Opened 5 years ago

Closed 5 years ago

#3973 closed defect (duplicate)

Map fitting: fmap is None

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

Description 

The following bug report has been submitted:
Platform:        Linux-4.15.0-118-generic-x86_64-with-debian-buster-sid
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/scipion/.cache/.fr-sRpfcI/6eig.pdb1

Summary of feedback from opening /home/scipion/.cache/.fr-sRpfcI/6eig.pdb1  
---  
warnings | Start residue of secondary structure not found: HELIX 10 AB1 CYS B
36 GLU B 41 1 6  
Start residue of secondary structure not found: HELIX 11 AB2 THR B 45 THR B 74
1 30  
Start residue of secondary structure not found: HELIX 12 AB3 GLU B 82 GLU B
101 1 20  
Start residue of secondary structure not found: HELIX 13 AB4 GLN B 117 SER B
136 1 20  
Start residue of secondary structure not found: HELIX 14 AB5 SER B 146 ALA B
169 1 24  
6 messages similar to the above omitted  
Cannot find LINK/SSBOND residue SER (256 )  
Cannot find LINK/SSBOND residue LYR (257 )  
Start residue of secondary structure not found: HELIX 10 AB1 CYS B 36 GLU B 41
1 6  
Start residue of secondary structure not found: HELIX 11 AB2 THR B 45 THR B 74
1 30  
Start residue of secondary structure not found: HELIX 12 AB3 GLU B 82 GLU B
101 1 20  
Start residue of secondary structure not found: HELIX 13 AB4 GLN B 117 SER B
136 1 20  
Start residue of secondary structure not found: HELIX 14 AB5 SER B 146 ALA B
169 1 24  
6 messages similar to the above omitted  
  
6eig.pdb1 title:  
Crystal structure of N24Q/C128T mutant of channelrhodopsin 2 [more info...]  
  
Chain information for 6eig.pdb1  
---  
Chain | Description  
1.1/A | No description available  
1.2/A | No description available  
  

> style sphere

Changed 4136 atom styles  

> style sphere

Changed 4136 atom styles  

> color bychain

> show surfaces

> open2 /home/scipion/Downloads/cryosparc_P52_J713_class_00_final_volume.mrc

Opened cryosparc_P52_J713_class_00_final_volume.mrc, grid size 128,128,128,
pixel 2.08, shown at level 0.428, step 1, values float32  

> select #2

2 models selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode translate

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> volume #2 style mesh

> ~select #2

Nothing selected  

> select #1

4136 atoms, 4208 bonds, 4 pseudobonds, 5 models selected  

> ui mousemode rightMode "translate selected models"

> toolshed show "Fit in Map"

Average map value = 0.5327 for 2068 atoms, 531 outside contour  
Fit molecule 6eig.pdb1 (#1.1) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5721, steps = 72  
shifted from previous position = 4.36  
rotated from previous position = 8.7 degrees  
atoms outside contour = 355, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.05265193 -0.98784350 -0.14626342 131.31220122  
-0.00514982 0.14673323 -0.98916269 143.38278903  
0.99859964 -0.05132810 -0.01281301 133.40411497  
Axis 0.52791309 -0.64445074 0.55316455  
Axis point 74.63357316 0.00000000 177.60504445  
Rotation angle (degrees) 117.34619496  
Shift along axis 50.71271327  
  
Fit molecule 6eig.pdb1 (#1.1) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5721, steps = 48  
shifted from previous position = 1.02  
rotated from previous position = 1.46 degrees  
atoms outside contour = 351, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.04875094 -0.98836022 -0.14410907 132.09360223  
0.01972429 0.14329984 -0.98948275 142.88919021  
0.99861619 -0.05108066 0.01250870 133.54033282  
Axis 0.52436532 -0.63853811 0.56330284  
Axis point 74.56024836 0.00000000 180.25700875  
Rotation angle (degrees) 116.51750411  
Shift along axis 53.24875898  
  
Fit molecule 6eig.pdb1 (#1.1) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5721, steps = 48  
shifted from previous position = 0.352  
rotated from previous position = 0.254 degrees  
atoms outside contour = 352, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.04437752 -0.98848296 -0.14467924 132.04229276  
0.01934702 0.14394439 -0.98939664 142.72209371  
0.99882747 -0.04670609 0.01273631 133.85817352  
Axis 0.52599518 -0.63804503 0.56234118  
Axis point 74.42454409 0.00000000 180.31426073  
Rotation angle (degrees) 116.34968412  
Shift along axis 53.66445044  
  
