[phenixbb] using reference model for low resolution refinement

Jeff Headd jjheadd at lbl.gov
Sun Feb 6 20:45:54 PST 2011


Hi,

On Sun, Feb 6, 2011 at 8:32 PM, crystallogrphy <qunwan1 at gmail.com> wrote:
> Hi,
> I am refining a hexamer model using low resolution data (4.7A). I want to
> use a high resolution model (2.4A) which is a dimer as the reference model.
> The sequence identity is 100%.
>
> Does anyone know how to select the residue range from the reference model
> for my refinement?

In this case, it will depend on how you want to assign the reference
model to the working model. Do you want to assign one chain from the
reference model as the reference for each protein in the working
hexamer, or do you want to assign the dimer in the reference model to
each pair of proteins in the working model? For you first case, you'll
want something like this:

refinement {
  main {
    reference_model_restraints=True
  }
  reference_model.file=reference.pdb
  reference_model.reference_group {
     reference = chain A
     selection = chain A
   }
   reference_model.reference_group {
     reference = chain A
     selection = chain B
   }
   reference_model.reference_group {
     reference = chain A
     selection = chain B
   }
   etc...
}
If you want to assign the reference pairings in a different way, use a
similar construction but with different selections for the
reference_model.reference_group entries.

You can read more about this in the phenix documentation:

http://www.phenix-online.org/documentation/refinement.htm#anch28

If you have further questions please let me know.

Thanks,
Jeff


> Thanks!
>
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