[phenixbb] energy minimization

Pavel Afonine PAfonine at lbl.gov
Fri Dec 11 14:05:23 PST 2009

For example:

phenix.refine model.pdb data.mtz strategy=individual_sites 
main.bulk_solvent_and_scale=false refine.sites.individual="chain A and 
backbone" main.number_of_macro_cycles=10

where you can use a fake mtz file (using pbbtools).


phenix.pdbtools model.pdb --geometry-regularization

but I forgot if it takes the atom selection - you can quickly try it out.


On 12/11/09 1:57 PM, Raja Dey wrote:
> Hi,
>    Does PHENIX has the option to simply minimize the energy of a homolgy model with C-alpha atoms or backbone fixed (in absence of x-ray data)? 
>    Thanks...
> Raja 
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