Opened 4 years ago

Closed 3 years ago

#4706 closed defect (fixed)

Peptide flip: Simulation must be running!

Reported by: jporta@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax_isolde.cxs

Opened cryosparc_P182_J525_chain_A.mrc as #6, grid size 400,400,400, pixel
0.98, shown at level 0.45, step 1, values float32  
Log from Sun May 30 23:08:48 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Opened cryosparc_P182_J525_map_sharp.mrc as #1, grid size 400,400,400, pixel
0.98, shown at level 0.4, step 1, values float32  
Opened cryosparc_P182_J525_map_sharp.mrc 0 as #3.1, grid size 400,400,400,
pixel 0.98, shown at level 0.4, step 1, values float32  
Opened cryosparc_P182_J525_map_sharp.mrc 1 as #3.2, grid size 400,400,400,
pixel 0.98, shown at level 0.34, step 1, values float32  

Frozen name "chaina" not restored: nothing is selected by specifier  

Log from Sun May 30 22:22:03 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 254, in event  
if event.file() in self._bad_drop_events:  
AttributeError: 'UI' object has no attribute '_bad_drop_events'  
  
AttributeError: 'UI' object has no attribute '_bad_drop_events'  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 254, in event  
if event.file() in self._bad_drop_events:  
  
See log for complete Python traceback.  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P182_J322_map_sharp.mrc as #4, grid size 400,400,400, pixel
0.98, shown at level 0.45, step 1, values float32  
Opened cryosparc_P182_J525_map_sharp.mrc as #2, grid size 400,400,400, pixel
0.98, shown at level 0.568, step 1, values float32  
Log from Sun May 23 18:08:30 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Opened cryosparc_P182_J322_map_sharp.mrc as #4, grid size 400,400,400, pixel
0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_colorzone_2.mrc as #5, grid size 400,400,400, pixel
0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_colorzone_3.mrc as #6, grid size 400,400,400, pixel
0.98, shown at level 0.25, step 1, values float32  
Log from Sat May 22 18:47:25 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Opened cav1_11mer_real_space_refined_043_molmap.mrc as #3, grid size
400,400,400, pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc as #4, grid size 400,400,400, pixel
0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 0 as #2.1, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 1 as #2.2, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_colorzone_2.mrc as #5, grid size 400,400,400, pixel
0.98, shown at level 0.25, step 1, values float32  
Log from Sat May 22 13:34:06 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Opened cryosparc_P182_J322_013_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.98, shown at level 0.35, step 1, values float32  
Opened cav1_11mer_real_space_refined_043_molmap.mrc as #3, grid size
400,400,400, pixel 0.98, shown at level 0.307, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc as #4, grid size 400,400,400, pixel
0.98, shown at level 0.35, step 1, values float32  
Log from Sat May 22 13:17:54 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 254, in event  
if event.file() in self._bad_drop_events:  
AttributeError: 'UI' object has no attribute '_bad_drop_events'  
  
AttributeError: 'UI' object has no attribute '_bad_drop_events'  
  
File
"/Applications/ChimeraX-1.2.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 254, in event  
if event.file() in self._bad_drop_events:  
  
See log for complete Python traceback.  
  
Opened cryosparc_P182_J322_013_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.98, shown at level 0.35, step 1, values float32  
Opened cav1_11mer_real_space_refined_043_molmap.mrc as #3, grid size
400,400,400, pixel 0.98, shown at level 0.307, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc as #4, grid size 400,400,400, pixel
0.98, shown at level 0.35, step 1, values float32  
Log from Fri May 21 16:19:17 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open chimerax.cxs

Opened cryosparc_P182_J322_013_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.98, shown at level 0.35, step 1, values float32  
Opened cav1_11mer_real_space_refined_043_molmap.mrc as #3, grid size
400,400,400, pixel 0.98, shown at level 0.307, step 1, values float32  
Log from Fri May 21 14:22:44 2021UCSF ChimeraX version: 1.2.4 (2021-05-14)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Cav1_11mer_real_space_refined_043.pdb

