gt;> > >> _______ >
>> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >>
Bijvoet Center for Biomolecular Research > >> Utrecht University > >> Padualaan
8, 3584 CH U
ake sure to add sufficient and correct meta data. > >> > >> Best wishes, >
>> Loes > >> > >> ___ >
>> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistr
red to our everyday use of > >> cloud services. And as Graeme
mentioned: when archiving raw data > >> make sure to add sufficient and correct
meta data. > >> > >> Best wishes, > >> Loes > >> > >>
__________________________
gt;>
> >> Best wishes,
> >> Loes
> >>
> >> ___________
> >> Dr. Loes Kroon-Batenburg
> >> Dept. of Crystal and Structural Chemistry
> >> Bijvoet Center for Biomolecular Research
> &
Dear all,
as a follow-up to our initial message (and similar to other activities
from the MX community), we added some content to our BUSTER wiki at
https://www.globalphasing.com/buster/wiki/index.cgi?Covid19
to show interested users how to (re-)refine existing PDB entries with
BUSTER and how
: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
Dear colleagues,
Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there mi
Dear Colleagues,
I would like to add my voice to those advocating making available raw
diffraction images and point out another resource for raw data deposition,
https://cxidb.org, particularly for the case of emerging methods such as
serial crystallography.
Cheers,
Filipe
On Thu, 19 Mar 2020 at
Hi
> While those text files would be heavy, they'd be still lighter than raw
> images and the whole useless white space they carry with them between
> reflections.
At the risk of extending this thread into a different direction, the "white
space (the images) carry with them between reflections
This last, very important point made by Graeme gives me the chance to plug
a satellite workshop at the IUCr Congress (end of August, so fingers
crossed that this will go ahead) on "MX raw image data formats, metadata
and validation". This is organized by Herbert Bernstein, Loes
Kroon-Batenburg, Br
___
>> Dr. Loes Kroon-Batenburg
>> Dept. of Crystal and Structural Chemistry
>> Bijvoet Center for Biomolecular Research
>> Utrecht University
>> Padualaan 8, 3584 CH Utrecht
>> The Netherlands
>>
>> E-mail : l.m.j.kroon-batenb...@uu.nl
>&g
AIL.AC.UK>>
namens Gerard Bricogne mailto:g...@globalphasing.com>>
Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
mailto:CCP4BB@JISCMAIL.AC.UK>>
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
Dear
Dear Julien,
On Thu, Mar 19, 2020 at 08:47:20AM +, Julien Cappèle wrote:
> Though I agree with you Clemens that raw images are amazing to work
> with as you can use any software you are confortable with, we cannot
> forget that depositing several TB of data for each lab would be bad
> for ecol
Dear all,
On Thu, 19 Mar 2020, Winter, Graeme (DLSLtd,RAL,LSCI) wrote:
Date: Thu, 19 Mar 2020 09:08:21
From: "Winter, Graeme (DLSLtd,RAL,LSCI)"
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
No matter how much data we pr
Van: CCP4 bulletin board namens Gerard Bricogne
Verzonden: woensdag 18 maart 2020 23:30
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
Dear colleagues,
Perusal and some initial (re-)refinement of the various SARS
Hi Folks,
Quick note on "Like a super raw image diet-plan for the incoming summer” - the
bslz4 compression used with Eiger works really well, and the data are pretty
close to entropy limit in terms of size - which means if you measure your data
carefully (i.e. low background etc.) you can reali
Hi everyone,
There are some very interesting ideas.
Though I agree with you Clement that raw images are amazing to work with as you
can use any software you are confortable with, we cannot forget that depositing
several TB of data for each lab would be bad for ecological reason. And because
d
Hi Clemens,
this is curious. You are right that there's a direct link to the raw data
on 6vs4, but there isn't one on http://www.rcsb.org/structure/6H56. I'll
contact RCSB to see where the problem lies.
All best.
Andreas
On Thu, Mar 19, 2020 at 8:34 AM Clemens Vonrhein
wrote:
> Hi Andrea
Dear Petr,
On Thu, Mar 19, 2020 at 06:45:31AM +, Petr Kolenko wrote:
> For those of you who are in touch with these data, would deposition
> of unmerged intensities in P1 in the whole detector range instead of
> complete dataset be good enough to „correctly“ re-evaluete the
> structure? Or is
Hi Andreas,
On Thu, Mar 19, 2020 at 07:06:32AM +0100, Andreas Förster wrote:
> - The link to the raw data can be found inside the mmCIF file under
> _pdbx_related_exp_data_set.data_reference. Whether it's also shown on one
> of the PDB sites is up to the designers of these sides. I cannot find a
people could offer
their spare time to help the others with someting?
Best regards,
Petr
From: CCP4 bulletin board On Behalf Of Andreas Förster
Sent: Thursday, March 19, 2020 7:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
As
As someone who's done this (for one structure of minor significance), I
would like to make a few comments:
- I highly encourage deposition of raw data. Why would you not? Now that
many labs are shut is the time to do it for all these datasets hiding
somewhere on abandoned hard disk. These disks
A wonderful idea Gerard and Clemens.
Sent from my iPhone
> On Mar 18, 2020, at 6:31 PM, Gerard Bricogne wrote:
>
> EXTERNAL EMAIL – Use caution with any links or file attachments.
>
> Dear colleagues,
>
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structure
(fax)
From: CCP4 bulletin board on behalf of Eleanor Dodson
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
Sent: Wednesday, March 18, 2020 5:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures
EXTERNAL
What a great idea? Have you approached the depositors? Eleanor
On Wed, 18 Mar 2020 at 22:31, Gerard Bricogne
wrote:
> Dear colleagues,
>
> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
> structures in the PDB seems to indicate that that there might be potential
> to
Dear colleagues,
Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease
structures in the PDB seems to indicate that that there might be potential
to improve these if refinements could be repeated after some reprocessing
and further analysis of the raw diffraction images, rath
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