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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