Hi Robbie,
> I agree that you bias R-free after the real-space refinement
> >
> >
> > well, ok, isn't it enough to realize that this is bad and should be
> avoided ? (I
> > guess we all know we should never bias Rfree!)
> >
> >
> > My point was that we normally do not calculate R-free
Hi Pavel,
> I agree that you bias R-free after the real-space refinement
>
>
> well, ok, isn't it enough to realize that this is bad and should be avoided ?
> (I
> guess we all know we should never bias Rfree!)
>
>
> My point was that we normally do not calculate R-free after re
Hi Robbie,
I agree that you bias R-free after the real-space refinement
well, ok, isn't it enough to realize that this is bad and should be avoided
? (I guess we all know we should never bias Rfree!)
> My point was that we normally do not calculate R-free after real-space
> refinement,
It's
; To: Robbie Joosten
> Cc: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] coot problems to decrease R FREE
>
> Hi Robbie,
>
>
> I agree with Ed that you probably should not leave out your free
> reflections in real-space under normal circumstances.
>
>
> Phoebe is
Hi Pavel
When you say "I can clearly demonstrate it", does "it" refer to the fact
that Rfree gets biased? Have you explored how strong the effect is?
To date, I'd laboured under the impression that real and reciprocal
space are numerically very different things, i.e. what you refer to as
"m
Hi Robbie,
I agree with Ed that you probably should not leave out your free
> reflections in real-space under normal circumstances.
>
Phoebe is right: you should not use free-r reflections in calculation of
map that you are going to use for real-space refinement. Otherwise you will
be biasing Rfr
nt from my Windows Phone
Van: Edward A. Berry
Verzonden: 24-4-2014 15:58
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] coot problems to decrease R FREE
On 04/24/2014 08:33 AM, Phoebe A. Rice wrote:
> If you are doing real-space refinement of the entire model
>
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>>
>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robbie
>> Joosten [robbie_joos...@hotmail.com]
>> Sent: Monday, April 21, 2014 4:4
4BB@JISCMAIL.AC.UK] on behalf of Robbie Joosten
> [robbie_joos...@hotmail.com]
> Sent: Monday, April 21, 2014 4:40 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] coot problems to decrease R FREE
>
> Dear Peter,
>
>> I'm a novice of coot and ccp4. Now I'm doing refi
bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robbie Joosten
[robbie_joos...@hotmail.com]
Sent: Monday, April 21, 2014 4:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coot problems to decrease R FREE
Dear Peter,
> I'm a novice of coot and ccp4. Now I'm doing refinement us
??
Gesendet: Montag, 21. April 2014 02:34
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] coot problems to decrease R FREE
Dear all,
I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5 and
coot.Here are some problems I'm facing. Really hope you can give me some
Hello Peter,
1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of
> refmac5 I got R factor which is 0.26 and R FREE which is 0.31. My question
> is what the final R factor and R FREE should be after several rounds of
> refinement by refmac5 and coot.
>
answer can be found here
Dear Peter,
> I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5
> and coot.Here are some problems I'm facing. Really hope you can give me
> some suggestions.
>
> 1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of
> refmac5 I got R factor which is 0.26
Dear all,
I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5 and
coot.Here are some problems I'm facing. Really hope you can give me some
suggestions.
1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of refmac5
I got R factor which is 0.26 and R FREE w
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