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Hello Michael-- > > 1. I have an X-ray structure to which I would like to add a > derivatized amino acid (ie: MTSL) for which I have the topology and > parameter files. I know how to create an extended structure > incorporating this residue but so far have not figured out how I can > read in the crystal coordinates, substitute coordinates for this > residue only and write out a new coordinate file maintaining the > accuracy of the crystal structure. you should 1) read in the good coordinates. 3) assign semi-random coordinates to the MTSL. 4) regularize. Steps 3 and 4 can be accomplished using somthing like import protocol protocol.genExtendedStructure(sel="resid XX") in the Python interface. > 2. I want to then use that derivatized structure to perform a > rigid-body minimization of this two-domain protein based on RDC data > and inter-domain long-range paramagnetic restraints to the derivatized > residue, again without changing the crystal coordinates of the two > domains. I had a look in the "prot-prot" example in "eginputs" and > will start from there. Since I can specify which residues have torsion > angle freedom (in our case the linker only) will this protocol be > sufficient for maintaining the accuracy of the crystal structure? > you might also look at eginputs/dock_dipolar_chemshift for an example using the Python interface, but the other should work too. Just make sure that the regions away from the interface are fixed or grouped so that the individual domains do not get distorted. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFDYiduPK2zrJwS/lYRAmt/AJ4qy7uIfaPlEZmuyoQ7wu4z1H7JlACfYNKn MzagaN/SiZ+YyzqqP5ZOSWQ= =eQgu -----END PGP SIGNATURE-----
