[phenixbb] running geometry regularization on side chains only

Nathaniel Echols nechols at lbl.gov
Wed Jul 27 11:39:34 PDT 2011

On Tue, Jul 26, 2011 at 11:48 PM, Francois Berenger <berenger at riken.jp> wrote:
> Thanks for the workaround Pavel.
> However, I just wanted to know if it could be done using geometry only
> with phenix.pdbtools.
> If it was possible and fast, I or some colleague may have needed to wrap the
> functionality into some code as a compiled library.
> Maybe I should rather look for some tool that can add sidechains
> to a backbone model (without introducing clashes in the process).

Try PULCHRA (http://www.pirx.com/pulchra/index.shtml) - since it is
open-source, we distribute it with Phenix (phenix.pulchra).  My guess
is it won't be able to avoid all clashes for a poor starting
structure, but it is incredibly fast, and it can even start from
C-alpha coordinates alone.  It appears to only work with a single
chain at a time, but a little bit of scripting will fix that problem.


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