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 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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On Tue, Mar 5, 2013 at 11:55 PM, Pavel Afonine wrote:

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.

Two further points: 1) If you're trying to preserve a crystallographic trimer anyway, one option is to set wxc_scale to a small but non-zero number, i.e. essentially defining an envelope around your protein with the fake data. This will allow your model geometry to refine but limit how far it can move. 2) The reference model restraints could also be useful here (with or without "data"). -Nat