Quick navigation:        Home   |    Site Map   ||    References   |    Biography   ||    Copyright   |    Other copyright   |    Contact us   |   
Protein structure
 

Re: [ccp4bb] Question about freeR tag
 

Basic tutorials: 		 
 

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 23 January 2008
Previous message:
Subject: Re: problem on protein precipitation
From: Lisa A Nagy lisanagy {- at -} UAB {- dot -} EDU
Date: 2008-01-23 		Next message:
Subject: Re: Why there are difference density when occupancy is 1.00
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-01-23


Subject: Re: Question about freeR tag
From: Roger Rowlett rrowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2008-01-23
Zheng Zhou wrote:
> Hi, All
>
> Could any tell me how CCP4 handle free R flag? I know It is important
> to select the same** FreeR reflections if I move to next step of
> refinement. But everytime I start from fresh, the freeR Flag remains
> unchanged. The Rwork and Rfree of my models are fine ( 20.7% and
> 22.9%). I thought Rfree was randomly generated. I asked more
> experienced people in the lab and neighbor labs, and didn't get a
> straight answer. Did I do something wrong?
>
> Thanks and sorry to bother others.
>
> Zheng (Joe)
You have two options for setting the FreeR flag in CCP4i. You can do it
at the time of scaling in SCALA by ticking the button "Ensure unique
data & add FreeR column for x.xx fraction of data." 5% of the data is
the default, which may be excessive depending on the number of total
reflections you have.

If you did not set the FreeR flag during scaling, you can do it later
using the Convert to MTZ & Standardise task under Reflection Utilities
in the GUI. Tick "Create a full unique set of reflections and generate
FreeR data" and select your FreeR fraction in the box near the bottom of
the task window.

Once the FreeR flag is set it should not change, and you should not
generate a new set of FreeR flags again during the refinement. The idea
is to set aside some data early on that is never used to refine the
model so that it is as unbiased as possible in evaluating your
refinement statistics and guarding against model bias. When refining
with Refmac5, tick the "Exclude data with freeR label FreeR_flag with
value of 0" to ignore the FreeR data during refinement.

Cheers,

--
------------------------------------------------------------------------
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowlett@mail.colgate.edu

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 23 January 2008
Previous message:
Subject: Re: problem on protein precipitation
From: Lisa A Nagy lisanagy {- at -} UAB {- dot -} EDU
Date: 2008-01-23 		Next message:
Subject: Re: Why there are difference density when occupancy is 1.00
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-01-23


ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd