Opened 4 years ago

Closed 4 years ago

#4675 closed defect (duplicate)

tape measure using closed model

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

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/bajic/Downloads/run_class001 (3).mrc"

Opened run_class001 (3).mrc, grid size 384,384,384, pixel 1.12, shown at level
0.00575, step 2, values float32  

> volume #1 step 1

> set bgColor white

> lighting soft

> volume #1 level 0.008455

> volume #1 level 0.007992

> volume #1 level 0.007761

> Segment Map

Unknown command: Segment Map  

> segger

Unknown command: segger  

> open "/Users/bajic/Downloads/run_class001 (1).mrc"

Opened run_class001 (1).mrc, grid size 72,72,72, pixel 5.81, shown at level
0.117, step 1, values float32  

> close #2

> volume #1 level 0.006834

> volume #1 level 0.004981

> volume #1 level 0.006139

> volume #1 level 0.007143

> volume #1 level 0.00668

> volume #1 level 0.009614

> volume #1 level 0.002897

> volume #1 level 0.01262

> volume #1 level 0.01556

> volume #1 level 0.01795

> volume #1 level 0.01618

> open /Users/bajic/Downloads/spike+fab.pdb

Chain information for spike+fab.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
H | No description available  
L | No description available  
  

> fitmap #2 inMap #1

Fit molecule spike+fab.pdb (#2) to map run_class001 (3).mrc (#1) using 50227
atoms  
average map value = 0.006881, steps = 252  
shifted from previous position = 21.6  
rotated from previous position = 25.7 degrees  
atoms outside contour = 44928, contour level = 0.016176  
  
Position of spike+fab.pdb (#2) relative to run_class001 (3).mrc (#1)
coordinates:  
Matrix rotation and translation  
0.90664556 0.12047670 0.40432561 -80.03759430  
-0.07677941 0.98947365 -0.12266551 61.61279942  
-0.41484787 0.08017026 0.90635202 92.40116082  
Axis 0.23404339 0.94520873 -0.22760527  
Axis point 176.56766269 0.00000000 249.41436893  
Rotation angle (degrees) 25.67903902  
Shift along axis 18.47369527  
  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> select #2

50227 atoms, 50796 bonds, 46 pseudobonds, 2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right select

> fitmap #2 inMap #1

Fit molecule spike+fab.pdb (#2) to map run_class001 (3).mrc (#1) using 50227
atoms  
average map value = 0.0115, steps = 364  
shifted from previous position = 7.99  
rotated from previous position = 63.9 degrees  
atoms outside contour = 37519, contour level = 0.016176  
  
Position of spike+fab.pdb (#2) relative to run_class001 (3).mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.19682974 -0.90661060 0.37324966 360.75407275  
0.37417554 -0.42134415 -0.82611248 396.33861649  
0.90622886 -0.02294261 0.42216457 -52.97195880  
Axis 0.50104632 -0.33249164 0.79900056  
Axis point 71.89486531 299.33017229 0.00000000  
Rotation angle (degrees) 126.72712462  
Shift along axis 6.65059846  
  

> hide sel atoms

> show sel cartoons

> select clear

Drag select of 1 run_class001 (3).mrc , 14 residues  

> select clear

> volume #1 color #b2b2b2c4

> volume #1 color #b2b2b2c3

> volume #1 color #b2b2b2bb

> volume #1 color #b2b2b2b8

> volume #1 color #b2b2b2b7

> volume #1 color #b2b2b2b1

> volume #1 color #b2b2b2af

> volume #1 color #b2b2b2b0

> select /B:61

14 atoms, 13 bonds, 1 model selected  

> select clear

> open 7L2C

Summary of feedback from opening 7L2C fetched from pdb  
---  
notes | Fetching compressed mmCIF 7l2c from
http://files.rcsb.org/download/7l2c.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
Fetching CCD CAC from http://ligand-expo.rcsb.org/reports/C/CAC/CAC.cif  
Fetching CCD PGE from http://ligand-expo.rcsb.org/reports/P/PGE/PGE.cif  
  
7l2c title:  
Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-
CoV-2 spike N-terminal domain (NTD) [more info...]  
  
Chain information for 7l2c #3  
---  
Chain | Description  
A B | Spike glycoprotein  
C H | 2-51 heavy chain  
D L | 2-51 light chain  
  
Non-standard residues in 7l2c #3  
---  
ACT — acetate ion  
CA — calcium ion  
CAC — cacodylate ion (dimethylarsinate)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PGE — triethylene glycol  
  
7l2c mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_and_software_defined_assembly  
  

> select #3

11329 atoms, 11559 bonds, 22 pseudobonds, 3 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ~select #3

Nothing selected  

> select #3

11329 atoms, 11559 bonds, 22 pseudobonds, 3 models selected  

> fitmap #3 inMap #1

Fit molecule 7l2c (#3) to map run_class001 (3).mrc (#1) using 11329 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 11329, contour level = 0.016176  
  
Position of 7l2c (#3) relative to run_class001 (3).mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 -54.43625408  
0.00000000 1.00000000 0.00000000 -114.53563030  
0.00000000 0.00000000 1.00000000 50.87722825  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 50.87722825  
  

