is sounds like you have 2 options: 1) bug/pester/inquire with the Morph people and see if they can tweak their input. My guess is they have fielded these questions before. 2) there are options within PyMol to fit to an external reference frame, and read this back in. You might have to output the alignment from an initial reference frame and then read this back in for every pdb. Hopefully someone more Python-y will have a script......As you have found out, simple fitting of backbone atoms will not give you what you want, due to these fluctuations. Please post any helpful response from the Yale folks, as I am also dealing with these issues. Mike Ford Michael G. Ford, Ph.D. Postdoctoral Research Fellow Department of Molecular Cardiology/NB20 Lerner Research Institute Cleveland Clinic Foundation 9500 Euclid Ave. Mail Stop NB20 Cleveland, OH 44195 216.444.8464 fo...@ccf.org
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Today's Topics:
1. Alignment and Translations/Rotations (Joshua L. Adelman)
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Message: 1
To: pymol-users@lists.sourceforge.net
From: "Joshua L. Adelman" <jadel...@ocf.berkeley.edu>
Date: Mon, 27 Dec 2004 13:09:45 -0800
Subject: [PyMOL] Alignment and Translations/Rotations
I am trying to string together several sequences of PDB files outputted
from the Yale Morph Server in order to make a movie. Basically there
are 3 groups of trajectories and I want to make a continuous movie. The
problem is that the Morph Server rotated one set of structures relative
to the other groups and I need to align them.
I have tried to use the align and pair_fit commands, but because the
protein is undergoing a conformational change, even aligning fairly
static residues or atoms in the protein induces motion in the movie
which is an artifact of the alignment (it looks like a rigid body
rotation of the protein). Ideally what I want to do is do a single
alignment of the last frame of the first sequence with the first frame
of the second sequence (they should be nearly identical structures) and
then get the translation and rotation matrices that were used and then
apply them to all of the .pdb files that compose the frames of the the
second group of structures.
If anyone had any suggestions of how do this or perhaps an alternative
work-around, I would greatly appreciate you passing along your insight.
Thanks in advance,
Josh
_________________________________________
Joshua L. Adelman
Biophysics Graduate Group
University of California - Berkeley
218 Wellman Hall
Berkeley, CA 94720
_________________________________________
E-mail : jadel...@ocf.berkeley.edu
Webpage : http://www.ocf.berkeley.edu/~jadelman
_________________________________________
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