[phenixbb] Using Phenix Refine for Hypothetical Models

Pavel Afonine pafonine at lbl.gov
Tue Mar 5 23:55:00 PST 2013

Hi Sam,

if it is a crystallographic symmetry then you can just use 
phenix.geometry_minimization like this:

phenix.geometry_minimization model.pdb

If it is a non-crystallographic symmetry or/and you want to use some 
extra exotic restraints (such as secondary-structure, ncs restraints, 
etc), then using phenix.refine is a better option (better because there 
is no other way of doing it in Phenix.

Step 1: fake the Fobs data:

phenix.fmodel model.pdb high_res=5 type=real label=F-obs r_free=0.1

Step 2: run phenix.refine without using x-ray data:

phenix.refine model.pdb data.mtz wxc_scale=0 main.bulk_solv=false 
strategy=individual_sites main.number_of_mac=10

If you need to use NCS, add to above: main.ncs=true ncs.type=cartesian

You can do all this using the GUI.

Also note that geoemtry terms in phenix.refine are not designed for 
simulations, they are very basic just enough to make refinement work 
well, and almost certainly not suitable to do simulations purely based 
on them. For example there is no electrostatic terms, which means if you 
don't carefully specify secondary structure restraints your model will 
unfold.. etc.


On 3/5/13 1:48 PM, Sam Stampfer wrote:
> Dear Phenix Community,
> Is it possible to use phenix.refine to do simulated annealing and 
> energy minimization of a hypothetical model? I am currently using 
> pyrosetta relax for minimization; however, my hypothetical model is 
> based on a homologous protein whose structure is a crystallographic 
> trimer. I would like to preserve my model's symmetry, which I know is 
> possible in phenix.refine but not in pyrosetta (the symmetry controls 
> are only supported in regular rosetta, as far as I know).
> Is there a way to have phenix ignore x-ray data and just do energy 
> minimization functions? How would I go about doing that? Would I need 
> a file containing fake/dummy x-ray data?
> Thanks for your help!
> -Sam Stampfer
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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