[phenixbb] Unrestrained refinement and reported RMSD values
pafonine at lbl.gov
Mon Apr 9 18:17:56 PDT 2012
you can turn off some restraints selectively (that is for selected atoms
only) by using:
angles = None
dihedrals = None
chiralities = None
planarities = None
Replace "None" with atom selection defining atoms for which you want to
turn off restraints.
angles = (chain A and resseq 123) or (chain B and resname TYR)
dihedrals = (chain A and resseq 1:10)
will remove angle restrains for all atoms in residue 123 in chain A, and
for all atoms belonging to TYR residues in chain B. Also, dihedral angle
restraints will be turned off for all atoms in residues from 1 to 10 in
There are multiple ways of checking the geometry. For example:
phenix.pdb_interpretation model.pdb write_geo_files=true
and then inspect the output geo file, that lists all the geometry
restraints for all atoms, as well as ideal and model values.
Let me know if you have questions.
On 4/6/12 10:15 AM, Yuri wrote:
> Hi all,
> I wonder if there is a way of turning off (loosening) restraints for
> certain residues and a ligand specifically, and will the bond/angle rmsd
> be printed out somewhere?
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