Hi Jianhui Song,
With a bit of scripting it's not that hard:
## python code
from pymol import cmd
import numpy
def princalign(obj):
R = numpy.zeros((4,4))
x = numpy.array(cmd.get_model(obj).get_coord_list())
R[3,:3] = -x.mean(axis=0)
x += R[3,:3]
R[:3,:3] = numpy.linalg.eig(numpy.dot(x.T,x))[1].T
cmd.transform_object(obj,R.flatten())
for obj in cmd.get_object_list():
princalign(obj)
##=== end of python code
Do note that the direction along the principal axes is arbitrary.
Hope it helps,
Tsjerk
On Wed, Oct 1, 2014 at 9:25 PM, SongJianHui <gigi...@hotmail.com> wrote:
> Hi, all,
>
> I'm wondering if it is possible to align a number of unfolded
> conformations (C-alpha based backbone only) according to their principal
> axis. Thanks.
>
> Dr. Jianhui Song
> Postdoctoral Fellow
> Department of Biochemistry
> University of Toronto
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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