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: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html You'll need a Chimera daily build to use this command: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom 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