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Re: [ccp4bb] process SeMet labelled data
 

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CCP4bb <-- 2007 <-- February 2007 <-- 28 February 2007
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From: emmanuelprata {- at -} GMAIL {- dot -} COM
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Subject: Solubility of ligands
From: I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-02-28


Subject: Re: process SeMet labelled data
From: vonrhein {- at -} GLOBALPHASING {- dot -} COM
Date: 2007-02-28
>On Feb 28, 2007, at 14:37, shivesh kumar wrote:
>
>Dear all,
>I have a data set at 2.2A, of the selenomethionene labelled
>protein.How should I process the data.

Some hopefully useful remarks (fairly random and not complete and
exhaustive):

1. make sure to mask out the backstop and beamstop holder
correctly. Although various integration software claims to do this
fairly automatic it is always better to do a good job on this.

2. check the rejected reflections (at the scaling/merging step): is
there some system in those rejections? The two files produced by
SCALA (ROGUES and a xmgr file that plots the detector position of
rejected reflections) are very helpful. It can show ice-rings, bad
beamstop-masking (see point 1) etc.

3. heavy atom detection/phasing software will also write out some
helpful information about outliers: if there are some suspicious
messages (e.g. warnings in autoSHARP) they usually point back to
problems in data processing (see point 1).

4. if you collected several datasets/wavelengths: you can give those
to SCALA for some 'local scaling'. This will also show you those
really helpful CC(Dano) plots. But be careful with absorption
correction: all datasets/sweeps need to be indexed identically.

5. always remember what your first reaction was when looking at the
images: 'great' images should give you good statistics further down
the pipeline. But if 'awfull' images give you good statistics I
would be suspicious ...

6. unless you really know what's going on: stick with program
defaults. Usually the developers have a very good idea why the
program is doing things in a specific way.

Cheers

Clemens

--

***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************

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CCP4bb <-- 2007 <-- February 2007 <-- 28 February 2007
Previous message:
Subject: video zueras do tooby
From: emmanuelprata {- at -} GMAIL {- dot -} COM
Date: 2007-02-28 		Next message:
Subject: Solubility of ligands
From: I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-02-28


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