Hi all,
I have read recent SERCA paper on IUCrJ and found their discussion
interesting.
"Structural studies of P-type ATPase–ligand complexes using an X-ray
free-electron laser" by Maike Bublitz et al.
http://journals.iucr.org/m/issues/2015/04/00/jt5009/index.html
In addition to CC1/2 and paired refinement, they scrambled indices
of reflections and showed Rfree indeed went up.
If we repeat permutations many times and calculate CC1/2 every time,
we can obtain empirical distribution of CC1/2 under null hypothesis
and thus calculate p-value. This is called permutation test in
statistics. I am wondering how this p-value compares with p-values
calculated by Student's t-test. Since t-test does not take the effect
of multiplicity into the account, I think the permutation test
gives more accurate value. (That is, CC1/2 calculated from a dataset
with multiplicity 30 should be more accurate and "reliable" than
that calculated from a dataset with multiplicity 2, but this difference
is ignored in t-test.)
Did anyone try this?
Best regards,
Takanori Nakane
On 2015年07月03日 04:41, Tim Gruene wrote:
Hi Robbie,
I have been wondering how much information would be present in a
weighted CC1/2 with weights from the ML refinement program.
As I understand the concept behind paired refinement, one can use much
higher resolution data in refinement than you would expect from the
(classical) scaling statistics, because refinement programs down-weight
the outliers.
Maybe a weighted CC1/2 would be a convenient short cut the more time
consuming paired refinemement? How easily could the calculation of a
weighted CC1/2 be implemented in refmac? Refmac would have to merge the
data internally, but that's just a simple formula to implement.
Best,
Tim
On 07/02/2015 08:28 PM, Robbie Joosten wrote:
Hi Jacob,
You need unmerged data to calculate cc1/2. That's not the sort of data you get
from the PDB. But anyway, we have a fairly simple automated test that we can
use on a case-by-case basis. I would argue that that is nicer than a empirical
cut-off that may or may not be correct for you case.
Cheers,
Robbie
Sent with my Windows Phone
________________________________
Van: Keller, Jacob<mailto:[email protected]>
Verzonden: 2-7-2015 20:12
Aan: [email protected]<mailto:[email protected]>
Onderwerp: Re: [ccp4bb] paired refinement
Well, in that case, one could simply look at the plot of CC1/2 versus
resolution and see the step up to one, conclude something was off.
I wonder whether PDB REDO was able to get some empirically-determined values
for CC1/2 cutoffs by comparing paired refinement versus CC1/2 versus other
parameters?
JPK
-----Original Message-----
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dale
Tronrud
Sent: Thursday, July 02, 2015 1:46 PM
To: [email protected]
Subject: Re: [ccp4bb] paired refinement
While I was puzzling over an entry in the PDB some years ago (since
obsoleted) I noticed that all the high resolution amplitudes were equal to
11.0! This was before CC1/2 but for this structure it would have been equal to
one, and yet the outer data were useless. A practical test like paired
refinement can't be fooled in this way.
Dale Tronrud
On 7/2/2015 10:25 AM, Edward A. Berry wrote:
My take on this-
No one has been willing to specify a cutoff (and probably there is no
rigorous way to mathematically define the cutoff) and say "If CC* (or
CCfree or
whatever) is below X
then it will not improve your structure, if above X then it will".
Probably depends
among other things on how strong the lower resolution data is, how
good the structure is without the added data.
On the other hand in paired refinement, if adding the data improves
the structure as measured by Rfree in a zone excluding the added data,
then it is hard to deny that that data are worth including.
eab
On 07/02/2015 12:52 PM, Keller, Jacob wrote:
Wasn’t all of this put to bed through the implementation of CC measures?
JPK
*From:*CCP4 bulletin board [mailto:[email protected]] *On Behalf
Of *Robbie Joosten
*Sent:* Thursday, July 02, 2015 12:46 PM
*To:* [email protected]
*Subject:* Re: [ccp4bb] paired refinement
But it is not the R-free of the shell here. In paired refinement you
take the R-free of the reflections outside the shell.
Cheers,
Robbie
Sent with my Windows Phone
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*Van: *Edward A. Berry <mailto:[email protected]>
*Verzonden: *2-7-2015 18:43
*Aan: *[email protected] <mailto:[email protected]>
*Onderwerp: *Re: [ccp4bb] paired refinement
Another criterion for cutoff, also requiring the structure to be
solved, is the agreement between data and structure, e.g. Rfree or CCfree.
I think it is very unlikely that you could get Rfree =.2493 in a
shell which contains only noise. So I would suggest doing paired
refinement to 2.2 and 2.1 A (if the data is available).
On 07/01/2015 07:15 PM, Eric Karg wrote:
> Hi all,
>
> I have a dataset processed in XDS to 2.3 A (based on CC1/2). I'm
trying to do "paired refinement" to determine the optimal resolution
cutoff. Here is what I get at different resolutions set in Phenix:
>
> Final Rfree/Rwork:
> 2.7—> 0.2498/0.2027
> 2.6—> 0.2519/0.2009
> 2.5—> 0.2567/0.2025
> 2.4 —> 0.2481/0.2042
> 2.3 —> 0.2493/0.2075
>
> The geometry of all output structures are similar.
>
> 1. What is the high resolution cutoff based on these data? I know
that Rfree/Rwork at different resolution should not be compared, but
is there a simple way to do the test as described in the K&D 2012
Science paper using Phenix GUI?
>
> 2. For refining a structure at a lower resolution (lower than the
initial dataset), do I simply set the resolution limit in the
refinement or I need to reprocess the data starting from the images?
Do I need to do anything with Rfree flags? Based on the discussions
on this forum I know I should deposit the highest resolution dataset
but my question is about the mtz file which will be used for refinement.
>
> Thank you very much for your help!
>