Fit molecule 6eig.pdb1 (#1.1) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5721, steps = 48  
shifted from previous position = 0.0724  
rotated from previous position = 0.068 degrees  
atoms outside contour = 355, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.04454870 -0.98839572 -0.14522159 131.99535945  
0.01833412 0.14453253 -0.98933018 142.76046765  
0.99883896 -0.04673588 0.01168263 133.83784019  
Axis 0.52603408 -0.63846646 0.56182624  
Axis point 74.38174257 0.00000000 180.19192772  
Rotation angle (degrees) 116.37004134  
Shift along axis 53.47989817  
  
Fit molecule 6eig.pdb1 (#1.1) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5721, steps = 28  
shifted from previous position = 0.0205  
rotated from previous position = 0.0525 degrees  
atoms outside contour = 353, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.04368317 -0.98839041 -0.14552037 131.98869399  
0.01836401 0.14484040 -0.98928460 142.74734798  
0.99887664 -0.04588743 0.01182373 133.85397574  
Axis 0.52629092 -0.63842226 0.56163589  
Axis point 74.35603901 0.00000000 180.20484867  
Rotation angle (degrees) 116.32801791  
Shift along axis 53.50856423  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 160  
shifted from previous position = 17.1  
rotated from previous position = 54.4 degrees  
atoms outside contour = 667, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.59797857 -0.80148008 0.00716367 139.65478782  
-0.47457458 -0.36125100 -0.80266847 131.20346332  
0.64591067 0.47657885 -0.59638243 150.75950509  
Axis 0.87216796 -0.43548629 0.22287832  
Axis point 0.00000000 68.21671163 101.08401994  
Rotation angle (degrees) 132.83015934  
Shift along axis 98.26614705  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 68  
shifted from previous position = 6.93  
rotated from previous position = 8.25 degrees  
atoms outside contour = 668, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.51751405 -0.85556030 0.01399204 138.66090444  
-0.57421885 -0.35936576 -0.73561468 132.98315598  
0.63439097 0.37265644 -0.67725569 144.99187048  
Axis 0.85193352 -0.47690375 0.21626857  
Axis point 0.00000000 77.88350327 92.65259798  
Rotation angle (degrees) 139.42486836  
Shift along axis 86.06689128  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 64  
shifted from previous position = 1.2  
rotated from previous position = 1.62 degrees  
atoms outside contour = 668, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50380937 -0.86315178 0.03383974 138.74957741  
-0.56402388 -0.35837862 -0.74393671 133.15611734  
0.65425773 0.35571586 -0.66739272 143.93170712  
Axis 0.84748484 -0.47814633 0.23053314  
Axis point 0.00000000 78.79862673 91.08948371  
Rotation angle (degrees) 139.55075600  
Shift along axis 87.10108309  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 48  
shifted from previous position = 0.218  
rotated from previous position = 0.307 degrees  
atoms outside contour = 667, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50523667 -0.86235090 0.03296708 138.89473294  
-0.56050912 -0.35696024 -0.74726763 133.12868282  
0.65617485 0.35906866 -0.66370495 144.07926087  
Axis 0.84765495 -0.47749057 0.23126574  
Axis point 0.00000000 78.56244220 91.39580987  
Rotation angle (degrees) 139.26310452  
Shift along axis 87.48771310  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 40  
shifted from previous position = 0.0795  
rotated from previous position = 0.148 degrees  
atoms outside contour = 669, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50700248 -0.86137357 0.03136954 138.91403209  
-0.56061566 -0.35718429 -0.74708063 133.05720843  
0.65472022 0.36118548 -0.66399283 144.10341582  
Axis 0.84818833 -0.47706843 0.23017879  
Axis point -0.00000000 78.42549696 91.51776954  
Rotation angle (degrees) 139.20809102  
Shift along axis 87.51741762  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 48  
shifted from previous position = 0.0605  
rotated from previous position = 0.0846 degrees  
atoms outside contour = 667, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50630335 -0.86174441 0.03245749 138.87084357  
-0.56086705 -0.35765111 -0.74666849 133.10107297  
0.65504585 0.35983642 -0.66440400 144.12879443  
Axis 0.84802806 -0.47715324 0.23059314  
Axis point 0.00000000 78.49579693 91.44379273  
Rotation angle (degrees) 139.27729660  
Shift along axis 87.49187526  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 44  
shifted from previous position = 0.0167  
rotated from previous position = 0.0275 degrees  
atoms outside contour = 667, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50618378 -0.86181793 0.03237025 138.88432332  
-0.56065240 -0.35735255 -0.74697258 133.10792633  
0.65532196 0.35995695 -0.66406636 144.12033212  
Axis 0.84796361 -0.47721229 0.23070792  
Axis point 0.00000000 78.49665162 91.45627346  
Rotation angle (degrees) 139.25461557  
Shift along axis 87.49781618  
  
