[phenixbb] Using Reference Structure in Phenix Refine

[Jeff Headd]

Hi John,

For your situation you will only need one reference chain in your
reference PDB, and then you will need to add selection statements to
your parameter file to tell Phenix how you want to proceed.  In the
case where your working model has four chains (A, B, C, D) and your
reference model has only chain A, the selections would look like this:

refinement.reference_model.reference_group {
     reference = chain A
     selection = chain A
   }
refinement.reference_model.reference_group {
     reference = chain A
     selection = chain B
   }
refinement.reference_model.reference_group {
     reference = chain A
     selection = chain C
   }
refinement.reference_model.reference_group {
     reference = chain A
     selection = chain D
   }

If you look at the documentation for a more recent installer, there is
more comprehensive documentation for adding a reference model that
will be included in the next release.  You can find a copy here:

http://www.phenix-online.org/version_docs/dev-598/refinement.htm#anch28

If you have any further questions please let me know.

Thanks,
Jeff





On Sat, Dec 4, 2010 at 11:18 AM, John Pascal
<John.Pascal at kimmelcancercenter.org> wrote:
> Hello Everyone,
>
> I am refining against low resolution data, and I would like to use a
> higher resolution model that is available as a reference structure.
>
> There are multiple copies of the molecule in the asymmetric unit, each
> with a different chain ID.  Does the reference PDB file need to
> contain multiple copies, such that there is a match for each chain
> (e.g. RESIDs and SEGIDs)?
> Or does phenix figure out that the reference structure refers to
> several copies of the molecule, and you only need a single copy in
> the reference molecule PDB file?  Or will NCS restraints take care of
> this?
>
>
> Thanks.
> -John
>
>
> --
> John Pascal, PhD                       ph 215.503.4596
> Assistant Professor                    fx 215.923.2117
> Thomas Jefferson University
> Biochemistry & Molecular Biology
> 233 South 10th Street, BLSB 804
> Philadelphia, Pennsylvania  19107
>
>
>
>
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