[phenixbb] Using Phenix Refine for Hypothetical Models
pafonine at lbl.gov
Wed Mar 6 07:34:20 PST 2013
yes. But as I mentioned in previous email, since the geometry targets
have no electrostatic term, I'm not sure how much sense this would make.
For this kind of things we really do need to implement a proper force
field, or at least add missing terms to currently used one.
On 3/6/13 7:05 AM, Shya Biswas wrote:
> 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.
> On Wed, Mar 6, 2013 at 2:55 AM, Pavel Afonine <pafonine at lbl.gov
> <mailto: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.
> 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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