Chain information for Cav1_11mer_real_space_refined_043.pdb #1  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> open cryosparc_P182_J322_013_volume_map_sharp.mrc

Opened cryosparc_P182_J322_013_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.98, shown at level 0.06, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.197

> select #1

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> transparency 50

> select clear

> volume #2 level 0.25

> volume #2 level 0.3

> volume #2 level 0.35

> volume #2 level 0.4

> volume #2 level 0.45

> volume #2 level 0.5

> view

> view

> select #1/c

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> show sel atoms

> style ssel stick

Expected a keyword  

> style sel stick

Changed 1049 atom styles  

> color sel byhetero

> select clear

> volume style mesh

> select #2

2 models selected  

> ~select #2

Nothing selected  

> select #1/c

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> color sel yellow

> color sel byhetero

> select clear

> volume #2 level 0.4772

> volume #2 level 0.4

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

> help help:user

> view

> select #1/c

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> hide sel cartoons

> ui mousemode right select

> select clear

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

> select #1

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> color sel cornflower blue

> select #2

2 models selected  

> color sel grey

> volume sel style surface

> select clear

> transparency 50

> select #1/c

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> show sel cartoons

> hide sel atoms

> select clear

> volume #2 level 0.35

> volume #2 level 0.4

> volume #2 level 0.35

> color zone #2 near #1 distance 3

> color zone #2 near #1 distance 2

> color zone #2 near #1 distance 1

> color zone #2 near #1 distance 1.5

> color zone #2 near #1 distance 2

> color zone #2 near #1 distance 2.5

> color #2 grey

> transparency 50

> molmap #1 3.8 onGrid #2

Opened Cav1_11mer_real_space_refined_043.pdb map 3.8 as #3, grid size
400,400,400, pixel 0.98, shown at level 0.0846, step 1, values float32  

> volume #3 color #6e7b8b

> transparency 0

> transparency 50

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #1 models

> volume #3 level 0.3074

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

> save cav1_11mer_real_space_refined_043_molmap.mrc #3

> open cav1_11mer_real_space_refined_043_molmap.mrc

Opened cav1_11mer_real_space_refined_043_molmap.mrc as #4, grid size
400,400,400, pixel 0.98, shown at level 8.1e-05, step 2, values float32  

> close #4

> save chimerax.cxs

——— End of log from Fri May 21 14:22:44 2021 ———

opened ChimeraX session  

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> open cryosparc_P182_J322_map_sharp.mrc

Opened cryosparc_P182_J322_map_sharp.mrc as #4, grid size 400,400,400, pixel
0.98, shown at level 0.06, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.238

> volume #4 level 0.3

> volume #4 level 0.35

> view

> save chimerax.cxs

——— End of log from Fri May 21 16:19:17 2021 ———

opened ChimeraX session  

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

——— End of log from Sat May 22 13:17:54 2021 ———

opened ChimeraX session  

> hide #!3 models

> lighting simple

> transparency #4.1 50

> show #1 models

> volume #2 level 0.3

> volume #3 level 0.25

> close #2

> volume #4 level 0.3

> volume #4 level 0.325

> volume #4 level 0.25

> volume #4 level 0.26

> volume #4 level 0.27

> volume #4 level 0.28

> volume #4 level 0.29

> volume #4 level 0.23

> volume #4 level 0.3

> ui tool show "Fit in Map"

Fit molecule Cav1_11mer_real_space_refined_043.pdb (#1) to map
cryosparc_P182_J322_map_sharp.mrc (#4) using 11539 atoms  
average map value = 0.4906, steps = 48  
shifted from previous position = 0.0806  
rotated from previous position = 0.0365 degrees  
atoms outside contour = 2982, contour level = 0.3  
  
Position of Cav1_11mer_real_space_refined_043.pdb (#1) relative to
cryosparc_P182_J322_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999981 -0.00060315 -0.00015146 0.13766296  
0.00060313 0.99999981 -0.00013591 -0.13362611  
0.00015155 0.00013582 0.99999998 -0.12284771  
Axis 0.21344211 -0.23800992 0.94751979  
Axis point 243.42159161 247.70073432 0.00000000  
Rotation angle (degrees) 0.03647139  
Shift along axis -0.05521322  
  

