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
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 real-
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-
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 using both refmac5
, 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 using both refmac5
and coot.Here are some problems I'm facing. Really hope you can give me
some suggestions.
1
]
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 using both refmac5
and coot.Here are some problems I'm facing. Really hope you can give me
some suggestions
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 against a map
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
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
model
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 right: you should not use free-r reflections in calculation
??
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
suggestions.
1
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 and R
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:
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