[phenixbb] Unrestrained refinement and reported RMSD values

Pavel Afonine pafonine at lbl.gov
Mon Apr 9 18:17:56 PDT 2012

Hi Yuri,

you can turn off some restraints selectively (that is for selected atoms 
only) by using:

refinement.geometry_restraints.remove {
     angles = None
     dihedrals = None
     chiralities = None
     planarities = None

Replace "None" with atom selection defining atoms for which you want to 
turn off restraints.

For example,

refinement.geometry_restraints.remove {
     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 
chain A.

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?
> Thanks

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