On Jan 26, 2009, at 12:58 PM, Tsjerk Wassenaar wrote:
Hi XAvier,
Unfortunately, you're out of luck. The coordinates do not contain
information regarding the proper orientation with respect to the
coordinate system.
No they don't.
May be I should have mentioned that I know for each
conformation of the system (protein embedded in a membrane
bilayer) the exact transformation that has been that has
been operated: a rotation around the z axis.
That's the short answer. I guess you did save all atoms, at least of
proteins and lipids, in which case you could do a search for a
rotation matrix that restores your PBC. If you have a brick or
triclinic representation of your atoms the easiest solution is to fit
planes through the sides, from which you can infer the original
coordinate system. Then you can rotate that back to match the one
stored.
The other option I found is to duplicate the system on x and y
directions, then center a copy of the protein and finally put everything
inside the new cell (made up from 4 copies of the original cell).
Then when rotating the pbc and included on the x and y directions.
Thanks for you thoughts I knew you'd had but I hope for a magic
solution.
Best,
XAvier
Hope it helps,
Tsjerk
On Sun, Jan 25, 2009 at 7:43 PM, XAvier Periole <x.peri...@rug.nl>
wrote:
Dears,
I need to rerun a trajectory that has been rotated to orient a
molecule
according to a reference. The pbc are therefore broken.
Would anyone know how to restore the correct position of the atoms
inside
the unit cell after the rotation is applied. The rotation is actually
applied around
only one axis (z, membrane normal).
Thanks for any suggestion.
XAvier.
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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