problems with "resfit" in 2017 movie-making tutorial

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-21)
Description
problems with "resfit" in 2017 movie-making tutorial

using the click-to-execute links in
http://www.rbvi.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html

there are other things in this tutorial that need updating for a few syntax changes, but the "resfit" problems appear to be bugs:  besides the traceback in log, there seems to be problem positioning the residues in the window (or maybe another symptom of same problem), see attached movie from following tutorial instructions

Log:
UCSF ChimeraX version: 0.9 (2019-05-21)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open //www.cgl.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html
fromDatabase http

Opened http://www.cgl.ucsf.edu/chimera/data/wcpcw-mar2017/moviemaking.html  

> open 3gbp

3gbp title:  
Structure of the periplasmic glucose/galactose receptor of salmonella
typhimurium [more info...]  
  
Chain information for 3gbp #1  
---  
Chain | Description  
A | galactose-binding protein  
  
Non-standard residues in 3gbp #1  
---  
BGC — β-D-glucose  
CA — calcium ion  
  
  

> ks vd

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/meng/Desktop/movie3.mp4

Movie saved to /Users/meng/Desktop/movie3.mp4  
  

> hide ribbons

> show selAtoms ribbons

> ks hr

> hide selAtoms ribbons

> select zone :309 10 extend true

Selected 215 atoms  

> ks ha

> hide selAtoms

> select ligand

24 atoms, 24 bonds selected  

> ks sp

> style selAtoms sphere

Changed 24 atom styles  

> color ligand & C pink

> select clear

> cofr ligand

> turn y 0.5 rock 100

> stop

> open 3gbp fromDatabase eds

Summary of feedback from opening 3gbp fetched from eds  
---  
note | Fetching map 3gbp from
http://www.ebi.ac.uk/pdbe/coordinates/files/3gbp.ccp4  
  
Opened 3gbp.ccp4, grid size 97,68,86, pixel 0.787,0.777,0.802, shown at level
1.02, step 1, values float32  

> volume #2 level 0.5

Expected a keyword  
Expected a keyword  

> surface zone #2 nearAtoms ligand distance 8

> style ligand ball

Changed 24 atom styles  

> resfit #1 map #2

> resfit #1 map #2

> movie record

> movie encode /Users/meng/Desktop/resfit.mp4 framerate 25.0

Movie saved to /Users/meng/Desktop/resfit.mp4  
  

> close #2

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/residue_fit/tool.py", line 90, in models_closed_cb  
self.delete()  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/residue_fit/tool.py", line 102, in delete  
self._label.delete()  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 226, in delete  
session_labels(s).delete(self)  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 156, in delete  
del self.labels[label.name]  
KeyError: 'resfit'  
  
Error processing trigger "remove models": 'resfit':  
KeyError: 'resfit'  
  
File
"/Users/meng/Desktop/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 156, in delete  
del self.labels[label.name]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.
File attachment: resfit.mp4

resfit.mp4​

[Elaine Meng]

Added by email2trac

[Tom Goddard]

The traceback happens when running "resfit #1 map #2" twice creating two sliders. It was creating a single label that showed the residue number and when closing the map, both sliders tried to close the same label. No doubt creating two sliders was an accident. I made each slider create its own label fixing this error.

More serious issue is that movie record with resfit slider does not align residues correctly although they do get aligned correctly when not recording. Will look into that.

[Tom Goddard]

Fixed resfit movie recording. It was trying to do interpolated motion between consecutive residues when movie record is supposed to simply jump from one residue to the next.

[Elaine Meng]

Thanks, the residue positioning in the movie looks good now. The movie playback seems like it might be too fast to assess the fits, but perhaps that’s an intentional balance vs. not making the whole movie too long.

[goddard@…]

He idea of the movie is you hand scrub through it with a scrollbar to see whatever residue you want.  There is only one frame per residue.  But I’ll look at changing playback rate to maybe 2 frames per second.

[Tom Goddard]

I made resfit command default movie encoding playback frame rate be two frames per second.