> ~select #3

Nothing selected  

> select #3

11329 atoms, 11559 bonds, 22 pseudobonds, 3 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right translate

> ui mousemode right "translate selected models"

> ~select #3

Nothing selected  

> select #3

11329 atoms, 11559 bonds, 22 pseudobonds, 3 models selected  

> ui mousemode right select

> select #2/B:403

24 atoms, 23 bonds, 1 model selected  

> select clear

> select clear

> select #3

11329 atoms, 11559 bonds, 22 pseudobonds, 3 models selected  

> ui mousemode right "translate selected models"

> hide #!3 target m

> close #3

> select up

Nothing selected  

> select up

Nothing selected  

> open /Users/bajic/Downloads/7l2c.pdb

7l2c.pdb title:  
Crystallographic structure of neutralizing antibody 2-51 In complex with sars-
cov-2 spike N-terminal domain (NTD) [more info...]  
  
Chain information for 7l2c.pdb #3  
---  
Chain | Description  
A B | spike glycoprotein  
C H | 2-51 heavy chain  
D L | 2-51 light chain  
  
Non-standard residues in 7l2c.pdb #3  
---  
ACT — acetate ion  
CA — calcium ion  
CAC — cacodylate ion (dimethylarsinate)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
PGE — triethylene glycol  
  

> select #3

11329 atoms, 11559 bonds, 25 pseudobonds, 3 models selected  

> ~select #3

Nothing selected  

> select #3

11329 atoms, 11559 bonds, 25 pseudobonds, 3 models selected  

> show target m

> fitmap #3 inMap #1

Fit molecule 7l2c.pdb (#3) to map run_class001 (3).mrc (#1) using 11329 atoms  
average map value = 8.728e-07, steps = 96  
shifted from previous position = 20.2  
rotated from previous position = 14.5 degrees  
atoms outside contour = 11329, contour level = 0.016176  
  
Position of 7l2c.pdb (#3) relative to run_class001 (3).mrc (#1) coordinates:  
Matrix rotation and translation  
0.98196651 0.00470118 0.18899647 -18.02999927  
-0.03607975 0.98597715 0.16293344 -17.23221676  
-0.18558022 -0.16681412 0.96836616 -12.61932653  
Axis -0.65856820 0.74810045 -0.08144722  
Axis point -82.90178782 0.00000000 87.45224364  
Rotation angle (degrees) 14.49833510  
Shift along axis 0.01036413  
  

> fitmap #3 inMap #1

Fit molecule 7l2c.pdb (#3) to map run_class001 (3).mrc (#1) using 11329 atoms  
average map value = -0.0001489, steps = 96  
shifted from previous position = 4.62  
rotated from previous position = 4.55 degrees  
atoms outside contour = 11329, contour level = 0.016176  
  
Position of 7l2c.pdb (#3) relative to run_class001 (3).mrc (#1) coordinates:  
Matrix rotation and translation  
0.96788904 0.04640081 0.24705823 80.01929845  
-0.09333075 0.97889869 0.18178756 248.94198394  
-0.23340989 -0.19900832 0.95179594 190.04880802  
Axis -0.60559862 0.76411234 -0.22222205  
Axis point 999.43088153 0.00000000 -437.95361474  
Rotation angle (degrees) 18.32437026  
Shift along axis 99.52702820  
  

> fitmap #3 inMap #1

Fit molecule 7l2c.pdb (#3) to map run_class001 (3).mrc (#1) using 11329 atoms  
average map value = 0.006288, steps = 572  
shifted from previous position = 45.6  
rotated from previous position = 68.7 degrees  
atoms outside contour = 10666, contour level = 0.016176  
  
Position of 7l2c.pdb (#3) relative to run_class001 (3).mrc (#1) coordinates:  
Matrix rotation and translation  
0.70768396 -0.16418149 -0.68718837 220.18877476  
0.61767821 0.61596767 0.48893503 162.59992511  
0.34301174 -0.77047275 0.53732177 182.06874487  
Axis -0.69765792 -0.57068670 0.43311676  
Axis point 0.00000000 280.47145293 83.30445529  
Rotation angle (degrees) 64.50154878  
Shift along axis -167.55303217  
  

> hide sel atoms

> show sel cartoons

Must specify one map, got 0  

> open 7b62

Summary of feedback from opening 7b62 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7b62 from
http://files.rcsb.org/download/7b62.cif  
Fetching CCD BLA from http://ligand-expo.rcsb.org/reports/B/BLA/BLA.cif  
Fetching CCD PG4 from http://ligand-expo.rcsb.org/reports/P/PG4/PG4.cif  
Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif  
Fetching CCD 1PE from http://ligand-expo.rcsb.org/reports/1/1PE/1PE.cif  
  
7b62 title:  
Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex
with biliverdin [more info...]  
  
