Dear Jakob, On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen <jtoudahl.niel...@gmail.com> wrote:
> I would like to modify a protein pdb file with a "crankshaft" flip, which > is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta. > Such a change should leave the protein coordinates unchanged effecting only > atoms in residues i-1 and i. However implementation in pymol (see below) > changes the coordinates of _all_ residues from i-1 to the C-terminal. Can > you help me? Can I somehow do the two changes simultanious?... > > set_dihedral 21/n, 21/ca, 21/c, 22/n, 148.435 #was 168.4 > set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704 #was -103.7 I don't see how this change can leave the other coordinates unchanged. Even if the psi(i-1) and phi(i) bonds are exactly parallel (meaning that the angles CA-C-N and C-N-CA are exactly the same, which they are not necessarily), rotation of the psi(i-1) bond will move the N(i) and CA(i) atoms, so therefore while a rotation in the opposite direction of the phi(i) bond will tend to keep the rest of the change travelling in the direction it was before those two counter-rotations, the backbone itself will be shifted. One textbook I consulted lists the angles at the C(i-1) and N(i) atoms as 116 and 122, respectively, so the psi(i-1) and phi(i) bonds are not even theoretically going to be parallel. In practice, with "real" structures, they certainly are not usually going to be parallel. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
