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

Pavel Afonine pafonine at lbl.gov
Mon Sep 27 21:56:58 PDT 2010

  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, 

Does this answer your question ?


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