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

[Jeff Headd]

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 <rojan at riken.jp> 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
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