Chain information for 7b62 #4  
---  
Chain | Description  
A | Spike glycoprotein  
  
Non-standard residues in 7b62 #4  
---  
1PE — pentaethylene glycol (PEG400)  
BLA — biliverdine IX α  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
PEG — di(hydroxyethyl)ether  
PG4 — tetraethylene glycol  
PGE — triethylene glycol  
  

> hide #!3 models

> ~select #3

Nothing selected  

> select #4

3035 atoms, 2756 bonds, 1 model selected  

> open /Users/bajic/Downloads/run_it058_class001.mrc

Opened run_it058_class001.mrc, grid size 384,384,384, pixel 1.12, shown at
level 2.73e-06, step 2, values float32  

> volume #5 step 1

> volume #5 level 0.002996

> hide #!2 models

> volume #5 level 0.01103

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap #4 inMap #5

Fit molecule 7b62 (#4) to map run_it058_class001.mrc (#5) using 3035 atoms  
average map value = 0.003414, steps = 220  
shifted from previous position = 14.4  
rotated from previous position = 17.2 degrees  
atoms outside contour = 2397, contour level = 0.011032  
  
Position of 7b62 (#4) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.80851307 0.58607285 -0.05315265 267.04124526  
-0.52950167 -0.68510012 0.50026571 221.64185090  
0.25677726 0.43261579 0.86423897 258.53526897  
Axis -0.05832887 -0.26722669 -0.96186675  
Axis point 148.14015143 33.68259999 0.00000000  
Rotation angle (degrees) 144.55643658  
Shift along axis -323.48131046  
  

> volume #5 color #b2ffffb4

> volume #5 color #b2ffffb2

> volume #5 color #b2ffffa6

> volume #5 color #b2ffff99

> volume #5 color #b2ffff95

> volume #5 color #b2ffff92

> volume #5 color #b2ffff8f

> volume #5 color #b2ffff8e

> volume #5 color #b2ffff8d

> volume #5 color #b2ffff8f

> volume #5 color #b2ffff90

> volume #5 color #b2ffff92

> volume #5 color #b2ffff95

> volume #5 color #b2ffff96

> volume #5 color #b2ffff97

> volume #5 color #b2ffff99

> volume #5 color #b2ffff9c

> volume #5 color #b2ffff9d

> volume #5 color #b2ffffa0

> volume #5 color #b2ffffa9

> volume #5 color #b2ffffb3

> volume #5 color #b2ffffb7

> volume #5 color #b2ffffb9

> volume #5 color #b2ffffbb

> volume #5 color #b2ffffc0

> volume #5 color #b2ffffc1

> volume #5 color #b2ffffc2

> volume #5 color #b2ffffc3

> volume #5 color #b2ffffc4

> volume #5 color #b2ffffc5

> volume #5 color #b2ffffc9

> volume #5 color #b2ffffcf

> volume #5 color #b2ffffd2

> volume #5 color #b2ffffd3

> volume #5 color #b2ffffd4

> volume #5 color #b2ffffd5

> volume #5 color #b2ffffd6

> volume #5 color #b2ffffd9

> volume #5 color #b2ffffda

> volume #5 color #b2ffffdc

> volume #5 color #b2ffffde

> volume #5 color #b2ffffe0

> volume #5 color #b2ffffe1

> volume #5 color #b2ffffe2

> volume #5 color #b2ffffe3

> volume #5 color #b2ffffe4

> volume #5 color #b2ffffe5

> volume #5 color #b2ffffe7

> volume #5 color #b2ffffe8

> volume #5 color #b2ffffe7

> volume #5 color #b2ffffe4

> volume #5 color #b2ffffe0

> volume #5 color #b2ffffdc

> volume #5 color #b2ffffd9

> volume #5 color #b2ffffd8

> volume #5 color #b2ffffd7

> volume #5 color #b2ffffd6

> volume #5 color #b2ffffd5

> volume #5 color #b2ffffd2

> volume #5 color #b2ffffd1

> volume #5 color #b2ffffd2

> volume #5 color #b2ffffd3

> volume #5 color #b2ffffd4

> volume #5 color #8000ff

> volume #5 color #8000ffc5

> fitmap #4 inMap #5

Fit molecule 7b62 (#4) to map run_it058_class001.mrc (#5) using 3035 atoms  
average map value = 0.003989, steps = 136  
shifted from previous position = 5  
rotated from previous position = 10.7 degrees  
atoms outside contour = 2315, contour level = 0.011032  
  
Position of 7b62 (#4) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.73948570 0.67100663 -0.05395356 262.42387186  
-0.64167783 -0.67839286 0.35781653 215.15603962  
0.20349556 0.29922102 0.93223190 259.12776932  
Axis -0.04376147 -0.19227329 -0.98036519  
Axis point 156.02060903 33.38539674 0.00000000  
Rotation angle (degrees) 137.97247880  
Shift along axis -306.89266056  
  

> ~select #4

Nothing selected  

> volume #5 color #20ffff

> volume #5 color #20ffffcb

> volume #5 color #20ffffcc

> volume #5 color #20ffffcd

> volume #5 color #20ffffce

> volume #5 color #20ffffd0

> volume #5 color #20ffffd4

> volume #5 color #20ffffd6

> volume #5 color #20ffffd9

> volume #5 color #20ffffda

> volume #5 color #20ffffdb

> volume #5 color #20ffffdd

> volume #5 color #20ffffde

> volume #5 color #20ffffdf

> volume #5 color #20ffffe0

> volume #5 color #20ffffe2

> volume #5 color #20ffffe4

> volume #5 color #20ffffe7

> volume #5 color #20ffffe8

> volume #5 color #20ffffe9

> volume #5 color #20ffffe8

> lighting full

> lighting soft

> lighting simple

> fitmap #4 inMap #5

Fit molecule 7b62 (#4) to map run_it058_class001.mrc (#5) using 3035 atoms  
average map value = 0.01191, steps = 144  
shifted from previous position = 5.53  
rotated from previous position = 28.9 degrees  
atoms outside contour = 1447, contour level = 0.011032  
  
