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Re: [ccp4bb] question about processing data
 

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CCP4bb <-- 2008 <-- March 2008 <-- 17 March 2008
Previous message:
Subject: Re: problem installing arp/warp
From: Mario Sanches msanches {- at -} LNLS {- dot -} BR
Date: 2008-03-17 		Next message:
Subject: Re: question about processing data
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-03-17


Subject: Re: question about processing data
From: James Stroud jstroud {- at -} MBI {- dot -} UCLA {- dot -} EDU
Date: 2008-03-17
Redundancy of 4.8 for a 74% complete shell (if I understand which
shell these stats are for) suggests you have assumed too much symmetry
and are rejecting a lot of reflections during scaling. Is this the
case? The I/sigma suggests you could drop the symmetry and re-scale
without losing a lot of data if this is the case.


On Mar 17, 2008, at 4:03 AM, Melody Lin wrote:

> well, redundancy for the highest shell is 4.8, I/sigma is 3, Rmerge
> for overall is 0.08 for highest shell is 0.336. I/sigma and Rmerge
> don't seem quite nice...
>
> thanks.
>
> On Mon, Mar 17, 2008 at 11:51 AM, Partha Chakrabarti
> wrote:
> Hi Melody,
>
> There was a nice discussion in this year's ccp4 study weekend. In
> general, one needs to consider several factors.. If you were at 3A, or
> low symmetry, you would of course try to get the maximum out of it, on
> the other hand, there are requirements for experimental phasing.. in
> general, judge it from:
>
> 1. Completeness
> 2. Redundancy
> 3. I / Sigma
> 4. R merge statistics
>
> Not just one of them. If you are pushing it too far, you will see the
> effect in later refinement step..
> With 74% completeness, how does the other parameters look like?
>
> HTH, Partha
>
>
> On Mon, Mar 17, 2008 at 10:06 AM, Melody Lin
> wrote:
> > Hi all,
> >
> > I have always been wondering... for a data set diffracting to say
> 2.15
> > Angstrom but in the highest resolution shell (2.25-2.15) the
> completeness is
> > 74%, should I use merge all the data and call it a 2.15 A dataset
> or I
> > should cut the data set to say 2.25 A where the highest resolution
> shell has
> > better completeness (>85%)? What is an acceptable completeness
> value for the
> > highest resolution shell?
> >
> > Thank you.
> >
> > Best,
> > Melody
> >
>
>
>
> --
> MRC National Institute for Medical Research
> Division of Molecular Structure
> The Ridgeway, NW7 1AA, UK
> Email: pchakra@nimr.mrc.ac.uk
> Phone: + 44 208 816 2515
>

--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095

http://www.jamesstroud.com

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CCP4bb <-- 2008 <-- March 2008 <-- 17 March 2008
Previous message:
Subject: Re: problem installing arp/warp
From: Mario Sanches msanches {- at -} LNLS {- dot -} BR
Date: 2008-03-17 		Next message:
Subject: Re: question about processing data
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2008-03-17


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