[phenixbb] reference model

Jeff Headd jjheadd at lbl.gov
Thu Mar 24 09:19:12 PDT 2011

Hey Kendall,

> I would like to use a reference model in refinement, but the structure has two components with known higher resolution structures. Can I specify two reference models? How?

At present you can only submit one reference model file, but you can
have as many chains as you'd like in the reference model file, as long
as each chain has a unique chainID. In your case, you can combine the
two reference chains into one file and give each a unique chainID.
Then use the selection syntax to match each reference chain to the
matching chain in the working model. The syntax would look something
like this:

  main.reference_model_restraints = True
    file = reference.pdb
      reference = chain A
      selection = chain A
      reference = chain B
      selection = chain B

In the future you will be able to submit as many reference models as
you like, but I haven't gotten to adding that feature yet. It has be a
frequently requested feature, so I hope to add that soon.

> I'm also having trouble with the syntax. With the following params file, the run fails saying that reference model is an unused parameter.

The problem with your sytax below is that you need
refinement.reference_model{ } as your scope, similar to the example

> Lastly, what does "reference_xray_structure"  do?

I'm actually not sure what this option does. Pavel, do you know what
the reference_xray_structure option is used for?


> Thanks!
> Kendall
> refinement.main {
>    reference_model_restraints = True
> }
> refinement.refine {
>    strategy = *individual_sites \
>                        rigid_body \
>                        individual_sites_real_space \
>                        *individual_adp \
>                        group_adp \
>                        tls \
>                occupancies \
>                group_anomalous \
>                        none
> }
> reference_model {
>        file = 4.pdb }
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

More information about the phenixbb mailing list