[phenixbb] reference model restraints

Jeff Headd jjheadd at lbl.gov
Wed Dec 21 12:39:28 PST 2011


Hi Ursula,

For a case where you want to use one chain as a reference model for
multiple chains in your working model, you need to specify the
selections like this in your parameter file:

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
   }

This would restrain chains A, B, and C in your working model to chain
A in the reference model.

If you run into any further trouble, please let me know.

Thanks,
Jeff

On Wed, Dec 21, 2011 at 12:32 PM, Ursula Schulze-Gahmen
<uschulze-gahmen at lbl.gov> wrote:
> I am refining a 3.1 A structure and are trying to use model restraints for
> this. There are 3 molecules in the asymmetric unit of my structure. I input
> the high resolution structure of one molecule of the reference structure to
> create restraints during the refinement. From looking at the log file, it
> seems to me that the reference structure is aligned to only one of my
> molecules, but not the other 2. How can I make sure the restraints are valid
> for all 3 molecules.
>
> Ursula
>
> --
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
>
>
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