> view

> volume #4 level 0.2

> volume #4 level 0.25

> color zone #4 near #1 distance 3

> color zone #4 near #1 distance 2

> color zone #4 near #1 distance 1

> volume splitbyzone #4

Opened cryosparc_P182_J322_map_sharp.mrc 0 as #2.1, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 1 as #2.2, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  

> hide #1 models

> hide #!2.1 models

> volume #2.2 level 0.22

> show #!4 models

> hide #!2 models

> color zone #4 near #1 distance 2

> volume splitbyzone #4

Opened cryosparc_P182_J322_map_sharp.mrc 0 as #5.1, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 1 as #5.2, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  

> hide #!5 models

> show #!4 models

> color zone #4 near #1 distance 1.5

> volume splitbyzone #4

Opened cryosparc_P182_J322_map_sharp.mrc 0 as #6.1, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 1 as #6.2, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  

> hide #!6.1 models

> show #1 models

> select #6.2

2 models selected  

> color sel grey

> select clear

> transparency #6.2.1 50

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> help help:user

> close #6

> close #5

> show #!4 models

> color #4 grey

> transparency #4.1 50

> color zone #4 near #1 distance 2

> close #2

> volume splitbyzone #4 onGrid #4

Expected fewer arguments  

> volume splitbyzone #4

Opened cryosparc_P182_J322_map_sharp.mrc 0 as #2.1, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 1 as #2.2, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  

> hide #!2.1 models

> select #2.2

2 models selected  

> color sel grey

> select clear

> transparency #2.2.1 50

> volume resample #2.2 onGrid #4

Opened cryosparc_P182_J322_map_sharp.mrc 1 resampled as #5, grid size
400,400,400, pixel 0.98, shown at step 1, values float32  

> save cryosparc_P182_J322_colorzone_2.mrc #5

> close #5

> open cryosparc_P182_J322_colorzone_2.mrc

Opened cryosparc_P182_J322_colorzone_2.mrc as #5, grid size 400,400,400, pixel
0.98, shown at level 0.000135, step 2, values float32  

> select #5

2 models selected  

> color sel grey

> select clear

> transparency #5.1 50

> volume #5 step 1

> volume #5 level 0.2774

> volume #5 level 0.25

> show #!4 models

> save chimerax.cxs

——— End of log from Sat May 22 13:34:06 2021 ———

opened ChimeraX session  

> close #3

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

> hide #!2 models

> hide #!5 models

> color #4 grey

> transparency #4.1 50

> color zone #4 near #1 distance 3

> volume splitbymap #4

Expected a density maps specifier or a keyword  

> volume splitbyzone #4

Opened cryosparc_P182_J322_map_sharp.mrc 0 as #3.1, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  
Opened cryosparc_P182_J322_map_sharp.mrc 1 as #3.2, grid size 400,400,400,
pixel 0.98, shown at level 0.25, step 1, values float32  

> hide #!3.1 models

> volume resample #3.2 onGrid #4

Opened cryosparc_P182_J322_map_sharp.mrc 1 resampled as #6, grid size
400,400,400, pixel 0.98, shown at step 1, values float32  

> save cryosparc_P182_J322_colorzone_3.mrc #6

> close #6

> open cryosparc_P182_J322_colorzone_3.mrc

Opened cryosparc_P182_J322_colorzone_3.mrc as #6, grid size 400,400,400, pixel
0.98, shown at level 0.000148, step 2, values float32  

