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hello Lizhe-- > > I am using X-plor to refine a protein structure, and now I have some > questions: > > 1) The protein structure and its corresponding X-ray structure have > four copies in one unit cell. So which way is better? A: First build > up the unit cell containing four copies of the protein, then run MD > under periodic boundary condition (PBC) by Xplor-NIH. B: Start with > one protein copy, then define unit cell and the four symmetric > operations by Xrefin, then run MD under periodic boundary condition > (PBC) by Xplor-NIH. I am not an expert on crystal refinement, but I believe you want to use some sort of NCS restraint for this http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node339.html The strict ncs restraint will allow you to have only a single copy of the structure. > > 2) How can I set up a real periodic boundary condition by Xplor-NIH, (by > which command)? > Please check out the examples in tutorial/xtalrefine If you wish to use the Python interface, I do have an example, but it's for a system with only one protein copy per unit cell. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkpnepoACgkQPK2zrJwS/lanUgCfQ1rE3L6v6EduIcUSKNyLva2+ fGsAn3AkBm3PYBXaxr0aKEQhhr7pq/Cr =aSgC -----END PGP SIGNATURE-----
