[phenixbb] Using Phenix Refine for Hypothetical Models
pafonine at lbl.gov
Tue Mar 5 23:55:00 PST 2013
if it is a crystallographic symmetry then you can just use
phenix.geometry_minimization like this:
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
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
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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb