Hi Minh,
you define a rotation axis by the rotation axis x, y or z (first
argument in cmd.rotate) and a point in 3d (origin argument in cmd.rotate).
Instead of rotations around axes that are not parallel to the x, y or z
axis you can do composite rotations.
Btw, for the case of GroEL (PDB 2c7e), the structure is oriented along
the Z axis, so you can flap the flexible regions with a single rotation
around the axis that goes through the regions center of mass and is
parallel to the z-axis.
See the attached file.
repeat the last rotate command from the gray window
cmd.rotate("z", 30, "flexregion", camera=0, origin=rotationCenter)
hope that makes sense.
Minh Nhat wrote:
Hi everyone,
Is it possible to make a selection rotate about an arbitrary axis
(which we can actively define ourself (not x,y, z) ?)
Thanks,
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from pymol import cmd
from pymol.cgo import *
def centerOfMass(selection, createSphere=True):
## assumes equal weights (best called with "and name ca" suffix)
model = cmd.get_model(selection)
x,y,z=0,0,0
for a in model.atom:
x+= a.coord[0]
y+= a.coord[1]
z+= a.coord[2]
com = (x/len(model.atom), y/len(model.atom), z/len(model.atom))
if createSphere:
print "Center of mass: (%.1f,%.1f,%.1f)"% com
## Creating a sphere CGO
comS = [COLOR, 1.0, 0.5, 0.5, SPHERE]+list(com) + [1.0]
cmd.load_cgo(comS, "CoM")
return com
cmd.fetch("2c7e") ## requires a newer pymol
cmd.as("cartoon", "all") ## requires a newer pymol
cmd.create("flexregion", "chain A and resi 229-270")
cmd.color("red", "flexregion")
rotationCenter = list(centerOfMass("flexregion"))
cmd.rotate("z", 30, "flexregion", camera=0, origin=rotationCenter) ## repeat this!
cmd.zoom("flexregion")
