[phenixbb] DEN refinement under phenix

Jeff Headd jjheadd at lbl.gov
Fri Mar 2 07:53:40 PST 2012

Hi Melania,

On Fri, Mar 2, 2012 at 12:56 AM, Melania Strycharska
<melania at berkeley.edu>wrote:

> Hi All,
> I was wondering whether anybody has successfully run the DEN refinement
> under phenix yet. I am having some problems with my scripts stalling
> without any error messages.

Sorry to hear that you're running into trouble. I'm not sure why that would
be happening. If you send me your input files offline I am happy to help
you debug the problem.

What sort of reference models do people use? The following issues I am not
> quite clear on:
> - if I don't have a reference model should I call on my current pdb where
> the script calls for a reference model?
> If you don't have the reference model, you do not need to specify one. If
you run DEN refinement without a reference model, the method will
automatically use the input model to generate the starting network.

> - is it ok to use a single domain as a reference model or is it not enough
> to get the whole protein refined?
> Yes, you can do this, but restraints will only be generated for the part
of the model that matches. I have some ideas on how to cover the rest of
the molecule, too, but have not yet implemented that part.

> - is it possible to use more than one reference model; in a case where I
> had structures of each domain solved separately?
> Right now the only way to do this would be to combine them into one file.
It's a high priority to allow to multiple reference models for both DEN and
reference model refinement, so hopefully that will be available soon.

> - can a reference model be a different protein or does it have to have the
> same sequence?
> For DEN refinement it needs to be the same sequence, but I can imagine
cases where you'd like it to be a related model, and will add that ability
in the future.


> Thanks a lot!
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