Position of 7b62 (#4) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
-0.62855648 0.66443942 -0.40427340 256.95402059  
-0.72758816 -0.68600384 0.00376542 215.95138986  
-0.27483122 0.29651132 0.91463043 271.26620180  
Axis 0.20495327 -0.09062330 -0.97456738  
Axis point 199.02923713 29.76343911 0.00000000  
Rotation angle (degrees) 134.42419234  
Shift along axis -231.27385051  
  

> volume #5 color #20ffffe7

> volume #5 color #20ffffe6

> volume #5 color #20ffffe3

> volume #5 color #20ffffe1

> volume #5 color #20ffffdf

> volume #5 color #20ffffde

> volume #5 color #20ffffdc

> volume #5 color #20ffffdb

> volume #5 color #20ffffda

> volume #5 color #20ffffd9

> volume #5 color #20ffffd8

> volume #5 color #20ffffd7

> volume #5 color #20ffffd6

> volume #5 color #20ffffd5

> volume #5 color #20ffffd4

> volume #5 color #20ffffd3

> volume #5 color #20ffffd2

> volume #5 color #20ffffce

> volume #5 color #20ffffcb

> volume #5 color #20ffffca

> volume #5 color #20ffffc8

> volume #5 color #20ffffc6

> volume #5 color #20ffffc3

> volume #5 color #20ffffc2

> volume #5 color #20ffffc1

> volume #5 color #20ffffc0

> volume #5 color #20ffffbe

> volume #5 color #20ffffbd

> volume #5 color #20ffffbc

> volume #5 color #20ffffba

> volume #5 color #20ffffb9

> volume #5 color #20ffffb8

> volume #5 color #20ffffb7

> volume #5 color #20ffffb6

> volume #5 color #20ffffb5

> volume #5 color #20ffffb4

> volume #5 color #20ffffb3

> volume #5 color #20ffffb2

> volume #5 color #20ffffb1

> volume #5 color #20ffffad

> volume #5 color #20ffffaa

> volume #5 color #20ffffa8

> volume #5 color #20ffffa7

> volume #5 color #20ffffa6

> volume #5 color #20ffffa4

> volume #5 color #20ffffa2

> volume #5 color #20ffffa1

> volume #5 color #20ffffa0

> volume #5 color #20ffff9e

> volume #5 color #20ffff9b

> volume #5 color #20ffff98

> volume #5 color #20ffff97

> volume #5 color #20ffff96

> volume #5 color #20ffff94

> volume #5 color #20ffff91

> volume #5 color #20ffff88

> volume #5 color #20ffff83

> volume #5 color #20ffff82

> volume #5 color #20ffff81

> volume #5 color #20ffff80

> volume #5 color #20ffff76

> volume #5 color #20ffff73

> volume #5 color #20ffff6d

> volume #5 color #20ffff6b

> volume #5 color #20ffff6a

> volume #5 color #20ffff66

> volume #5 color #20ffff65

> volume #5 color #20ffff64

> volume #5 color #20ffff63

> volume #5 color #20ffff61

> volume #5 color #20ffff60

> volume #5 color #20ffff5f

> volume #5 color #20ffff60

> volume #5 color #20ffff61

> volume #5 color #20ffff62

> hide #4 models

> show #!1 models

> hide #!5 models

> volume #1 level 0.01085

> volume #1 level 0.009073

> volume #1 level 0.009073

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!5 models

> show #4 models

> show #!1 models

> hide #!5 models

> show #!5 models

> hide #!1 models

> volume #5 level 0.01702

> ui mousemode right select

> select #4/A:1301@C1D

1 atom, 1 model selected  

> select #4/A:126

7 atoms, 6 bonds, 1 model selected  

> select clear

> select clear

> open 7NTC

Summary of feedback from opening 7NTC fetched from pdb  
---  
note | Fetching compressed mmCIF 7ntc from
http://files.rcsb.org/download/7ntc.cif  
  
7ntc title:  
Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab [more info...]  
  
Chain information for 7ntc #6  
---  
Chain | Description  
A B C | Spike glycoprotein  
H | P008_056 Fab Heavy chain  
L | P008_056 Fab Light chain  
  
Non-standard residues in 7ntc #6  
---  
BLA — biliverdine IX α  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> fitmap #6 inMap #5

Fit molecule 7ntc (#6) to map run_it058_class001.mrc (#5) using 30005 atoms  
average map value = 0.0003132, steps = 172  
shifted from previous position = 10.8  
rotated from previous position = 9.74 degrees  
atoms outside contour = 29719, contour level = 0.017019  
  
Position of 7ntc (#6) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
0.98999776 -0.11453699 0.08237549 16.20690777  
0.12177808 0.98855657 -0.08902817 -13.93845975  
-0.07123582 0.09816922 0.99261688 1.19601756  
Axis 0.55325733 0.45399450 0.69842346  
Axis point 137.99622138 112.66803109 0.00000000  
Rotation angle (degrees) 9.74000079  
Shift along axis 3.47393316  
  

