Hi Melania,
On Fri, Mar 2, 2012 at 12:56 AM, Melania Strycharska
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.
Jeff
Thanks a lot!
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