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: 38th MidAtlantic Crystallography Meeting Announcement
From: "Edward J {- dot -} Collins" collins1 {- at -} MED {- dot -} UNC {- dot -} EDU
Date: 2008-01-23 		Next message:
Subject: meeting suggestions
From: Ingrid {- dot -} Mechin {- at -} SANOFI-AVENTIS {- dot -} COM Ingrid {- dot -} Mechin {- at -} SANOFI-AVENTIS {- dot -} COM
Date: 2008-01-23


Subject: Re: Question about freeR tag
From: Zheng Zhou zhengzhouzz {- at -} GMAIL {- dot -} COM
Date: 2008-01-23
Thank you all for fast replying. The reason that I am trying to use a
different set of FreeR flag from the very beginning of the refinement is
that for some data set, my colleague's CNS refinement gave converged Rfree
and R work, 3% difference. However both my CNS and CCP4 refinement gave a
difference of about 7%. I was trying to use the same parameter settings as
my colleague in simulated annealing. His program is from his previous lab
and all the input files for CNS are modified as a batch file. But mine are
just individual files downloaded from CNS website.

Among those things I tried, I thought about looking at the true input data
for computing Rfree and Rwork. It appeared to me the FreeR flags in my
"First" runs are never randomized. Thanks for your reply, I guess I could
use a different flag number other than 0 (I know I am not supposed to change
this in the middle of a refinement). I even tried to use my colleague's
cross-validation file .cv for CNS. It still diverge in my runs. Anyone met
similar problem before, where CNS and CCP4 give a quite different R factors?
Thanks for your insight.

Zheng (Joe)

On Jan 23, 2008 9:50 AM, 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)
>
ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd