[Chimera-users] Morph surfaces

Thomas Goddard goddard at cgl.ucsf.edu
Wed Apr 23 15:17:56 PDT 2008

Hi Craig,

   You can make a low resolution surface from atomic coordinates using 
the new molmap Chimera command (added in January 2008).  You can create 
such a surface for each frame of your morph using the MD Movie dialog 
menu entry Per-Frame / Define Script.  If your morph is model #2 the 
script would look like:

	molmap #2 8.5

where 8.5 is the desired resolution in Angstroms.  To produce a smoother 
surface, to color it (transparent red), and to set the volume step size 
(the surface is a contour surface of a map computed from the molecule) 
the script would look like

	molmap #2 8.5 gridSpacing 1.5
	volume #2 color 1,0,0,.5 step 1

The color spec is red,green,blue,opacity.  The molmap command replaces a 
previous map for the molecule by default so the surfaces will not 
accumulate.  More details on the molmap command are in the Chimera manual:


You'll need a Chimera daily build to use this command:



Craig Yoshioka wrote:
> Hi Dr. Goddard,
> I'm Craig, a graduate student in Clint and Bridget's lab at Scripps.  I 
> am trying to use Chimera to put together an animation movie.  I have 
> fitted a couple of crystal structures into different EM maps and have 
> used the Morph Conformations to interpolate between them (excellent 
> btw).  I want to do the animation using surfaces though, and have not 
> found a satisfactory way to do so.  The surfacing command under the 
> actions menu seems to fail half the time, but provides far too detailed 
> a surface for this animation anyways.  I really like the flexibility of 
> the surfacing used by the multi-scale model window (letting you set the 
> "resolution", etc.) but this surface does not update with the morph 
> conformations animation.  I have taken to saving the morph conformations 
> pdb to the disk as all frames, and reopening it to get access to all the 
> intermediate PDBs.  I then using multi-scale surfacing on this to 
> generate a large series of surfaces, and I generate the animation by 
> switching them on and off in series.  This is, of course, very time 
> consuming.  Is there a way for me to switch the algorithm used by the 
> surfacing in the actions menu to use the multi-scale models surfacing 
> instead?  That way the animation would be much easier.
> thanks for your help,
> -Craig

More information about the Chimera-users mailing list