> volume #6 step 1

> volume #6 level 0.2

> volume #6 level 0.25

> color #6 light blue

> color #6 medium blue

> color #6 blue

> color #6 royal blue

> color #6 dodger blue

> transparency #6.1 50

> hide #!3 models

> close #2-3

> save chimerax.cxs

——— End of log from Sat May 22 18:47:25 2021 ———

opened ChimeraX session  

> show #!4 models

> hide #!6 models

> select #4

2 models selected  

> color sel grey

> ~select #4

Nothing selected  

> transparency #4.1 50

> volume #4 level 0.3

> volume #4 level 0.35

> volume #4 level 0.4

> volume #4 level 0.45

> select #1

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> color sel bychain

> select clear

> view

> help help:user

> open
> /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan/local_refinement/cryosparc_P182_J525_map_sharp.mrc

Opened cryosparc_P182_J525_map_sharp.mrc as #2, grid size 400,400,400, pixel
0.98, shown at level 0.0854, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.2367

> hide #!4 models

> volume #2 level 0.25

> volume #2 level 0.3

> volume #2 level 0.4

> volume #2 level 0.45

> transparency #2.1 50

> hide #1 models

> show #!4 models

> select #2

2 models selected  

> color #2.1 cornflower blue

> select clear

> ui tool show "Fit in Map"

Fit map cryosparc_P182_J525_map_sharp.mrc in map
cryosparc_P182_J322_map_sharp.mrc using 54292 points  
correlation = 0.975, correlation about mean = 0.7846, overlap = 2.597e+04  
steps = 56, shift = 1.5, angle = 0.186 degrees  
  
Position of cryosparc_P182_J525_map_sharp.mrc (#2) relative to
cryosparc_P182_J322_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999476 -0.00323832 0.00002353 0.62177748  
0.00323832 0.99999476 -0.00003160 -0.61744297  
-0.00002343 0.00003167 1.00000000 -1.50424518  
Axis 0.00976856 0.00725039 0.99992600  
Axis point 187.62120199 196.23473434 0.00000000  
Rotation angle (degrees) 0.18555626  
Shift along axis -1.50253670  
  

> view

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!4 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #1 models

> volume #2 level 0.6953

> show #!4 models

> volume #2 level 0.4447

> ui tool show "Side View"

> volume #2 level 0.45

> select #1/k

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 1049 atom styles  

> color sel byhetero

> select clear

> select #1/k

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> hide sel cartoons

> select clear

> hide #!4 models

> volume #!2 style mesh

> volume #!2 step 1

> select #2

2 models selected  

> color sel dodger blue

> select clear

> volume #2 level 0.5684

> view

> view

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

——— End of log from Sun May 23 18:08:30 2021 ———

opened ChimeraX session  

> open
> /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan/Cav1_11mer_refined_final_014.pdb

Chain information for Cav1_11mer_refined_final_014.pdb #3  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> select #3

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #!2 models

> align #1 toAtoms #3 matchChainIds true reportMatrix true

Alignment matrix in structure Cav1_11mer_real_space_refined_043.pdb
coordinates  
Matrix rotation and translation  
0.99999913 0.00131674 -0.00002600 -0.26585113  
-0.00131674 0.99999913 -0.00006839 0.22377860  
0.00002591 0.00006842 1.00000000 1.43343055  
Axis 0.05187142 -0.01967964 -0.99845985  
Axis point 148.19058053 144.90059807 0.00000000  
Rotation angle (degrees) 0.07556006  
Shift along axis -1.44941680  
  
RMSD between 11539 atom pairs is 0.884 angstroms  

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> select #3/k:118-151

285 atoms, 294 bonds, 34 residues, 1 model selected  

> setattr #3/k:118-151 res ss_type 1

Assigning ss_type attribute to 34 items  

> setattr #3/k:117-152 res ss_type 1

Assigning ss_type attribute to 36 items  

> select #3/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> select clear

> open Cav1_chain_A.pdb

Summary of feedback from opening Cav1_chain_A.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 37 37 SER I
149 VAL I 155 1 7  
Start residue of secondary structure not found: HELIX 38 38 LEU I 159 LYS I
165 1 7  
Start residue of secondary structure not found: HELIX 39 39 THR J 90 TYR J 100
1 11  
Start residue of secondary structure not found: HELIX 40 40 PRO J 110 ILE J
117 1 8  
Start residue of secondary structure not found: HELIX 41 41 VAL J 152 VAL J
155 1 4  
47 messages similar to the above omitted  
  
