Here's an example script that scratch-builds such an animation. Note
that the "rotate" command seems broken in terms of the selections it
currently accepts -- selection macros don't currently work, so you'll
need to write them out long-hand as I have done below.
# create a 4 state molecule
fragment asp,mov
fragment asp,mov
fragment asp,mov
fragment asp,mov
# orient the camera parallel to the plane of motion
reset
turn x,-50
orient mov////CG+OD1+OD2
# get coordinates of the CG atom
crd = [0,0,0]
iterate_state 1,mov////CG, crd[0:3]=(x,y,z)
# now rotate atoms in states 2-4
frame 2
cmd.rotate("z",-4,"mov and name OD1",origin=crd)
cmd.rotate("z", 4,"mov and name OD2",origin=crd)
frame 3
cmd.rotate("z",-8,"mov and name OD1",origin=crd)
cmd.rotate("z", 8,"mov and name OD2",origin=crd)
frame 4
cmd.rotate("z",-4,"mov and name OD1",origin=crd)
cmd.rotate("z", 4,"mov and name OD2",origin=crd)
as sticks
set sphere_quality,2
set stick_radius, 0.1
show spheres
set sphere_scale, 0.25
mplay
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
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. South San Francisco, CA 94080 USA
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. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:[email protected]
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of
> Sven Lammers
> Sent: Wednesday, February 22, 2006 5:05 AM
> To: [email protected]
> Subject: [PyMOL] animate angle bending
>
> Dear pymol users,
>
> I'm struggling to figure out how to create an animation of an
> angle bending vibration with pymol, like this one
> http://www.ch.embnet.org/MD_tutorial/Images/Part2/a.gif
> My question is how do I correctly set the origin and axis so
> that I could use the rotate command to rotate one bond with
> respect to the other.
>
> Thanks a lot in advance and best regards, Sven
>
>
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