Re: [phenixbb] Does Phenix have the library or program to maintain bond angle and bond length to create an extended chain?

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.