Fit molecule 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 2068 atoms  
average map value = 0.5076, steps = 60  
shifted from previous position = 0.0104  
rotated from previous position = 0.0263 degrees  
atoms outside contour = 667, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.50649213 -0.86164413 0.03217332 138.89334028  
-0.56074881 -0.35750579 -0.74682687 133.09964854  
0.65500114 0.36022078 -0.66423979 144.11473872  
Axis 0.84806791 -0.47712516 0.23050467  
Axis point 0.00000000 78.48471813 91.46294558  
Rotation angle (degrees) 139.25541948  
Shift along axis 87.50491526  
  

> undo

> ~select #1.1

2068 atoms, 2104 bonds, 2 pseudobonds, 5 models selected  

> select #1

4136 atoms, 4208 bonds, 4 pseudobonds, 5 models selected  

> ~select #1

2 models selected  

> select #1.2

2068 atoms, 2104 bonds, 2 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> close #1

> open2 /home/scipion/Downloads/6ykm.pdb

6ykm.pdb title:  
Structure of C. Jejuni motab [more info...]  
  
Chain information for 6ykm.pdb #1  
---  
Chain | Description  
A B C D E | chemotaxis protein mota, putative  
F G | chemotaxis protein motb, putative  
  

> hide #1 target m

> close #1

> open2 /home/scipion/Downloads/6eig.pdb1

Summary of feedback from opening <_io.textiowrapper
name="/home/scipion/Downloads/6eig.pdb1" mode="rt" encoding="utf-8">  
---  
warnings | Start residue of secondary structure not found: HELIX 10 AB1 CYS B
36 GLU B 41 1 6  
Start residue of secondary structure not found: HELIX 11 AB2 THR B 45 THR B 74
1 30  
Start residue of secondary structure not found: HELIX 12 AB3 GLU B 82 GLU B
101 1 20  
Start residue of secondary structure not found: HELIX 13 AB4 GLN B 117 SER B
136 1 20  
Start residue of secondary structure not found: HELIX 14 AB5 SER B 146 ALA B
169 1 24  
6 messages similar to the above omitted  
Cannot find LINK/SSBOND residue SER (256 )  
Cannot find LINK/SSBOND residue LYR (257 )  
Start residue of secondary structure not found: HELIX 10 AB1 CYS B 36 GLU B 41
1 6  
Start residue of secondary structure not found: HELIX 11 AB2 THR B 45 THR B 74
1 30  
Start residue of secondary structure not found: HELIX 12 AB3 GLU B 82 GLU B
101 1 20  
Start residue of secondary structure not found: HELIX 13 AB4 GLN B 117 SER B
136 1 20  
Start residue of secondary structure not found: HELIX 14 AB5 SER B 146 ALA B
169 1 24  
6 messages similar to the above omitted  
  
6eig.pdb1 title:  
Crystal structure of N24Q/C128T mutant of channelrhodopsin 2 [more info...]  
  
