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 fe
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 rem
020 1:18 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 vi
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 05:
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 foun
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 https://journals.iucr.or
o believe in rules of thumb.
>
> best,
>
> Kay
>
> >
> >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?
> >>
> >
------------
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 safe
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
resol
>>> 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:CCP4BB@JISCM
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:CCP4BB@JISCMAIL.AC.UK] *On Behalf
>>> Of *Robbie Joosten
>>> *Sent:
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
>>
AC.UK
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/20
-off that may or may not be correct for you case.
Cheers,
Robbie
Sent with my Windows Phone
Van: Keller, Jacob<mailto:kell...@janelia.hhmi.org>
Verzonden: 2-7-2015 20:12
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp
mi.org>
> Verzonden: 2-7-2015 20:12
> Aan: CCP4BB@JISCMAIL.AC.UK<mailto: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 som
ell...@janelia.hhmi.org>
Verzonden: 2-7-2015 20:40
Aan: Robbie Joosten<mailto:robbie_joos...@hotmail.com>;
CCP4BB@JISCMAIL.AC.UK<mailto: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
7-2015 20:12
Aan: CCP4BB@JISCMAIL.AC.UK<mailto: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 empirica
r you case.
Cheers,
Robbie
Sent with my Windows Phone
Van: Keller, Jacob<mailto:kell...@janelia.hhmi.org>
Verzonden: 2-7-2015 20:12
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: Re: [ccp4bb] paired refinement
Well, in that case,
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
e 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
&
bject:* 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 Win
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 of
. Berry <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
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 or CCfree.
I think it is very unlikely that you could get Rfree =.2493 in a
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
On Thu, 2 Jul 2015 00:15:58 +0100, 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—>
Verzonden: 2-7-2015 01:28
Aan: CCP4BB@JISCMAIL.AC.UK<mailto: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. H
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 s
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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