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Re: [ccp4bb] Question about freeR tag
 

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CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008
Previous message:
Subject: Re: Why there are difference density when occupancy is 1.00
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-24 		Next message:
Subject: Summary solvent-resistant crystallisation plates
From: "Mark J {- dot -} van Raaij" vanraaij {- at -} USC {- dot -} ES
Date: 2008-01-24


Subject: Re: Question about freeR tag
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-24
You know you can convert the CNS FreeRflags to the mtz file?
Use Reflection utilities / convert to mtz and say you are inputted CNS /
Xplor data

Eleanor

But I believe there is an inevitable difference between CNS and Refmac
FreeRs - CNS scaled the work and free data seperately which for lower
resolution data will give a reduced difference between the 2 values.

Eleanor

Zheng Zhou wrote:
> 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)
>>
>>
>
>

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 24 January 2008
Previous message:
Subject: Re: Why there are difference density when occupancy is 1.00
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2008-01-24 		Next message:
Subject: Summary solvent-resistant crystallisation plates
From: "Mark J {- dot -} van Raaij" vanraaij {- at -} USC {- dot -} ES
Date: 2008-01-24


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