Chain information for 6eig.pdb1  
---  
Chain | Description  
1.1/A | No description available  
1.2/A | No description available  
  

> select #1.1

2068 atoms, 2104 bonds, 2 pseudobonds, 2 models selected  

> select #1.2

2068 atoms, 2104 bonds, 2 pseudobonds, 2 models selected  

> select #1

4136 atoms, 4208 bonds, 4 pseudobonds, 5 models selected  
Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 112  
shifted from previous position = 13.6  
rotated from previous position = 21.8 degrees  
atoms outside contour = 1238, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00296208 -0.99561861 0.09346018 132.30026512  
-0.14344067 -0.09291712 -0.98528736 133.34048035  
0.98965448 -0.01048749 -0.14308743 134.33791099  
Axis 0.61904768 -0.56912913 0.54117649  
Axis point 0.00000000 91.39620446 79.41816775  
Rotation angle (degrees) 128.06253948  
Shift along axis 78.71274033  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00296208 -0.99561861 0.09346018 132.30026512  
-0.14344067 -0.09291712 -0.98528736 133.34048035  
0.98965448 -0.01048749 -0.14308743 134.33791099  
Axis 0.61904768 -0.56912913 0.54117649  
Axis point 0.00000000 91.39620446 79.41816775  
Rotation angle (degrees) 128.06253948  
Shift along axis 78.71274033  
  
Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 44  
shifted from previous position = 0.00875  
rotated from previous position = 0.035 degrees  
atoms outside contour = 1239, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00272924 -0.99566777 0.09294212 132.29900881  
-0.14366113 -0.09236875 -0.98530680 133.34857497  
0.98962318 -0.01066303 -0.14329085 134.34186835  
Axis 0.61891405 -0.56940650 0.54103755  
Axis point 0.00000000 91.40922978 79.43914745  
Rotation angle (degrees) 128.05846026  
Shift along axis 78.63616573  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00272924 -0.99566777 0.09294212 132.29900881  
-0.14366113 -0.09236875 -0.98530680 133.34857497  
0.98962318 -0.01066303 -0.14329085 134.34186835  
Axis 0.61891405 -0.56940650 0.54103755  
Axis point 0.00000000 91.40922978 79.43914745  
Rotation angle (degrees) 128.05846026  
Shift along axis 78.63616573  
  
Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 44  
shifted from previous position = 0.0476  
rotated from previous position = 0.0573 degrees  
atoms outside contour = 1234, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00367585 -0.99563462 0.09326413 132.31061964  
-0.14368603 -0.09282284 -0.98526049 133.30372563  
0.98961650 -0.00977908 -0.14339999 134.35518994  
Axis 0.61932795 -0.56908933 0.54089761  
Axis point 0.00000000 91.34614661 79.46814422  
Rotation angle (degrees) 128.04451292  
Shift along axis 78.75433721  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00367585 -0.99563462 0.09326413 132.31061964  
-0.14368603 -0.09282284 -0.98526049 133.30372563  
0.98961650 -0.00977908 -0.14339999 134.35518994  
Axis 0.61932795 -0.56908933 0.54089761  
Axis point 0.00000000 91.34614661 79.46814422  
Rotation angle (degrees) 128.04451292  
Shift along axis 78.75433721  
  
Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 40  
shifted from previous position = 0.0162  
rotated from previous position = 0.0158 degrees  
atoms outside contour = 1236, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00344271 -0.99564723 0.09313826 132.30567692  
-0.14361109 -0.09266561 -0.98528622 133.31808748  
0.98962821 -0.00998363 -0.14330500 134.34908469  
Axis 0.61920854 -0.56917129 0.54094807  
Axis point 0.00000000 91.36064542 79.46577613  
Rotation angle (degrees) 128.04381861  
Shift along axis 78.71985591  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00344271 -0.99564723 0.09313826 132.30567692  
-0.14361109 -0.09266561 -0.98528622 133.31808748  
0.98962821 -0.00998363 -0.14330500 134.34908469  
Axis 0.61920854 -0.56917129 0.54094807  
Axis point 0.00000000 91.36064542 79.46577613  
Rotation angle (degrees) 128.04381861  
Shift along axis 78.71985591  
  
Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 60  
shifted from previous position = 0.0102  
rotated from previous position = 0.0122 degrees  
atoms outside contour = 1236, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00360714 -0.99563607 0.09325124 132.30901456  
-0.14368567 -0.09280023 -0.98526268 133.30955034  
0.98961680 -0.00984488 -0.14339338 134.35380158  
Axis 0.61929971 -0.56910888 0.54090938  
Axis point 0.00000000 91.35150555 79.46592194  
Rotation angle (degrees) 128.04594926  
Shift along axis 78.74451678  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00360714 -0.99563607 0.09325124 132.30901456  
-0.14368567 -0.09280023 -0.98526268 133.30955034  
0.98961680 -0.00984488 -0.14339338 134.35380158  
Axis 0.61929971 -0.56910888 0.54090938  
Axis point 0.00000000 91.35150555 79.46592194  
Rotation angle (degrees) 128.04594926  
Shift along axis 78.74451678  
  