Chain information for Cav1_chain_A.pdb #5  
---  
Chain | Description  
A | No description available  
  

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hide #5 models

> show #!2 models

> view

> show #!4 models

> select #4

4 models selected  

> volume sel style mesh

> transparency sel 0

> transparency sel 50

> select clear

> show #3 models

> hide #!4 models

> volume #2 level 0.6

> volume #2 level 0.65

> hide #!2 models

> show #5 models

> hide #3 models

> view

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:81

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #5/A:81-90

83 atoms, 86 bonds, 10 residues, 1 model selected  

> setattr #3/k:81-90 res ss_type 1

Assigning ss_type attribute to 10 items  

> show #3 models

> ui mousemode right select

> select clear

> hide #5 models

> setattr #3/a:81-90 res ss_type 1

Assigning ss_type attribute to 10 items  

> setattr #3/a:81-91 res ss_type 1

Assigning ss_type attribute to 11 items  

> select #5/A:105

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #5/A:105-109

36 atoms, 36 bonds, 5 residues, 1 model selected  

> select #5/A:104

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #5/A:104-110

49 atoms, 50 bonds, 7 residues, 1 model selected  

> setattr #3/a:104-110 res ss_type 1

Assigning ss_type attribute to 7 items  

> setattr #3/a:103-106 res ss_type 1

Assigning ss_type attribute to 4 items  

> select #5/A:170

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:170-176

60 atoms, 59 bonds, 7 residues, 1 model selected  

> select #5

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> ~select #5

Nothing selected  

> select #5/A:169-176

68 atoms, 67 bonds, 8 residues, 1 model selected  

> select #5/A:170

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:170-176

60 atoms, 59 bonds, 7 residues, 1 model selected  

> show #5 models

> hide #3 models

> select #5/A:170

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:170-176

60 atoms, 59 bonds, 7 residues, 1 model selected  

> select #5/A:91

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:91-117

228 atoms, 237 bonds, 27 residues, 1 model selected  

> show #3 models

> select #5

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> hide #5 models

> setattr #3/a:91-117 res ss_type 1

Assigning ss_type attribute to 27 items  

> ~select #5

Nothing selected  

> select #3/a:91-117

228 atoms, 237 bonds, 27 residues, 1 model selected  

> select #5/A:81

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #5/A:81-117

311 atoms, 324 bonds, 37 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:81

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #3/A:81-117

311 atoms, 324 bonds, 37 residues, 1 model selected  

> select #3/a:81-175

785 atoms, 812 bonds, 95 residues, 1 model selected  

> select #3/a:91-165

618 atoms, 640 bonds, 75 residues, 1 model selected  

> select #3/a:81-165

701 atoms, 727 bonds, 85 residues, 1 model selected  

> select up

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> select clear

> setattr #3/a:81-165 res ss_type 1

Assigning ss_type attribute to 85 items  

> setattr
> #3/b:81-165/c:81-165/d:81-165/e:81-165/f:81-165/g:81-165/h:81-165/i:81-165/j:81-165/k:81-165
> res ss_type 1

Assigning ss_type attribute to 850 items  

> view

> show #!2 models

> volume #2 level 0.55

> volume #2 level 0.6

> volume #!2 style surface

> volume #2 level 0.5

> volume #2 level 0.4

> ui tool show "Side View"

> volume #2 level 0.35

> volume #2 level 0.3

> volume #2 level 0.4

> view

> hide #!2 models

> view

> show #!2 models

> volume #2 level 0.45

> hide #3 models

> volume #2 level 0.4

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> view

> save Cav1_11mer_refined_final_014_1.pdb #3

> close #3

> open Cav1_11mer_refined_final_014.pdb

Chain information for Cav1_11mer_refined_final_014.pdb #3  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> hide #3 atoms

> show #3 cartoons

> show #!2 models

> volume #2 level 0.35

> volume #2 level 0.3

> view

> view

> view orient

> view

> volume #!2 style mesh

> volume #2 level 0.45

> select #3

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 11539 atom styles  

> hide sel atoms

> select #3/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> show sel atoms