> style #4#!6 sphere

Changed 33040 atom styles  

> style #4#!6 sphere

Changed 33040 atom styles  

> hide #4#!6 atoms

> show #4#!6 cartoons

> select #6

30005 atoms, 30809 bonds, 9 pseudobonds, 2 models selected  
Drag select of  

> select #6

30005 atoms, 30809 bonds, 9 pseudobonds, 2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap #6 inMap #5

Fit molecule 7ntc (#6) to map run_it058_class001.mrc (#5) using 30005 atoms  
average map value = 0.0002799, steps = 156  
shifted from previous position = 2.64  
rotated from previous position = 11 degrees  
atoms outside contour = 29697, contour level = 0.017019  
  
Position of 7ntc (#6) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
0.63322336 0.74898894 -0.19504803 -45.19057511  
-0.77262919 0.62654748 -0.10238359 293.48383088  
0.04552268 0.21553148 0.97543522 -70.74632541  
Axis 0.20211006 -0.15293946 -0.96734743  
Axis point 284.35525205 203.47345690 0.00000000  
Rotation angle (degrees) 51.85869454  
Shift along axis 14.41754655  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap #6 inMap #5

Fit molecule 7ntc (#6) to map run_it058_class001.mrc (#5) using 30005 atoms  
average map value = 0.0003607, steps = 236  
shifted from previous position = 5.54  
rotated from previous position = 12 degrees  
atoms outside contour = 29594, contour level = 0.017019  
  
Position of 7ntc (#6) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
0.45233452 0.68443965 -0.57178305 112.99516541  
-0.20244972 0.70318542 0.68157492 -63.49013138  
0.86856640 -0.19254255 0.45663965 -58.63956154  
Axis -0.45909249 -0.75648140 -0.46580037  
Axis point 119.02369806 0.00000000 102.45856314  
Rotation angle (degrees) 72.17686131  
Shift along axis 23.46820147  
  

> fitmap #6 inMap #5

Fit molecule 7ntc (#6) to map run_it058_class001.mrc (#5) using 30005 atoms  
average map value = 0.001541, steps = 264  
shifted from previous position = 12.4  
rotated from previous position = 20.2 degrees  
atoms outside contour = 28731, contour level = 0.017019  
  
Position of 7ntc (#6) relative to run_it058_class001.mrc (#5) coordinates:  
Matrix rotation and translation  
0.59562075 0.56664231 -0.56934384 75.14205535  
0.09533931 0.65390706 0.75054378 -165.37942044  
0.79758783 -0.50132030 0.33545732 58.49879464  
Axis -0.65455728 -0.71472221 -0.24642835  
Axis point 45.26461741 0.00000000 162.60241240  
Rotation angle (degrees) 72.99275860  
Shift along axis 54.59980440  
  

> ~select #6

Nothing selected  

> select #6

30005 atoms, 30809 bonds, 9 pseudobonds, 2 models selected  

> ~select #6

Nothing selected  

> hide #!6 models

> style #4 stick

Changed 3035 atom styles  

> show #4 atoms

> ui mousemode right select

> select #4/A:1301@C1D

1 atom, 1 model selected  

> select clear

> select #6.1

9 pseudobonds, 1 model selected  

> ~select #6.1

Nothing selected  

> hide #6.1 models

> show #6.1 models

> hide #6.1 models

> show #6.1 models

> hide #6.1 models

> hide #4 models

> show #4 models

> hide #!6 models

> select #4/A:1301@CBD

1 atom, 1 model selected  

> color byattribute heteroatom

No known/registered attribute heteroatom  

> color byhetero

> select clear

> show #!6 models

> hide #4 models

> hide #!6 models

> show #4 models

> show #!6 models

> hide #!5 models

> hide #4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!6 models

> show #4 models

> hide #4 models

> show #!6 models

> hide #!6 models

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #4 models

> hide #!5 models

> show #!5 models

> show #!1 models

> hide #4 models

> hide #!5 models

> volume #1 level 0.008069

> show #!5 models

> hide #!1 models

> show #4 models

> open /Users/bajic/Downloads/emd_23899.map

Opened emd_23899.map, grid size 300,300,300, pixel 1.16, shown at level
0.0113, step 2, values float32  

> hide #4 models

> volume #7 step 1

> volume #7 level 0.1875

> volume #7 level 0.3148

> volume #7 level 0.2267

> open /Users/bajic/Downloads/emd_23898.map

Opened emd_23898.map, grid size 300,300,300, pixel 1.16, shown at level
0.0192, step 2, values float32  

