[phenixbb] ncs_average output map

[Ursula Schulze-Gahmen]

That could be right. Would you suggest to do the averaging in CCP4 instead?

Ursula

On Mon, Dec 12, 2011 at 11:35 AM, Tom Terwilliger <terwilliger at lanl.gov>wrote:

> Hi Ursula,
>
> I am not sure if this is the (only) problem, but phenix.ncs_average does
> not know about NCS groups, so it only takes the first NCS group and
> averages it and writes out the map where that group has been averaged.
>
> So supposedly phenix.ncs_average should (1) average the density in the
> region where the 1st NCS group applies, and (2) leave original density
> elsewhere.
>
> Is that consistent with what you see?
>
> All the best,
> Tom T
>
>
> On Dec 12, 2011, at 12:27 PM, Ursula Schulze-Gahmen wrote:
>
> I am puzzled about my ncs-averaged output map.
> I determined the ncs relation using phenix.find_ncs with pdb and mtz
> input. The program finds 2 NCS groups with 3 molecules each and the rmsds
> are low. I then read in the ncs_spec file and an mtz file with map
> coefficients into phenix.ncs_average. I used the FOFCWT, PHFOFCWT
> coefficients. The output map seems cleaner than the unaveraged map and
> shows some of the same features, but the density around the 3 molecules is
> not identical. 2 of them look very similar, but the density around one of
> them is somewhat different. How is this possible if the map is averaged?
>
> Thanks for any suggestions or explanations.
>
> Ursula
>
>
>
> --
> Ursula Schulze-Gahmen, Ph.D.
> Assistant Researcher
> UC Berkeley, QB3
> 356 Stanley Hall #3220
> Berkeley, CA 94720-3220
>
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>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
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-- 
Ursula Schulze-Gahmen, Ph.D.
Assistant Researcher
UC Berkeley, QB3
356 Stanley Hall #3220
Berkeley, CA 94720-3220
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