> color sel yellow

> hide sel cartoons

> color sel byhetero

> select clear

> select #3/b/c/d/e/f/g/h/i/j/k

10490 atoms, 10810 bonds, 1280 residues, 1 model selected  

> hide sel cartoons

> select #3/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> color sel grey

> color zone #3 near sel distance 2

> volume #!2 style surface

> name frozen chaina sel

> color zone #3 near chaina distance 2

> show sel cartoons

> hide sel atoms

> color zone #2 near chaina distance 2

> color zone #2 near chaina distance 3

> view

> volume splitbyzone #2

Opened cryosparc_P182_J525_map_sharp.mrc 0 as #6.1, grid size 400,400,400,
pixel 0.98, shown at level 0.45, step 1, values float32  
Opened cryosparc_P182_J525_map_sharp.mrc 1 as #6.2, grid size 400,400,400,
pixel 0.98, shown at level 0.45, step 1, values float32  

> select #3

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> ~select #3

Nothing selected  

> hide #!6.2 models

> show #!6.2 models

> hide #!6.1 models

> view

> transparency #6.2.1 50

> volume #!6.2 style mesh

> select #3/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> color sel yellow

> show sel atoms

> hide sel cartoons

> color sel byhetero

> select #2

2 models selected  

> color sel blue

> select #6.2

2 models selected  

> color sel blue

> select clear

> color sel dodger blue

> select #6.2

2 models selected  

> color sel dodger blue

> select clear

> hide #3 models

> volume #6.2 level 0.5

> volume #6.2 level 0.6

> show #3 models

> select #3/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> show sel cartoons

> select clear

> volume #6.2 level 0.5

> volume #6.2 level 0.45

> show #1 models

> show #!2 models

> select #2

2 models selected  

> color sel dodger blue

> transparency sel 50

> ~select #2

Nothing selected  

> hide #3 models

> show #3 models

> close #1

> show #5 models

> hide #5 models

> show #5 models

> hide #!2 models

> show #!2 models

> hide #3 models

> setattr #5/a:81-165 ss_type 1

Missing or invalid "attrValue" argument: Expected a text string  

> setattr #5/a:81-165 res ss_type 1

Assigning ss_type attribute to 85 items  

> setattr #5/a:169-176 res ss_type 2

Assigning ss_type attribute to 8 items  

> view

> hide #!2 models

> view

> select #5

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> color yellow\

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color yellow

> select #6.2

2 models selected  

> color sel dodger blue

> select clear

> select #5

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> select clear

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> volume #6.2 level 0.4

> view

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for Cav1_11mer_refined_final_014.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F 1.2/G 1.2/H 1.2/I 1.2/J 1.2/K | No
description available  
  
Done loading forcefield  
Chain information for Cav1_chain_A.pdb  
---  
Chain | Description  
3.2/A | No description available  
  
Opened cryosparc_P182_J525_map_sharp.mrc 1 as #3.1.1.1, grid size 400,400,400,
pixel 0.98, shown at step 1, values float32  

> volume #3.1.1.1 level 0.5

> volume #3.1.1.1 level 0.45

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> show #!1.2 models

> hide #!1.2 models

Opened cryosparc_P182_J322_map_sharp.mrc as #3.1.1.2, grid size 400,400,400,
pixel 0.98, shown at step 1, values float32  

> close #1

> close #3.1

> close #3

> close #2

> view

> show #!6.1 models

> close #6#6.1

> open
> /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan/local_refinement/cryosparc_P182_J525_map_sharp.mrc
> /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan/Cav1_11mer_real_space_refined_043.pdb

Opened cryosparc_P182_J525_map_sharp.mrc as #1, grid size 400,400,400, pixel
0.98, shown at level 0.0854, step 2, values float32  
Chain information for Cav1_11mer_real_space_refined_043.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  
Chain information for Cav1_11mer_real_space_refined_043.pdb  
---  
Chain | Description  
2.2/A 2.2/B 2.2/C 2.2/D 2.2/E 2.2/F 2.2/G 2.2/H 2.2/I 2.2/J 2.2/K | No
description available  
  

