[Chimera-users] surftransparency

[Elaine Meng]

Hi Tom,
It depends what version of Chimera you are using.  In older versions  
it only works for molecular surfaces.  In newer versions (daily builds  
from late June 2009 onwards) it works for the kind of surface you have  
and has a "frames" argument for scripting gradual changes.

You might be looking at documentation that is not synchronized with  
your download. If you use the Help menu or "help" command, that will  
show documentation that goes with your downloaded version.  If you go  
to the Web, it may be for a totally different version.

It should work if you have a daily build from sometime in the last  
several weeks.  Here is the latest documentation:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surftransparency.html 
 >

You would just specify your surface by model number, for example  
"surftrans 100 #0 120" (change transparency of surface model #0 to  
completely transparent over 120 frames).

Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Aug 14, 2009, at 2:17 PM, Tom Guu wrote:

> Hi,
>
> I am trying to use the surftransparecy function on a EM-map  
> (surface), and don't seem to be able to get it to work.  I read on  
> the documentation page, is this command specific for atoms and not  
> for an entire EM map?  I know I can use show or hide for displaying  
> EM map, just wonder what other command can make the EM map gradually  
> disappear or appear.  Thanks a bunch.
>
> Regards,
> Tom