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. ;-) Regards, Tom -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Tuesday, August 18, 2009 3:08 PM To: tomguu@rice.edu Cc: chimera-users@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: <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