> volume #1 level 0.323

> volume #1 step 1

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> view

> transparency 50

> close

> open
> /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan/local_refinement/cryosparc_P182_J525_map_sharp.mrc
> /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan/Cav1_11mer_real_space_refined_043.pdb

Opened cryosparc_P182_J525_map_sharp.mrc as #1, grid size 400,400,400, pixel
0.98, shown at level 0.0854, step 2, values float32  
Chain information for Cav1_11mer_real_space_refined_043.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> volume #1 level 0.2382

> hide #2 models

> volume #1 step 1

> transparency 50

> view

> volume #1 level 0.4

> volume #1 level 0.5

> volume #1 level 0.45

> volume #1 level 0.4

> show #2 models

> hide atoms

> show cartoons

> close #2

> open Cav1_11mer_refined_final_014.pdb

Chain information for Cav1_11mer_refined_final_014.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> select #2

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> color zone #1 near sel distance 3

> volume splitbyzone #1

Opened cryosparc_P182_J525_map_sharp.mrc 0 as #3.1, grid size 400,400,400,
pixel 0.98, shown at level 0.4, step 1, values float32  
Opened cryosparc_P182_J525_map_sharp.mrc 1 as #3.2, grid size 400,400,400,
pixel 0.98, shown at level 0.4, step 1, values float32  

> select #2

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> ~select #2

Nothing selected  

> hide #!3.1 models

> transparency #3.2.1 50

> select #3.2

2 models selected  

> color sel dodger blue

> transparency sel 0

> transparency sel 50

> volume sel style mesh

> select clear

> select #2/a

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> save cav1_chain_a.pdb selectedOnly

Missing "selectedOnly" keyword's argument  

> save cav1_chain_a.pdb selectOnly

Expected a models specifier or a keyword  

> save cav1_chain_a.pdb selectOnly #2

Expected a models specifier or a keyword  

> close #2

Undo failed, probably because structures have been modified.  

> open Cav1_11mer_refined_final_014.pdb

Chain information for Cav1_11mer_refined_final_014.pdb #2  
---  
Chain | Description  
A B C D E F G H I J K | No description available  
  

> select #2

11539 atoms, 11891 bonds, 1408 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> open Cav1_chain_a.pdb

Summary of feedback from opening Cav1_chain_a.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 9 9 PHE B 81
THR B 90 1 10  
Start residue of secondary structure not found: HELIX 10 10 THR B 91 SER B 104
1 14  
Start residue of secondary structure not found: HELIX 11 11 ALA B 105 ILE B
109 1 5  
Start residue of secondary structure not found: HELIX 12 12 PRO B 110 ILE B
117 1 8  
Start residue of secondary structure not found: HELIX 13 13 TYR B 118 TYR B
148 1 31  
89 messages similar to the above omitted  
  
Chain information for Cav1_chain_a.pdb #4  
---  
Chain | Description  
A | No description available  
  

> hide #2 models

> view orient

> select #4

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> color sel yellow

> show sel stick

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show sel atoms

> color sel byhetero

> select clear

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> volume #3.2 level 0.3403

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax.cxs

——— End of log from Sun May 30 22:22:03 2021 ———

opened ChimeraX session  

> volume resample #3.2 onGrid #1

Opened cryosparc_P182_J525_map_sharp.mrc 1 resampled as #5, grid size
400,400,400, pixel 0.98, shown at step 1, values float32  

> hide #!3 models

> save cryosparc_P182_J525_chain_A.mrc #5

> save Cav1_chain_a.pdb #4

> open cryosparc_P182_J525_chain_A.mrc

Opened cryosparc_P182_J525_chain_A.mrc as #6, grid size 400,400,400, pixel
0.98, shown at level 0.000208, step 2, values float32  

