[Chimera-users] Movie Question

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 15 13:21:57 PDT 2006

Hi Jared,
You can make multiple models rotate about their own individual centers 
with the command "set independent" - I should probably add that to the 
movie commands list, thanks for the nudge.  A related command you may 
also be interested in is "select" (the old function, selection for 
motion).  Man pages for all these commands I mention can be accessed 
from here:

We are planning to add more/better transitioning commands for movies, 
but Chimera is currently rather limited in that respect. If you are 
using Chimera commands, there are some icky ways for fading things 
in/out that involve repeating a command many times because a "frames" 
argument is not available:
(1) the command "surftransparency" adjusts molecular surface (not 
volume surface) transparency. You can repeatedly use it to gradually 
make something 100% transparent.
(2) the command "colordef" allows you to define your own colors and 
includes a transparency value.  If you color something your new color, 
then you can repeatedly use colordef to redefine that color as more and 
more transparent. This would be rather painful for fading out 
multicolored things.

The programmers among my colleagues may be able to generate Python 
scripts that would be much less icky.

Finally, there are some experimental features of Chimera that can be 
downloaded separately from this page:

Look in this page for the one called "Animation Commands."  I suspect 
it does not have everything you need, but some of these may be of 
Vary volume data contour level. Make multiscale protein surfaces fly 
away radially. Smoothly change radius in icosahedral surface tool.

I hope this helps,

On Sep 15, 2006, at 12:56 PM, Jared Godar wrote:

> Hello there,
> I have a few technical questions about a movie I am trying to make 
> with chimera.
> I have PDB files for three predicted structural elements of a larger 
> protein whose structure my lab is resolving through cryo EM.  I've 
> converted these PDB files to MRC's of the desired resolution we are 
> trying to obtain with the reconstruction.  In an effort to produce 
> animation which highlights structural elements of these three 
> subdomains, I have encountered a couple difficulties translation the 
> movie I envision through Chimera.
> I would like to start with the three subunits spaced across the X axis 
> and rotating about the central y axis of each subunit. Then, one at a 
> time, have a single unit grow and translate to the center, then while 
> the other two subunits fade away, then return to it's original 
> position.
> I've been able to script this type of motion for each of the 
> individual subunits, but I hit a problem when I try to incorporate all 
> three.
> 	• 	Is there a way to have multiple proteins roll about their own 
> respective y axis instead of orbiting about the central y axis of the 
> scene?
> 	• 	Is there a way to selectively show / hide (fade over specified 
> number of frames) PDB's or MRC's like you can show / hide / fade text?
> Thank you in advance for your help.
> -Jared
> -- 
> Jared A. Godar
> Graduate Student: Stewart Lab
> Vanderbilt University Medical Center
> Molecular Physiology & Biophysics Dept.
> Light Hall 708
> Work: 615.322.7898
> Fax:   615.322.7236_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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