[PyMOL] mrock questions

[john l. <joh...@uc...>]

I have been trying to make a movie using the eMovie plugin. I have  
run into two problems with the util.mrock function:

1) I want to show a difference in conformation when a ligand binds.  
To do this I want to have both bound and unbound PDBs loaded with  
unbound displayed and bound hidden, and fade in the bound structure.  
I have been doing this by setting the transparency of the bound  
structure to 1 ("fading" in eMovie) until the frame I want it to  
appear in and fading from 0-100% over 5 frames or so (perhaps this is  
not the best way?). However, I want to fade into a rocking picture.  
If I execute the command "util.mrock(start-frame,end-frame,,,) I find  
that the bound structure will not fade in unless it is outside the  
mrock frame window--i.e. unless it is stationary. Is there any way  
around this? Is there a better way to fade in structures that can be  
ordered while the mrock command is active?

2) Is there a way to specify the speed at which the molecule rocks?  
It seems like it simply rocks at a speed that will make one full  
motion over the frame length specified, resulting in different  
rocking rates over the course of the movie.

JD Laughlin
University of Colorado Denver