> close #3

> volume #6 step 1

> volume #6 level 0.45

> close #1

> close #2

> select #6

2 models selected  

> color sel dodger blue

> ui mousemode right select

> select clear

> transparency 50

> close #5

> volume style mesh

> select #6

2 models selected  

> hide sel cartoons

> select #4

1049 atoms, 1081 bonds, 128 residues, 1 model selected  

> hide sel cartoons

> select clear

> view

> pwd

Current working directory is: /Users/jporta/Desktop/Cav1/Cav1_Myc/Erkan  

> save chimerax_isolde.cxs

——— End of log from Sun May 30 23:08:48 2021 ———

opened ChimeraX session  

> clipper associate #4 toModel #6

Invalid "toModel" argument: Must specify 1 structure, got 0 for "#6"  

> clipper associate #6 toModel #4

Opened cryosparc_P182_J525_chain_A.mrc as #1.1.1.1, grid size 400,400,400,
pixel 0.98, shown at level 0.621, step 1, values float32  
Drag select of 7 residues  

> select clear

> select clear

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> volume #1.1.1.1 level 0.598

> isolde start

> set selectionWidth 4

Done loading forcefield  

> select clear

> select clear

> open cryosparc_P182_J322_chain_A.mrc

No such file/path: cryosparc_P182_J322_chain_A.mrc  

> open cryosparc_P182_J525_chain_A.mrc as #2

'as' has no suffix  

> open cryosparc_P182_J525_chain_A.mrc

Opened cryosparc_P182_J525_chain_A.mrc as #2, grid size 400,400,400, pixel
0.98, shown at level 0.000208, step 2, values float32  

> volume #2 step 1

> select #2

2 models selected  

> volume #2 level 0.5

> color sel dodger blue

> select clear

> transparency 50

> volume style mesh

Opened cryosparc_P182_J525_chain_A.mrc as #1.1.1.2, grid size 400,400,400,
pixel 0.98, shown at step 1, values float32  

> open cryosparc_P182_J525_chain_A.mrc

Opened cryosparc_P182_J525_chain_A.mrc as #2, grid size 400,400,400, pixel
0.98, shown at level 0.000208, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.5

> select #2

2 models selected  

> color sel dodger blue

> select clear

> transparency 0

> transparency 50

> volume style mesh

ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to Cav1_chain_a.pdb #1.2  
---  
notes | No usable SEQRES records for Cav1_chain_a.pdb (#1.2) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ILE 49  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 176  
34 hydrogen bonds  
/A LYS 176 is not terminus, removing H atom from 'C'  
1055 hydrogens added  
  
Traceback (most recent call last):  
File "/Users/jporta/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2265, in _flip_peptide_bond  
self.flip_peptide_bond(res)  
File "/Users/jporta/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 3257, in flip_peptide_bond  
pf = Peptide_Bond_Flipper(self, res)  
File "/Users/jporta/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/manipulations/peptide_flip.py", line 44, in __init__  
raise TypeError('Simulation must be running!')  
TypeError: Simulation must be running!  
  
TypeError: Simulation must be running!  
  
File "/Users/jporta/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/manipulations/peptide_flip.py", line 44, in __init__  
raise TypeError('Simulation must be running!')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.21
OpenGL renderer: AMD Radeon Pro 575 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Intel Core i5
      Processor Speed: 3.5 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 32 GB
      Boot ROM Version: 180.0.0.0.0
      SMC Version (system): 2.41f1

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G3020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 10:04

Graphics/Displays:

    Radeon Pro 575:

      Chipset Model: Radeon Pro 575
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c4
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1P-025
      EFI Driver Version: 01.00.931
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (3)

comment:1 by Tristan Croll, 4 years ago

Platform: → all
Project: → ChimeraX

Hmm... now how did that get broken? Thanks for reporting - will look into it.

comment:2 by pett, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Status: new → assigned
Summary: ChimeraX bug report submission → Peptide flip: Simulation must be running!

comment:3 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

This was effectively fixed by ISOLDE's new GUI, which replaces essentially all that old code. Neglected to close out the ticket at the time, though.

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