Average map value = 0.5145 for 4136 atoms, 1236 outside contour  
Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 40  
shifted from previous position = 0.00644  
rotated from previous position = 0.017 degrees  
atoms outside contour = 1236, contour level = 0.42848  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00334685 -0.99564985 0.09311374 132.30728536  
-0.14365782 -0.09262713 -0.98528303 133.31508196  
0.98962176 -0.01007892 -0.14334289 134.35053046  
Axis 0.61917532 -0.56920971 0.54094568  
Axis point -0.00000000 91.36609042 79.45991368  
Rotation angle (degrees) 128.04728456  
Shift along axis 78.71350644  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
0.00334685 -0.99564985 0.09311374 132.30728536  
-0.14365782 -0.09262713 -0.98528303 133.31508196  
0.98962176 -0.01007892 -0.14334289 134.35053046  
Axis 0.61917532 -0.56920971 0.54094568  
Axis point -0.00000000 91.36609042 79.45991368  
Rotation angle (degrees) 128.04728456  
Shift along axis 78.71350644  
  

> volume #2 level 0.4215

Fit molecules 6eig.pdb1 (#1.1), 6eig.pdb1 (#1.2) to map
cryosparc_P52_J713_class_00_final_volume.mrc (#2) using 4136 atoms  
average map value = 0.5145, steps = 72  
shifted from previous position = 1.19  
rotated from previous position = 22.6 degrees  
atoms outside contour = 1167, contour level = 0.42146  
  
Position of 6eig.pdb1 (#1.1) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.21583551 -0.95727423 -0.19246058 131.57750877  
-0.25667772 0.24579866 -0.93471898 134.28918157  
0.94208894 -0.15234520 -0.29876305 134.83003977  
Axis 0.50605998 -0.73385654 0.45316429  
Axis point 72.89789396 0.00000000 146.52585524  
Rotation angle (degrees) 129.37549402  
Shift along axis 29.13727712  
  
Position of 6eig.pdb1 (#1.2) relative to
cryosparc_P52_J713_class_00_final_volume.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.21583551 -0.95727423 -0.19246058 131.57750877  
-0.25667772 0.24579866 -0.93471898 134.28918157  
0.94208894 -0.15234520 -0.29876305 134.83003977  
Axis 0.50605998 -0.73385654 0.45316429  
Axis point 72.89789396 0.00000000 146.52585524  
Rotation angle (degrees) 129.37549402  
Shift along axis 29.13727712  
  

> ui mousemode rightMode rotate

> ~select #1

Nothing selected  

> volume #2 color #729fcf

> volume #2 color #b2ffff

> volume #2 color #40a9bf

> ui mousemode rightMode clip

> volume #2 level 0.6273

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #2 level 0.4706

> show #!1 models

> volume #2 level 0.5852

> volume #2 level 0.4986

> open2 /home/scipion/Downloads/cryosparc_P52_J714_003_volume_map.mrc

Opened cryosparc_P52_J714_003_volume_map.mrc, grid size 320,320,320, pixel
0.832, shown at level 0.127, step 2, values float32  

> volume #3 color #6778ba

> select #2

3 models selected  

> select #3

2 models selected  

> ui mousemode rightMode "rotate selected models"

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 300, in _model_moved  
xf = self._relative_position()  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
Error processing trigger "model position changed":  
AttributeError: 'NoneType' object has no attribute 'scene_position'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/map/fit/fitgui.py", line 319, in _relative_position  
xfo = fmap.scene_position  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.33.01
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
CPU: 24 Intel(R) Core(TM) i9-7920X CPU @ 2.90GHz
Cache Size: 16896 KB
Graphics:
	17:00.0 VGA compatible controller [0300]: NVIDIA Corporation GV102 [10de:1e07] (rev a1)
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:37ab]
	Kernel driver in use: nvidia

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Map fitting: fmap is None

comment:2 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #3559. Fixed 4 months ago, fixed in ChimeraX 1.1.

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