Nigel, I am using PHENIX 1.4-6, which is newer that the most recent version on the PHENIX web site, other than "nightly build" versions. Nigel W Moriarty wrote:
Joe
I think you may need to upgrade your version of PHENIX. In the current version, the periodicity is 3. I have recently been using eLBOW, the Chemical Components library and the Monomer Library to improve any residue restraints that have short comings. These are freely available at Source Forge from a project called GeoStd at http://sourceforge.net/projects/geostd
Its included in more recent PHENIX versions in $PHENIX/chem_data/geostd
Nigel
On 9/28/09 11:45 AM, Joe Krahn wrote:
I found that residue TRS has different dihedral target angles for the three hydroxyl oxygens, which are actually all equivalent. They have a periodicity of 1, but should have a periodicity of 3. What is the best way to handle such discrepancies?
Most ligand parameters are probably auto-generated based on a reference structure, and there is probably a lot of conformation bias. In this case, it seems that parameterization should have been able to detect symmetry. It would be nice if parameters could include information about whether a human has done any validation. Actually, a ligand Wiki might be nice, where people can easily put comments, even if they are not sure about how to improve the parameters.
Joe Krahn _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb