[phenixbb] DEN Refinement in phenix 1.7.3

Das, Debanu debanu at slac.stanford.edu
Tue Jan 24 10:47:52 PST 2012


Although this is not really a Phenix list answer, since it has come up, I would like to announce that we recently implemented scripts to run the full grid search of DEN in CNS (parallelized to optimize gamma and weight) to run on a Linux cluster (as opposed to only Mac or SBGrid). They are documented and available under the "DEN Grid Searches" link (http://cns-online.org/wiki/index.php/DEN_Grid_Searches) on the CNS Wiki page (http://cns-online.org/wiki/index.php/Main_Page).


-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Jeff Headd
Sent: Tuesday, January 24, 2012 9:35 AM
To: PHENIX user mailing list
Subject: Re: [phenixbb] DEN Refinement in phenix 1.7.3

Hi Eike,

Yes, DEN restraints can be activated in phenix.refine from the
command-line with the current version and latest nightly builds, and
they are the same deformable elastic network restraints available in
CNS. We have been working closely with Axel Brunger and Gunnar
Schroder to implement DEN in Phenix.

We have not yet officially announced the DEN restraints as they are
still being tested and actively developed to get the implementation
just right, and the parameterization is still very much in flux. I
hope that by the next version it will become and a stable feature, and
at that point DEN will be added as an option in the GUI.

These restraints have been shown to be particularly useful at low
resolution, and there has been success in using at 4-5A and below. I'm
not sure how useful they would be at relatively high resolution (say
2.5A or higher), as there are other restraint methods that work well
at that resolution range that are far less computationally intensive.

In almost all cases it is best to optimize the gamma and weight
parameters, which is quite time intensive but is most likely to give
you the best results. Currently this can be parallelized, but only on
cores that share memory. I'm working on an implementation that will be
compatible with SGE, but that is not yet ready. If you do optimize the
gamma and weight parameters, you cannot simultaneously optimize B
factor weights, which is another limitation that will be overcome in
the future.

As soon as a stable version is announced in the context of a new
release, documentation will be available.

To use them with the current release (1.7.3), you can use a
parameterization such as this:

refinement {
 main {
   den_refinement = True
   number_of_macro_cycles = 1
   nproc = 8
 refine {
   strategy = *individual_sites individual_sites_real_space rigid_body \
              *individual_adp group_adp tls occupancies group_anomalous
 den {
   reference_file = reference.pdb
   optimize = True
   annealing_type = *torsion cartesian
   final_refinement_cycle = True

If you have specific questions on how to run a refinement, please let me know.


On Tue, Jan 24, 2012 at 5:19 AM, Eike Schulz <eike.schulz at embl.de> wrote:
> Dear phenixbb,
> I have noticed that in (since?) the latest release it is possible to
> activate DEN refinement in phenix.refine. I assume this refers to deformable
> elastic networks - right? What is your experience with DEN refinements ? As
> I could not find any reference to it in the documentation I would be happy
> to have feedback on when to use and when to avoid it e.g. resolution limits
> etc. and what to watch out for.
> Many thanks in advance
> Eike
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