[Chimera-users] morphing model extrapolation

Tom Goddard goddard at sonic.net
Wed Dec 12 15:25:19 PST 2012

Hi Stefan,

  If you are willing to change a couple lines of  code you can make the Chimera Morph Conformations dialog extrapolate beyond both ends of a morph between two structures.  You would edit the following text file in your copy of Chimera


(on Mac this is Chimera.app/Contents/Resources/share/morph/Interoplate.py) replacing

		f = (rate[i] - lo) / interval


#		f = (rate[i] - lo) / interval
		f = -0.5 + 2*rate[i]

and replacing line

		mol.activeCoordSet = cs


#		mol.activeCoordSet = cs

This will make the morph extend from -0.5 to 1.5 where 0 corresponds to the first structure and 1 the second structure.  So you get 50% more motion on each end.  To change those values just change the "f = …" line, for example to go from -1 to 2 use "f = -1 + 3*rate[i]".  The rate[i] value goes from 0 to 1.  Make sure to save the file as plain text, and don't change the indentation of the lines.  Restart Chimera and it will use the new code.

  I tried this on maltotriose binding protein conformations 2gha and 2ghb.  The one glitch is that the very first frame of the morph is still the first input structure and the very last frame is still the second input structure.  You'd want those to be the extreme ends of the extrapolation but that would require changing more lines of code.  Instead I suggest just leaving out the end frames when you play the trajectory.


On Dec 11, 2012, at 9:37 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Stefan,
> Sorry, no -- the morphing calculation can only interpolate between the input structures.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 10, 2012, at 6:16 PM, Gajewski, Stefan wrote:
>> Hi!
>> I have two .pdb files on hand. Both are in between two biologically relevant conformations. When I create a morph between them, I can see them permuting between the two crystal structures but only half way to the two relevant conformations.
>> The morphing model should generate a trajectory between the two coordinate sets. Is it possible to let the morphing model generate more coordinate files/frames beyond the target structure?  Let’s say 120 frames morph A to B and compute 60-100 more frames beyond B based on the previous trajectories?
>> Thanks,
>> Stefan
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