Hi, you may want to read this before (yes, I remember, you deal with low resolution structure and the information from this link may not be 100% relevant to your case, but it is good to have a look anyway): http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19554.html Cheers, Pavel. Ralf W. Grosse-Kunstleve wrote:
Hi Jianghai,
I am refining a low resolution huge protein structure. There are about 20% residues in the disallowed region of ramachandran plot. Is there a way in phenix.refine to refine the phi, psi angles to get a better ramachandran plot? or a phi, psi restraints in refinement?
If you add
discard_psi_phi=False
to the phenix.refine command line the psi and phi dihedral angles are restraint according to the CCP4 monomer library definitions in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get the full path name). Look for data_link_TRANS and data_link_CIS, scroll down to _chem_link_tor.value_angle, to see the restraint definitions.
We don't have much experience using the phi, psi restraints. If you don't mind, please let us know how it goes!
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb