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Hi Folks-- > Are you using the xplor-nih in python mode? If so, I'd suggest that you > use protocol.AddUnknownAtoms() to add the MSC ligand. HBUILD is unable to > handle adding heavy atoms, and that's the problem that you are seeing. > Addunknownatoms() basically gives random positions to every unknown atom > and then refines based on the covalent geometry. > > When I was doing this, I also found that I needed to use > protocol.FixupCovalentGeometry() to really get things right. Your mileage > may vary. > this seems like good advise to me. To be precise, the necessary python statements are import protocol protocol.addUnknownAtoms() protocol.fixupCovalentGeom() be aware that fixupCovalentGeom will slightly modify the initial input coordinates. Please let us know if this is unacceptable, and I will suggest an alternative approach. regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.5 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFFH9u6PK2zrJwS/lYRAhMFAJwIxfsAI8FJ958pPnY5h8aWVnWx2QCePDL3 WRLEz9f994htKlZDDOv7TNk= =L22L -----END PGP SIGNATURE-----
