[Chimera-users] ESP surface, DelphiController

[Elaine Meng]

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 at 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