[Chimera-users] morph shape/bild objects

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 25 12:26:20 PST 2011

On Feb 25, 2011, at 7:50 AM, Do-Nyun Kim wrote:
> Hello,
> I'm using shapes in bild format to make spheres and cylinders in Chimera.
> Is there a way of morphing these shapes, spheres in one conformation to spheres in another conformation?
> Thanks you. 
> Best regards,
> Do-Nyun Kim.
Hi Do-Nyun,
It sounds like you want the positions of the objects to change but their shapes to stay the same, is that right?  In that case, and if you only need spheres and cylinders, it might be possible with fake atoms and bonds instead of BILD objects.

The initial creation of the fake atoms (spheres) and bonds (cylinders) would be more trouble than reading in a BILD file, because setting colors and radii would require additional commands ("vdwdefine" etc.) or selecting them and using the Selection Inspector.  Also, since bonds are only between two atoms, you would need to have additional atoms at the ends of the cylinders, which might be visible even if they are only drawn as dots. 

(A) One approach is to use morphing, as you suggested.
Chimera has two kinds of morphing, one for atoms/bonds and another for density maps.  I don't see a reasonable way to use the latter for your problem.  For atoms/bonds, you would need to make two PDB files with the starting and ending positions of the objects in which the corresponding atoms have the same names and are in the same order.  You would open both files (don't bother adjusting the display yet), then use Morph Conformations (under Tools... Structure Comparison) to generate a morph trajectory.  I haven't tried this process on disconnected fake atoms, and don't know how well it would work. Then you could hide the input structures, adjust the display of the morph trajectory, and play that trajectory with MD Movie. 

(B) An alternative approach is to open each object as a separate model.  In other words, each sphere (one "atom") and each cylinder (two bonded "atoms") would be in a separate PDB file.  Models can be moved relative to one another in Chimera, and each arrangement of the models saved as a "position."  Then you can reset to any of the saved positions gradually over a number of frames.  The saving and resetting are done with the commands "savepos" and "reset" and these positions are included in saved Chimera sessions.  I guess the hard part in that case might be getting the objects in the desired positions, using the mouse or movement commands such as "move" and "turn".

Now, neither of these approaches handles changes in color, display style, size or shape.  They only handle the positions of the atoms.

There is development work going on in Chimera to save "scenes" which include more of these properties in addition to positions, and to restore or animate between the saved scenes (see Tools... Utilities... Animation in recent version 1.6 daily builds, but be aware it is only early development).  Currently this does include atom colors and styles, but not BILD objects, surfaces from the "shape" command, density map displays, or changes in atomic radii; also, gradual transitions in properties other than position are not yet available.

Finally, it probably could be done with BILD objects or surfaces from the "shape" command plus a fair amount of Python coding, but that is beyond my skills.

Unfortunately I can't think of a short/easy way to do what you want, but maybe some of these ideas will help.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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