[Chimera-users] thanks

Tom Guu tomguu at rice.edu
Tue Aug 18 13:19:00 PDT 2009

Hi Elaine,

Thanks for both replies (last Friday and today).  You and Tom Goddard are
"life-saver," considering I had no prior knowledge on how to make
animations.  I am forever grateful for y'all's help.  I eventually got the
animations to work, at least for what I intended to show on the defense
(things like zoom in, rocking, turning, etc).  I LOVE chimera, and have so
much appreciation for UCSF crew, who put in so much effort to make this
terrific program.  I will try out the surftransparency a bit later to see if
the gradually disappearing command would work on our machine (well, instant
disppearing of the EM map works, just not as cool).  Again, thanks a bunch.


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, August 18, 2009 3:08 PM
To: tomguu at rice.edu
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] surftransparency

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:

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).

Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of
Pharmaceutical Chemistry University of California, San Francisco

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

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