[phenixbb] Omit map

[Nathaniel Echols]

On Tue, Nov 22, 2011 at 7:35 PM, Rajesh kumar <ccp4_sc at hotmail.com> wrote:
> I am new to Phenix. I have a structure 2.74 A structure with R/freeR
> 22.7/27.9%. But the molprobity score is 50th percentile.
> If I fix the outliers they wouldn't go away and molprobity score remains
> same or get worst.

Which version of Phenix are you using, and what are your current
RMS(bonds) and RMS(angles)?  Do you have NCS, and have you optimized
the weights?

> I  added my .pdb and .mtz and do SA-composit omit map. This is running from
> morning and I have feeling that I will get results after thanksgiving. Is
> this the correct way of doing a omit map for the purpose I mentioned?

Yes.  If you have a system with multiple processor cores, or a
queueing system, I'd recommend taking advantage of these when running
AutoBuild - although the SA omit maps are very slow, the composite
omit map procedure parallelizes very nicely.

-Nat