[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".


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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> phenixbb at phenix-online.org
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