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<div class="moz-cite-prefix">Hi Shya,<br>
<br>
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.<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
On 3/6/13 7:05 AM, Shya Biswas wrote:<br>
</div>
<blockquote
cite="mid:CAP3ssmHs82hDt+ZaHQmeEXO9ZgHZczf7Q6QtvLB4=BwmAKpswQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>Hi Pavel,</div>
<div>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.</div>
<div>thanks,</div>
<div>Shya</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Mar 6, 2013 at 2:55 AM, Pavel
Afonine <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi Sam,<br>
<br>
if it is a crystallographic symmetry then you can just
use phenix.geometry_minimization like this:<br>
<br>
phenix.geometry_minimization model.pdb<br>
<br>
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.<br>
<br>
Step 1: fake the Fobs data:<br>
<br>
phenix.fmodel model.pdb high_res=5 type=real label=F-obs
r_free=0.1<br>
<br>
Step 2: run phenix.refine without using x-ray data:<br>
<br>
phenix.refine model.pdb data.mtz wxc_scale=0
main.bulk_solv=false strategy=individual_sites
main.number_of_mac=10<br>
<br>
If you need to use NCS, add to above: main.ncs=true
ncs.type=cartesian<br>
<br>
You can do all this using the GUI.<br>
<br>
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.<br>
<br>
Pavel<br>
<br>
On 3/5/13 1:48 PM, Sam Stampfer wrote:<br>
</div>
<blockquote type="cite">Dear Phenix Community,<br>
<br>
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).<br>
<br>
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?<br>
<br>
Thanks for your help!<br>
<br>
-Sam Stampfer<br>
<br>
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