waters, then repeat the above test.
Hope this helps.
-- Ian
> -Original Message-
> From: U Sam [mailto:[EMAIL PROTECTED]
> Sent: 22 June 2008 04:47
> To: Ian Tickle
> Subject: RE: [ccp4bb] How many reflections for Rfree?
>
>
> Hi Ian,
> I have nearly 610
ver is the expected value.
Cheers
-- Ian
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of U Sam
> Sent: 20 June 2008 21:23
> To: Mark J. van Raaij; ccp4bb@jiscmail.ac.uk
> Subject: RE: [ccp4bb] How many reflections for Rfree?
>
I use CCP4i, refmac5 for the refinement using data of 2.45 angstrom. My R and
Rfree is 0.182 and 0.267 respectively. For calculating Rfree ,5% of random data
(1715 reflections) was used . So I see there is a difference of about 8.5%
between R and Rfree. Is this difference reasonable ?
Any idea h
Hi Tassos,
I tried to summarize the discussion (or rather, some parts of it) in
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Test_set
Anybody is welcome to improve on this!
Kay
Anastassis Perrakis schrieb:
Hi-
I am afraid that the real issue might be that the real question is:
Randy Read wrote:
But there's another important issue: how many reflections do you need
to get a good estimate of the sigmaA values (as a function of
resolution) needed to calibrate the likelihood target? I know I've
discussed this in talks, but it doesn't look like I ever published
anything
Hi,
Apart from the issue of what to tell referees, there are two slightly
different practical issues. One question that has been addressed is
how precise the estimate of Rfree will be for a certain number of test
set reflections, and this has been discussed in papers by Axel and by
Ian T
u/
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Mark J. van Raaij
Sent: Monday, June 16, 2008 11:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How many reflections for Rfree?
Dear All,
It has recently been put to me that 5-10% of reflections shou
When we ran into reviewer complaints a while back we referred to Methods
in Enzymology, 277:366-396. I can't lay my hands onto this to verify
the statement, but back then it was good enough to placate the reviewer.
Full QnA with reviewer:
3) Why were only 1% of the reflections included in t
On Tue, 17 Jun 2008, Anastassis Perrakis wrote:
been highly correlated with the phase accuracy of the atomic model. In
practice, about 5-10% of the observed diffraction data (chosen at random
from the unique reflections) become sequestered in the test set. The size
of the test set is a compromis
Anastassis Perrakis wrote:
CCP4 [User Community] Wiki
The 'user' one has links to the IUcr Wiki and the "test set" article is
still not written.
The 'official' one does not touch the subject either.
Time to write it (with appropriate references!!!) ?
Good idea!
What are you looking at me
Hi-
I am afraid that the real issue might be that the real question is:
'How do I tell the referee of my paper that 1500 reflections are
enough?'
Something along the lines of a statement like:
"It is generally accepted by the X-ray crystallography community that
1000-1500 are far enough f
J. van Raaij
> Sent: Monday, June 16, 2008 11:22 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] How many reflections for Rfree?
>
> Dear All,
>
> It has recently been put to me that 5-10% of reflections should always
> be set aside for calculation of Rfree. Howe
Mark J. van Raaij wrote:
On a related note, how to refine a structure with only 5000
reflections, which could happen when you have a small a.u. and modest
resolution? Could, exceptionally, a lower absolute amount of
reflections be used for Rfree, say 500?
Eleanor (mostly) answered my identical
Dear All,
It has recently been put to me that 5-10% of reflections should always
be set aside for calculation of Rfree. However, when one has, say, 200
000 reflections (high resolution and/or large asymmetric unit), that
seems to me to be a waste, because it would mean removing 10 000 to 20
14 matches
Mail list logo
