RE: [PyMOL] animate angle bending

[Warren D. <wa...@de...>]

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 =3D [0,0,0]

iterate_state 1,mov////CG, crd[0:3]=3D(x,y,z)

# now rotate atoms in states 2-4

frame 2
cmd.rotate("z",-4,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 4,"mov and name OD2",origin=3Dcrd)

frame 3
cmd.rotate("z",-8,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 8,"mov and name OD2",origin=3Dcrd)

frame 4
cmd.rotate("z",-4,"mov and name OD1",origin=3Dcrd)
cmd.rotate("z", 4,"mov and name OD2",origin=3Dcrd)

as sticks
set sphere_quality,2
set stick_radius, 0.1
show spheres
set sphere_scale, 0.25
mplay

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Sven Lammers
> Sent: Wednesday, February 22, 2006 5:05 AM
> To: pym...@li...
> Subject: [PyMOL] animate angle bending
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> Dear pymol users,
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> I'm struggling to figure out how to create an animation of an=20
> angle bending vibration with pymol, like this one=20
> http://www.ch.embnet.org/MD_tutorial/Images/Part2/a.gif
> My question is how do I correctly set the origin and axis so=20
> that I could use the rotate command to rotate one bond with=20
> respect to the other.
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> Thanks a lot in advance and best regards, Sven
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