> volume #8 step 1

> volume #8 level 0.1406

> volume #8 level 0.3529

> volume #7 level 0.06543

> volume #7 level 0.06039

> volume #7 level 0.1612

> volume #7 level 0.06039

> volume #7 level 0.2821

> volume #7 color #b2b2fffe

> volume #7 color #b2b2fffc

> volume #7 color #b2b2fff9

> volume #7 color #b2b2fff4

> volume #7 color #b2b2ffe9

> volume #7 color #b2b2ffdd

> volume #7 color #b2b2ffd6

> volume #7 color #b2b2ffd2

> volume #7 color #b2b2ffd0

> volume #7 color #b2b2ffce

> volume #7 color #b2b2ffc9

> volume #7 color #b2b2ffc0

> volume #7 color #b2b2ffba

> volume #7 color #b2b2ffb8

> volume #7 color #b2b2ffb7

> volume #7 color #b2b2ffb4

> volume #7 color #b2b2ffb3

> volume #7 color #b2b2ffb2

> volume #7 color #b2b2ffaf

> volume #7 color #b2b2ffa8

> volume #7 color #b2b2ffa3

> volume #7 color #b2b2ffa1

> volume #7 color #b2b2ff9f

> volume #7 color #b2b2ff9a

> volume #7 color #b2b2ff97

> volume #7 color #b2b2ff91

> volume #7 color #b2b2ff8e

> volume #7 color #b2b2ff8c

> volume #7 color #b2b2ff87

> volume #7 color #b2b2ff84

> volume #7 color #b2b2ff83

> volume #7 color #b2b2ff82

> volume #7 color #b2b2ff81

> volume #7 color #b2b2ff80

> volume #7 level 0.06543

> volume #7 level 0.1864

> volume #7 color #108080

> close #7

> volume #8 level 0.07089

> close #8

> volume #5 level 0.01056

> volume #1 level 0.01587

> ui mousemode right "tape measure"

> marker segment #7 position 280,179.6,266.3 toPosition 311.2,258.5,265.8
> color yellow radius 0.28 label 84.81 labelHeight 8.481 labelColor yellow

> close #7

> marker segment #7 position 269.1,190.7,264.3 toPosition 314.9,253.9,255.2
> color yellow radius 0.28 label 78.51 labelHeight 7.851 labelColor yellow

> marker delete #7

> marker segment #7 position 230.4,165.9,173.6 toPosition 158.4,279.1,268.4
> color yellow radius 0.28 label 164.3 labelHeight 16.43 labelColor yellow

> marker segment #7 position 159.7,168.5,167.6 toPosition 280.3,175.4,274.1
> color yellow radius 0.28 label 161 labelHeight 16.1 labelColor yellow

> close #7

> open "/Users/bajic/Dropbox
> (Personal)/Clara/Ab090/deepmemhancer_NU_refined.mrc"

Opened deepmemhancer_NU_refined.mrc, grid size 384,384,384, pixel 1.06, shown
at level 0.0087, step 2, values float32  

> volume #7 step 1

> volume #7 level 0.3636

> volume #7 level 0.5765

> volume #7 level 0.3704

> volume #7 color #ffb2b2d2

> volume #7 color #ffb2b2d1

> volume #7 color #ffb2b2cf

> volume #7 color #ffb2b2cd

> volume #7 color #ffb2b2cb

> volume #7 color #ffb2b2c5

> volume #7 color #ffb2b2c2

> volume #7 color #ffb2b2c0

> volume #7 color #ffb2b2be

> volume #7 color #ffb2b2bd

> volume #7 color #ffb2b2b3

> volume #7 color #ffb2b2ac

> volume #7 color #ffb2b295

> volume #7 color #ffb2b291

> volume #7 color #ffb2b290

> volume #7 color #ffb2b294

> volume #7 color #ffb2b295

> volume #7 color #ffb2b294

> lighting soft

> lighting full

> lighting soft

> volume #7 color #fc0280

> volume #7 color #8000ff

> volume #7 color #8000ff7d

> volume #7 color #cc66ff

> volume #7 color #cc66ffac

> volume #7 color #cc66ffaa

> volume #7 color #cc66ffa7

> volume #7 color #cc66ff9f

> volume #7 color #cc66ff9d

> volume #7 color #cc66ff9c

> volume #7 color #cc66ff9b

> volume #7 color #cc66ff9a

> volume #7 color #cc66ff99

> volume #7 color #cc66ff98

> volume #7 color #cc66ff96

> volume #7 color #cc66ff92

> volume #7 color #cc66ff81

> volume #7 color #cc66ff7f

> volume #7 color #cc66ff7c

> volume #7 color #cc66ff7d

> volume #7 color #cc66ff7e

> volume #7 color #cc66ff80

> open "/Users/bajic/Dropbox (Personal)/Clara/Ab090/RBD_and_Fab-coot-1.pdb"

Chain information for RBD_and_Fab-coot-1.pdb #8  
---  
Chain | Description  
E | No description available  
H | No description available  
L | No description available  
  

> open "/Users/bajic/Dropbox (Personal)/Clara/Ab090/051221-coot-2.pdb"

Chain information for 051221-coot-2.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
H | No description available  
L | No description available  
  

> hide #8#!9 atoms

> show #8#!9 cartoons

> hide #!9 models

> show #!9 models

> hide #!9 models

> select up

Nothing selected  
Must specify one map, got 0  

> fitmap #8 inMap #7

Fit molecule RBD_and_Fab-coot-1.pdb (#8) to map deepmemhancer_NU_refined.mrc
(#7) using 3110 atoms  
average map value = 0.5002, steps = 84  
shifted from previous position = 8.61  
rotated from previous position = 4.6 degrees  
atoms outside contour = 996, contour level = 0.37035  
  
