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

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Mon Sep 27 20:03:45 PDT 2010

Hi Rojan,

phenix.refine (mostly) uses the CCP4 monomer library to determine ideal bond, 
angle, dihedral, chirality, and planarity restraints. You can also add "custom" 
restraints via the phenix.refine parameter file (see phenix.refine docs). The 
procedure for determining the restraints is fairly complex, but all results are 
written to the .geo file which is meant to be human readable.

> The torsion angles of residue and xyz of each atoms are already known. I want 
> juxtapose residue or residues to create an extended chain.

This sounds like something you'd want to do in COOT... but I'm not sure I fully 
understand your question.


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