-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hello Jinzhong-- > I manually modeled a protein-RNA complex which I am confident that it is > basically right. This protein has two domains which bind different sites > of a RNA. One of the domain has a ligand and one atom of the ligand has > a constant distance with a specific base of the RNA. Now I want to > refine this model but there are some constraints must be concerned. > First the relative position of the two domain can be adjusted that is > the linker between the domain can be flexible. Second, the sidechains in > the protein-RNA interface can be refined but for the rest of the domain > and ligand i just want to do rigid-body refinement. And last the > distance between the two atoms of protein and rna must be restrained in > 2A. So here is my quension: can Xplor-nih do this work for me? if can, > which script should i use and how to define these constraints. You might try eginput/dock_dipolar_chemshift/dock_tor_rigid.py or eginput/EIN_HPr_diffTens/dock.py These are both probably overkill. Make sure you disable rigid-body rotational/translational randomization if using dock.py. I'm not 100% sure about your 2A distance restraint- are you referring to repulsive restraints? If so, these can be implemented in terms of the standard NOE term by using a very large upper bound, and a 2A lower bound. I hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFJmFBgPK2zrJwS/lYRApFSAJ9gi5Hs7eL56sSmAs7JN09WWHwlKACdEvjK Ax0CpVD/3Q/vseU4qjk7uEk= =1O5a -----END PGP SIGNATURE-----