Position of RBD_and_Fab-coot-1.pdb (#8) relative to
deepmemhancer_NU_refined.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99960028 0.02403111 0.01489235 0.32820205  
-0.02284399 0.99689769 -0.07532032 21.16907226  
-0.01665618 0.07495001 0.99704818 -14.10307447  
Axis 0.93601836 0.19651258 -0.29198019  
Axis point 0.00000000 164.64185325 251.87411161  
Rotation angle (degrees) 4.60414537  
Shift along axis 8.58501050  
  

> show #!9 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> hide #8 models

> show #8 models

> open "/Users/bajic/Dropbox (Personal)/Clara/Ab090/run_it059_class001.mrc"

Opened run_it059_class001.mrc, grid size 384,384,384, pixel 1.06, shown at
level 4.36e-07, step 2, values float32  

> volume #10 step 1

> volume #10 level 0.006434

> volume #10 level 0.0126

> volume #10 color #b2ffb2bc

> volume #10 color #b2ffb2bd

> volume #10 level 0.01182

> fitmap #10 inMap #7

Fit map run_it059_class001.mrc in map deepmemhancer_NU_refined.mrc using 86807
points  
correlation = 0.8356, correlation about mean = 0.2665, overlap = 631.2  
steps = 80, shift = 8.42, angle = 4.68 degrees  
  
Position of run_it059_class001.mrc (#10) relative to
deepmemhancer_NU_refined.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99968039 0.01111563 0.02270598 0.57472525  
-0.00932172 0.99693802 -0.07763823 20.28729937  
-0.02349945 0.07740176 0.99672300 -13.75941684  
Axis 0.95078946 0.28335677 -0.12533295  
Axis point 0.00000000 174.31341876 225.16196434  
Rotation angle (degrees) 4.67664439  
Shift along axis 8.01949479  
  

> hide #!9 models

> volume #10 level 0.01287

> volume #10 color #20ffff

> volume #10 color #20ffffae

> volume #10 color #20ffffad

> volume #10 color #20ffffab

> volume #10 color #20ffffaa

> volume #10 color #20ffffa9

> volume #10 color #20ffffa8

> volume #10 color #20ffffa9

> volume #10 color #20ffffaa

> volume #10 color #20ffffab

> volume #10 color #20ffffae

> volume #10 color #20ffffaf

> volume #10 color #66ccff

> volume #10 color #66ccffb7

> volume #10 color #66ccffb6

> volume #10 color #66ccffb4

> volume #10 color #66ccffb2

> volume #10 color #66ccffb1

> volume #10 color #66ccffb0

> volume #10 color #66ccffaf

> volume #10 color #66ccffb0

> volume #10 color #66ccffb1

> volume #10 color #66ccffb2

> volume #10 color #66ccffb5

> volume #10 color #66ccffb3

> volume #10 color #66ccffab

> lighting full

> volume #10 level 0.01208

> volume #10 level 0.01379

> style #8 stick

Changed 3110 atom styles  

> show #8 atoms

> color byhetero

> show #!9 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> volume #7 level 0.5235

