[phenixbb] Using Phenix Refine for Hypothetical Models

[Shya Biswas]

Hi Pavel,
Is it possible to do the same with protein ligand complex the protein is a
homology model obtained from swiss modeller and the ligand is modelled into
the active site.
thanks,
Shya


On Wed, Mar 6, 2013 at 2:55 AM, Pavel Afonine <pafonine at lbl.gov> wrote:

>  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.
>
> Pavel
>
> 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
>
>
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