[Chimera-users] Save session for movie

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 27 12:57:33 PDT 2010

Hi Francesco,

On Apr 19, 2010, at 12:29 AM, Francesco Pietra wrote:

> If at all, I did not understand if a continuous trace of the centroid
> (instead of a series of balls) can be obtained in the context of the
> protein. That would improve the presentation further. Otherwise, the
> series of balls for the centroid, with appropriate choice of radius
> and step size, shows the pathway of the ligand through the protein
> adequately.

Nothing simple comes to mind.  One way that's a bit of work would be  
to save the centroid information to a file (the 'Save' button on the  
Axes/Planes/Centroids interface) and the use a text editor to create a  
BILD file (BILD format) showing lines/cylinders connecting the  
centroid centers.

> As a minor point, I was unable to render helices transparent.
> Transparency would help to to see the centroid trajectory in between
> helices.

Should be possible unless there's something wrong with your graphics  
cards.  Try this:

Select->Structure->secondary structure->helix
Actions->Color->from editor

This will bring up a color editor.  Try making a transparent red.  For  
me, the editor looks like this when I do that:

(note the "Opacity" box is checked)

and the structure looks like this:


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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