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
Hi Craig,
the script would look like
molmap #2 8.5 gridSpacing 1.5 volume #2 color 1,0,0,.5 step 1
You might want to string those two commands together on the same line, separated by a semicolon, to avoid display of the intermediate state (before you colored the surface red). I haven't tried doing that inside a per-frame script, but as far as I know it would work! Elaine
On Apr 23, 2008, at 3:26 PM, Elaine Meng wrote:
Hi Craig,
the script would look like
molmap #2 8.5 gridSpacing 1.5 volume #2 color 1,0,0,.5 step 1
You might want to string those two commands together on the same line, separated by a semicolon, to avoid display of the intermediate state (before you colored the surface red).
You don't need to put them on the same line. The MD Movie tool executes these scripts as if they were being handled by the 'read' command (no display updates between commands) rather than the 'source' command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Thanks, is there a way I can specify different chains as separate maps using molmap? I'm trying to create three distinctly colored regions, one semi-transparent. Chimera is fantastic software, btw. Thanks to all of you. On Apr 23, 2008, at 3:40 PM, Eric Pettersen wrote:
On Apr 23, 2008, at 3:26 PM, Elaine Meng wrote:
Hi Craig,
the script would look like
molmap #2 8.5 gridSpacing 1.5 volume #2 color 1,0,0,.5 step 1
You might want to string those two commands together on the same line, separated by a semicolon, to avoid display of the intermediate state (before you colored the surface red).
You don't need to put them on the same line. The MD Movie tool executes these scripts as if they were being handled by the 'read' command (no display updates between commands) rather than the 'source' command.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Craig, You can create a surface for a chain or any set of atoms. You just need to specify the atoms in the molmap command. To specify chain B of model 2 (model numbers are shown using Favorites / Model Panel) use: molmap #2:.B 8.5 Any set of atoms can be specified using more complex atom specifier text as described in the manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html For only residues 10 through 50 of chain A use: molmap #2:10-50.A Tom
participants (4)
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Craig Yoshioka -
Elaine Meng -
Eric Pettersen -
Thomas Goddard