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

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 to 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. Ralf