[phenixbb] a few questions
PAfonine at lbl.gov
Fri Aug 4 14:45:52 PDT 2006
Hi Jianghai Zhu,
thanks for your questions!
> <>I have a structure refined to 2.5 A. After simulated annealing
> (start temp = 5000, cool rate = 25, final temp = 100, include TLS
> refinement and NCS restraint), my R and Rfree are 24.6% and 28.7%
> respectively. I then turned off the SA in the generated def file and
> carried on the combined refinement. My R and Rfree went up to 25% and
> 29.2% respectively. Why did the Rfree go up after refinement?
The difference between 28.7% and 29.2% is not large (=0.5%). If you run
a set of identical refinement jobs with different random seed you will
get the distribution of final R-factors ranging within 0.5%. So I would
not worry too much about this.
However, I would try different refinement strategy, for example:
1) you do SA refinement first;
2) then you do regular refinement + TLS.
> The RMSD of bonds and angles after either SA or combined refinement
> are about 0.006 and 0.851 respectively. Don't you guys think the
> geometry restraints are too tight?
At 2.5A resolution I wouldn't worry about these values. The resolution
is low enough to keep the geometry tight.
> How do I change the weight in PHENIX?
However, if you want you can play with the target weights. The total
target function in phenix.refine for the coordinates refinement is :
T = wxc_scale * wxc * Exray + wc * Egeom, where wxc is determined
automatically and wxc_scale is a parameter that the user can modify. So,
if you want to make the X-ray term stronger, then obviously you need to
increase the wxc_scale value. By default it is 0.5 (see parameters file
under the scope refinement.target_weights). Try several wxc_scale and
pick the refinement outcome you like best.
Let us know if you have more problems / questions.
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