MR in CNS

Jack Tanner tannerjj at missouri.edu
Tue Mar 14 10:45:05 EST 2000


I'd be concerned with an MR answer with CC=0.22.  What's the R-factor?

My MR experience is with X-plor, but this probably applies for CNS too:

Did you do Patterson Correlation filtering of the rotation function peaks?
If not, try it.  I (and many others, of course) have found that the top
rotation function peak often is NOT the correct solution.

You should also try AMoRe.


You might want to check out these two references:

Brünger, Axel T.
Patterson correlation searches and refinement
Methods in Enzymology
276, 558-580
1997

J. Navaza, P. Saludjian
AMoRE:  An automated molecular replacement program package
Methods in Enzymology
276, 581-594
1997



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>From: Yu Wai Chen <ywc at mrc-lmb.cam.ac.uk>
>X-Newsgroups: bionet.software.x-plor
>Subject: Re: MR in CNS!
>Date: Tue, 14 Mar 2000 13:49:46 +0000
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>Miljan Simonovic wrote:
>>
>> I ran rf (first peak 0.08, second 0.06, sigma 0.014) and tf in CNS
>> (v1.0). I got the best peak with following values:
>> corr.coeff.=0.22, packing =0.53. Other peaks have lower values (0.14,
>> 0.41 respectively). I am searching for one molecule per asymmetric unit.
>> Should I expect higher values for the correct solution or should I just
>> proceed further?
>
>In MR, values are relative and case dependent.  You look at
>signal-to-noise ratio rather than absolute value of the corr.coef.
>Looks like yours has a high s/n ratio.  If I were you, I'll check the
>crystal packing to make sure there is no steric overlap and calculate
>sigmaA-weighted maps.  If you see a good map, then you are on the right
>track.  Mind you I've come across very high s/n ratio yet the solution
>is wrong...
>
>--
>===================================================================
>Yu Wai CHEN, Ph.D. ..................   email:ywc at mrc-lmb.cam.ac.uk
> Centre for Protein Engineering,             tel:+44-(0)1223-402148
> MRC Centre, Hills Rd, Cambridge CB2 2QH, UK fax:+44-(0)1223-402140
> WWW homepage: http://www.mrc-cpe.cam.ac.uk/~ywc
>
-------------------------------------------------------------------------------
Dr. John J. Tanner
Department of Chemistry
University of Missouri - Columbia
125 Chemistry Building
Columbia, MO 65211
USA

office: 573-884-1280
lab:    573-884-1281
fax:    573-882-2754
tannerjj at missouri.edu
http://www.chem.missouri.edu/TannerGroup/tanner.html
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