This advance brings deep new meaning to crystallographic data having both a
real and an imaginary component!
On 3/31/20, 11:36 PM, "CCP4 bulletin board on behalf of Petr Kolenko"
wrote:
Dear colleagues,
We, the developers of a program for paired refinement, have found a
remarkable
NMR spectroscopists are ~50 years ahead of us on this. They call it
"zero filling". Fortunately, these extra data compress very well.
-James Holton
MAD Scientist
On 3/31/2020 9:36 PM, Petr Kolenko wrote:
Dear colleagues,
We, the developers of a program for paired refinement, have found a
:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Paired refinement proves data quality goes beyond the
spatial limits of the detector
That is awesome. It means we can add data up to a kilometer out, and
start modelling quarks?
I urge the community to deposit all raw data to a virtual
Center is operational and
prioritizing Covid-19 projects - http://getacrystal.org)
From: CCP4 bulletin board on behalf of Frank von Delft
Sent: Wednesday, April 1, 2020 1:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Paired refinement proves
That is awesome. It means we can add data up to a kilometer out, and
start modelling quarks?
I urge the community to deposit all raw data to a virtual detector of
1km in size - I'm sure Google will happily stump up for the storage
costs, the business case is unarguable.
On 01/04/2020
Dear colleagues,
We, the developers of a program for paired refinement, have found a remarkable
feature that should be shared with the community. The fact that data beyond the
arbitrary cutoff may cause an improvement of electron density and make your
models better is generally accepted. We
Dear CCP4BB-ers,
A recent discussion on the CPP4BB made it clear that people want an easy way to
run paired refinement on their data. This option has always been available in
the PDB-REDO webserver (https://pdb-redo.eu), but it was (un)cleverly hidden in
automation (see
measures?
JPK
*From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
Of *Robbie Joosten
*Sent:* Thursday, July 02, 2015 12:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] paired refinement
But it is not the R-free of the shell here. In paired refinement you
*To:* CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*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
Dear Eric Karg,
if you want to cut the resolution by only a few tenth of A, it is
sufficient to simply cut the resolution, e.g. within the refinement
program. If the data you want to exclude are quite some part of the
data, e.g. 30% or more, I would probably reprocess and rescale to be on
the
Thank you for all your comments! I think it would be great to have the paired
refinement implemented in future updates of refinement programs.
Coming back to my original questions: if I have overestimated the high
resolution cutoff, what is the correct procedure to refine against lower
mailto:ber...@upstate.edu
*Verzonden: *2-7-2015 18:43
*Aan: *CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*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
] *On Behalf
Of *Robbie Joosten
*Sent:* Thursday, July 02, 2015 12:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*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
*To:* CCP4BB@JISCMAIL.AC.UK
*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
On Thu, 2 Jul 2015 00:15:58 +0100, Eric Karg harvard...@yahoo.com 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
Subject: Re: [ccp4bb] paired refinement
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
for you case.
Cheers,
Robbie
Sent with my Windows Phone
Van: Keller, Jacobmailto:kell...@janelia.hhmi.org
Verzonden: 2-7-2015 20:12
Aan: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] paired refinement
Well, in that case, one could
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
parameters?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale
Tronrud
Sent: Thursday, July 02, 2015 1:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] paired refinement
While I was puzzling over an entry in the PDB some years ago (since
] *On Behalf
Of *Robbie Joosten
*Sent:* Thursday, July 02, 2015 12:46 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*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
mailto:ber...@upstate.edu
*Verzonden: *2-7-2015 18:43
*Aan: *CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
*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
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
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
mailto:ber...@upstate.edu
Verzonden: 2-7-2015 18:43
Aan: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] paired refinement
Another criterion for cutoff, also requiring the structure
Wasn’t all of this put to bed through the implementation of CC measures?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie
Joosten
Sent: Thursday, July 02, 2015 12:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] paired refinement
But it is not the R-free
...@janelia.hhmi.org
Verzonden: 2-7-2015 20:40
Aan: Robbie Joostenmailto:robbie_joos...@hotmail.com;
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Onderwerp: RE: [ccp4bb] paired refinement
You need unmerged data to calculate cc1/2. That's not the sort of data you get
from the PDB.
Yes, good point; I
@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
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
-7-2015 01:28
Aan: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] paired refinement
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
Hi,
In order to do a paired refinement you need 2 sets of Rwork/Rfree at each
resolution. The first is just the normal figures from refinement, the second
is from the structure refined at higher resolution but with the R/Rfree
calculated at the lower resolution. You can calculate this using
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 —
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