> view matrix models
> #6,-0.77365,0.53335,0.34206,107.86,-0.45633,-0.84354,0.28319,341.37,0.43958,0.062997,0.89599,-36.371

> fitmap #6 inMap #4

Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.1568, steps = 180  
shifted from previous position = 22  
rotated from previous position = 24 degrees  
atoms outside contour = 526, contour level = 0.1137  
  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.55089174 0.78378919 0.28669288 63.83872163  
0.49992602 0.58498019 -0.63864870 87.89127912  
-0.66827560 -0.20850106 -0.71409736 407.81195656  
Axis 0.39639134 0.88002631 -0.26158670  
Axis point 80.27327853 0.00000000 206.00581471  
Rotation angle (degrees) 147.14058981  
Shift along axis -4.02643108  
  

> view matrix models
> #6,-0.39814,-0.8258,0.39942,235.31,0.73085,-0.5487,-0.40595,230.7,0.55439,0.13029,0.82199,-52.011

> ui tool show "Command Line Interface"

> map fit #6 in_Map #4 search 50

Unknown command: map fit #6 in_Map #4 search 50  

> vop fit #6 in_Map #4 search 50

> volume fit #6 in_Map #4 search 50

Expected a density maps specifier or a keyword  

> mapfit #6 in_Map #4 search 50

Unknown command: mapfit #6 in_Map #4 search 50  

> fitmap #6 inMap #4 search 50

Found 22 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (22 of 50).  
  
Average map values and times found:  
0.2284 (1), 0.2087 (1), 0.2076 (1), 0.2017 (1), 0.2013 (1), 0.1983 (1), 0.1977
(1), 0.1896 (1), 0.1887 (1), 0.1855 (1), 0.1631 (1), 0.1447 (1), 0.1405 (1),
0.1391 (1), 0.1324 (1), 0.129 (1), 0.1229 (1), 0.1085 (1), 0.1036 (1), 0.0818
(1), 0.0299 (1), 0.02156 (1)  
  
Best fit found:  
Fit molecule udglike-apo.pdb (#6) to map
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) using 1293 atoms  
average map value = 0.2284, steps = 220  
shifted from previous position = 18.5  
rotated from previous position = 29.6 degrees  
atoms outside contour = 433, contour level = 0.1137  
Position of udglike-apo.pdb (#6) relative to
cryosparc_P8_J1985_006_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.76054230 -0.43887654 -0.47850064 405.51868114  
-0.36288004 0.89843177 -0.24726198 147.08411880  
0.53841761 -0.01441487 -0.84255486 239.00719966  
Axis 0.22260718 -0.97219719 0.07265440  
Axis point 184.51908902 0.00000000 185.02812925  
Rotation angle (degrees) 148.46629919  
Shift along axis -35.35847225  
  
Found 22 fits.  

> select down

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2181, in
_forward_keystroke  
self.tool_instance.session.ui.forward_keystroke(event)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 323, in
forward_keystroke  
run(self.session, 'select down')  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36,
in run  
results = command.run(text, log=log, return_json=return_json)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/std_commands/select.py", line
138, in select_down  
session.selection.demote(session)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 64, in
demote  
self._promotion.demote_selection()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 200, in
demote_selection  
p.demote()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1876,
in demote  
s.atoms.selected = self._prev_atom_sel_mask  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 210, in
set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 9079 does not match objects array length 7858  
  
ValueError: Values array length 9079 does not match objects array length 7858  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 210, in
set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> select down

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2181, in
_forward_keystroke  
self.tool_instance.session.ui.forward_keystroke(event)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 323, in
forward_keystroke  
run(self.session, 'select down')  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 36,
in run  
results = command.run(text, log=log, return_json=return_json)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line
2856, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/std_commands/select.py", line
138, in select_down  
session.selection.demote(session)  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 64, in
demote  
self._promotion.demote_selection()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/core/selection.py", line 200, in
demote_selection  
p.demote()  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/structure.py", line 1876,
in demote  
s.atoms.selected = self._prev_atom_sel_mask  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 210, in
set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
ValueError: Values array length 9079 does not match objects array length 7858  
  
ValueError: Values array length 9079 does not match objects array length 7858  
  
File "/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-
ChimeraX/lib/python3.9/site-packages/chimerax/atomic/molc.py", line 210, in
set_prop  
raise ValueError('Values array length %d does not match objects array length
%d'  
  
See log for complete Python traceback.  
  

> select down

1293 atoms, 1326 bonds, 165 residues, 1 model selected  

> select down

1293 atoms, 1326 bonds, 165 residues, 1 model selected  

> select down

1293 atoms, 1326 bonds, 165 residues, 1 model selected  

> select down

1293 atoms, 1326 bonds, 165 residues, 1 model selected  




OpenGL version: 3.3.0 NVIDIA 470.57.02
OpenGL renderer: Quadro K2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T3610
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v2 @ 3.50GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G         13G        7.0G        523M         10G         16G
	Swap:           32G         15G         16G

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK107GL [Quadro K2000] [10de:0ffe] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:094c]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    biopython: 1.79
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RIBFIND: 0.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    ribfind: 2.0.2
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 21 months ago

Component: Unassigned → General Controls
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → sel down: array length mismatch

comment:2 by Tom Goddard, 21 months ago

Resolution: → duplicate
Status: assigned → closed

User tried to revert the selection with down arrow after expanding it and deleting some of the atoms involved. This no longer gives an error in current ChimeraX. Report is with old ChimeraX 1.3.

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