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 [email protected]
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