On Sep 1, 2008, at 9:14 AM, James Fethiere wrote:

Once the .dx file is loaded in Chimera, I get a nice ESP map. However, it seems sensitive!! how? well, when I color the surface of a transcription factor bound to DNA (1DH3) according to the dx ESP loaded file, it's nice. But when I display the ribbons of the bound DNA in the same model and color these ribbons, the previous surface reverts to the default Chimera colors and I loose the ESP from the dx file. Quite strange no?

Hi James, The reason is that the surface cannot have "custom" colors (e.g. ESP coloring) and coloring to match the underlying atoms at the same time, even in different areas of the surface. If you make sure to color only ribbon and not surface, the surface should stay ESP-colored. If you are using the Actions... Color menu, make sure to check only "ribbons" as what will be colored, color the ribbons, and then change it back to the default "all of the above" coloring targets. If you are using a command, then something like color red,r :30-50 specifies coloring ribbons only (the ",r" part). The alternative is to do all the ribbon/atom coloring first, ESP-color the surface last.

It is also not possible to select this dx ESP file in a command file to make a movie. And if it is displayed before movie record starts, I get a black frame movie with the avi encoding (yes I did modify the video acceleration in media player). So I guess it will be still pictures. Check out the session attached.

What are you trying to do with the surface in this movie (why are you trying to select or specify it?). Most command-line selections are based on specifying a set of atoms, so you would just specify the atoms associated with the molecular surface. However, I would need to know which commands you are trying to use to be more specific/ concrete, or let you know if what you want to do is possible with commands.

Thanks

James

I am unable to deal with that attached session because it is just shown as a zillion lines of text beneath the mail message. My cut- paste attempts failed. You could instead use Help... Report a Bug and attach the session to it to illustrate the black movie problem. We may or may not be able to reproduce it, but having the session (and perhaps also your movie script?) would help. It may only let you attach one thing, so I'd say attach the session and put the script (or some short version that exhibits the problem) as part of the message text. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu 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