[phenixbb] phenix - can phenix perform simulated annealing w/o data?
Pavel Afonine
PAfonine at lbl.gov
Fri Apr 18 16:42:23 PDT 2008
Hi Sue,
just to add to Nigel's reply... Yes, you can do geometry regularization
using this command:
phenix.pdbtools --geometry-regularization model.pdb
There are two important parameters that define how far phenix.pdbtools
will go with your model idealization: "max_iterations=500" and
"macro_cycles=1" (500 and 1 are the default values).
If you want to get an almost ideal model, then use something like this:
"max_iterations=100" and "macro_cycles=1000".
Cheers,
Pavel.
On 4/18/2008 1:42 PM, Sue Roberts wrote:
> Hello
>
> I'm trying to minimize a (hypothetical) protein ligand complex where
> the ligand is very large. I can build a dictionary from the smiles
> description using elbow.builder (I love this capability!)). Can
> phenix perform minimization (or preferably simulated annealing)
> without real data? How? (This sort of thing could be done using
> xplor). (I have looked at the phenix documentation but didn't find
> the answer. I'm pretty sure the answer is in the documentation
> somewhere and I'm just not seeing it.)
>
> Thanks,
>
> Sue
>
> Dr. Sue A. Roberts
> Biochemistry & Biophysics
> University of Arizona
> 520 621 8171
> suer at email.arizona.edu
>
>
>
>
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