Hi Rojan, Phenix does use a library to restrain geometry, including bond lengths, angles, and dihedrals. These restraints are applied by default during refinement. I'm not completely sure what you're trying to do, but are you trying to restrain your working model to the coordinates of another model? We have a method for that called 'reference_model' that allows you to submit the coordinates of a related model to your working model which is used to generate an additional set of dihedral restraints. You can read about this method here: http://www.phenix-online.org/documentation/refinement.htm#anch26 Is this what you are trying to do? Thanks, Jeff On Mon, Sep 27, 2010 at 7:07 PM, Rojan Shrestha wrote:

Hello:

I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain.

Thanks

Regards,

Rojan _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Rojan,

I am wondering whether Phenix has the library or program to maintain the ideal bond length and bond angle. The torsion angles of residue and xyz of each atoms are already known. I want to juxtapose residue or residues to create an extended chain.

if you have a PDB file containing your structure (let's say it's called model.pdb) then the command phenix.pdbtools model.pdb --geometry-regularization will idealize the geometry of your model, where the geometry is defined as described here: Grosse-Kunstleve RW, Afonine PV, Adams PD: cctbx news: Geometry restraints and other new features Newsletter of the IUCr Commission on Crystallographic Computing 2004, 4, 19-36. Does this answer your question ? Pavel.