> hide #8 atoms

> volume #10 level 0.006171

> volume #10 level 0.01405

> volume #10 level 0.009191

> volume #7 level 0.2799

> hide #8 models

> lighting soft

> volume #7 color #cc66ff81

> volume #7 color #cc66ff8e

> volume #7 color #cc66ff99

> volume #7 color #cc66ffa2

> volume #7 color #cc66ffab

> volume #7 color #cc66ffb0

> volume #7 color #cc66ffb1

> volume #7 color #cc66ffb3

> volume #7 color #cc66ffb4

> volume #7 color #cc66ffb5

> volume #7 color #cc66ffb6

> volume #7 color #cc66ffb7

> volume #7 color #cc66ffba

> volume #7 color #cc66ffc1

> volume #7 color #cc66ffc3

> volume #7 color #cc66ffc5

> volume #7 color #cc66ffca

> volume #7 color #cc66ffce

> volume #7 color #cc66ffcf

> volume #7 color #cc66ffd1

> volume #7 color #cc66ffd4

> volume #7 color #cc66ffda

> volume #7 color #cc66ffe7

> volume #7 color #cc66fffb

> volume #7 color #cc66ff

> volume #7 color #cc66fff7

> volume #7 color #cc66fff6

> volume #7 color #cc66fff5

> volume #7 color #cc66fff4

> volume #7 color #cc66fff3

> volume #7 color #cc66fff1

> volume #7 color #cc66fff0

> volume #7 color #cc66ffef

> volume #7 color #cc66ffec

> volume #7 color #cc66ffeb

> volume #7 color #cc66ffe9

> volume #7 color #cc66ffe8

> volume #7 color #cc66ffe9

> volume #7 color #cc66ffea

> volume #7 color #cc66ffed

> volume #7 color #cc66ffee

> volume #7 color #cc66fff0

> volume #7 color #cc66fff1

> volume #7 color #cc66fff4

> volume #7 color #cc66fff2

> volume #7 color #cc66ffef

> volume #7 color #cc66ffee

> volume #7 color #cc66ffea

> volume #7 color #cc66ffe9

> volume #7 color #cc66ffe8

> volume #7 color #cc66ffea

> volume #7 color #cc66ffee

> volume #7 color #cc66ff

> volume #7 level 0.3077

> lighting full

> lighting soft

> volume #7 level 0.3924

> volume #7 level 0.3019

> volume #7 color #cc66ffda

> volume #7 color #cc66ffd9

> volume #7 color #cc66ffd3

> volume #7 color #cc66ffb9

> volume #7 color #cc66ffa0

> volume #7 color #cc66ff98

> volume #7 color #cc66ff95

> volume #7 color #cc66ff94

> volume #7 color #cc66ff93

> volume #7 color #cc66ff91

> volume #7 color #cc66ff8e

> volume #7 color #cc66ff7d

> volume #7 color #cc66ff65

> volume #7 color #cc66ff4f

> volume #7 color #cc66ff4b

> volume #7 color #cc66ff4c

> volume #7 color #cc66ff4e

> volume #7 color #cc66ff51

> volume #7 color #cc66ff55

> volume #7 color #cc66ff5b

> volume #7 color #cc66ff5c

> volume #7 color #cc66ff5f

> volume #7 color #cc66ff65

> volume #7 color #cc66ff69

> volume #7 color #cc66ff6b

> volume #7 color #cc66ff6c

> volume #7 color #cc66ff6d

> volume #7 color #cc66ff6f

> volume #7 color #cc66ff70

> volume #7 color #cc66ff72

> volume #7 color #cc66ff74

> volume #7 color #cc66ff79

> volume #7 color #cc66ff7c

> volume #7 color #cc66ff7d

> volume #7 color #cc66ff80

> volume #7 color #cc66ff89

> volume #7 color #cc66ff8c

> volume #7 color #cc66ff90

> volume #7 color #cc66ff91

> volume #7 color #cc66ff92

> volume #7 color #cc66ff9d

> volume #7 color #cc66ffa0

> volume #7 color #cc66ffa2

> volume #7 color #cc66ffa4

> volume #7 color #cc66ffa6

> volume #7 color #cc66ffa7

> volume #7 color #cc66ffa6

> volume #7 color #cc66ffa3

> volume #7 color #cc66ff9d

> volume #7 color #cc66ff89

> volume #7 color #cc66ff83

> volume #7 color #cc66ff7e

> volume #7 color #cc66ff7c

> volume #7 color #cc66ff7b

> volume #7 color #cc66ff7a

> volume #7 color #cc66ff79

> volume #7 color #cc66ff78

> volume #7 color #cc66ff75

> volume #7 color #cc66ff6d

> volume #7 color #cc66ff6b

> volume #7 color #cc66ff6c

> volume #7 color #cc66ff6f

> volume #7 color #cc66ff85

> volume #7 color #cc66ff8f

> volume #7 color #cc66ff93

> volume #7 color #cc66ff9f

> volume #7 color #cc66ffa6

> volume #7 color #cc66ffab

> volume #7 color #cc66ffb4

> volume #7 color #cc66ffba

> volume #7 color #cc66ffbe

> volume #7 color #cc66ffc2

> volume #7 color #cc66ffcb

> volume #7 color #cc66ffed

> volume #7 color #cc66ff

> volume #7 color #cc66fff6

> volume #7 color #cc66fff5

> volume #7 color #cc66ffe5

> volume #7 color #cc66ffd8

> volume #7 color #cc66ffce

> volume #7 color #cc66ffca

> volume #7 color #cc66ffc5

> volume #7 color #cc66ffbf

> volume #7 color #cc66ffbd

> volume #7 color #cc66ffbb

> volume #7 color #cc66ffba

> volume #7 color #cc66ffb8

> volume #7 color #cc66ffb4

> volume #7 color #cc66ffb3

> volume #7 color #cc66ffb2

> volume #7 color #cc66ffae

> volume #7 color #cc66ffaa

> volume #7 color #cc66ffa9

> volume #7 color #cc66ffa7

> volume #7 color #cc66ffa6

> volume #7 color #cc66ffa5

> volume #7 color #cc66ffa4

> volume #7 color #cc66ffa1

> volume #7 color #cc66ffa0

> volume #7 color #cc66ff8e

> volume #7 color #cc66ff8c

> volume #7 color #cc66ff8a

> volume #7 color #cc66ff89

> volume #7 color #cc66ff8a

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 475, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 396, in
_dispatch_mouse_event  
lm.mouse_up(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 477, in <lambda>  
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 402, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 103, in mouse_up  
self._clear()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 51, in _clear  
self._log_clear_command()  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/tape_measure/tape.py", line 122, in _log_clear_command  
log_equivalent_command(mset.session, cmd)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 43, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Structure' object has no attribute 'session'  
  
AttributeError: 'Structure' object has no attribute 'session'  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.0/chimerax_extlib/chimerax-1.0-3mrx/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.13
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini8,1
      Processor Name: 6-Core Intel Core i7
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1030)
      Kernel Version: Darwin 19.6.0
      Time since boot: 16 days 2:47

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0000
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Dell U4919DW:
          Resolution: 6400 x 1800
          UI Looks like: 3200 x 900 @ 59 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: J0QYTY2     
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No
          Adapter Firmware Version: 2.19

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Structure Analysis
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → tape measure using closed model

Possibly already fixed.

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #3457

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