Hi all,
Sorry for contributing to the noise as well as the signal in the discussion.
To clarify:
It is not an issue of not having a place to put the data as we certainly have
definitions for this and for intermediate phasing data sets. You cannot simply
put the data into the current REFLN category which is where we presently
collect reflection data.
At present, there is no official wwPDB policy in place describing how this
data is to be processed, validated and distributed. Stuffing it into the
structure factor files, as has been done informally by some depositors, is not
a good long term solution as there is no way for people to easily find the
information. What we'll likely end up doing is store these data in separate
files (just like for NMR the raw NOE peak lists and distance restraints are
likely to be archived and distributed as separate files).
As I tried to explain yesterday, the case for both unmerged Is and unassigned
NOE peak lists has been made, and this will get implemented. It will just take
a bit of time.
--Gerard
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
On Tue, 17 Sep 2013, Miller, Mitchell D. wrote:
Hi Martyn,
I too was puzzled by the statement that "unmerged data
cannot be handled properly as part of a PDB deposition."
We have deposited the unmerged original index intensities
for the refinement wavelength (and for additional wavelengths
used for phasing in the case of MAD) since 2005.
This was based on recommendation #2 from the "Report of Task Force
on Numerical Criteria in Structural Genomics" from the 2001
Airlie meeting (2nd Intl. Struct. Genomics Mtg.).
http://www.nigms.nih.gov/NR/rdonlyres/14937E88-B916-4503-A29E-FA11E4B3D445/0/numerical.doc
http://www.isgo.org/organization/members07/010410.html
Which states that "For X-ray data, unmerged integrated intensities (omitting
outliers but including systematically-absent axial reflections) should be
deposited
along with the final, merged intensities and amplitudes for all wavelengths
and/or
derivatives."
We worked the RCSB staff to refine the format of the mmCIF formatted
reflection containing multiple data loops for our depositions and this
has been used for more than 1300 JCSG depositions and the data is retrievable
from all wwPDB partner sites.
Regards,
Mitch
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn
Symmons
Sent: Tuesday, September 17, 2013 3:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] What kind of reflection data to deposit to PDB
Sorry to contradict,
But the mmCIF data model certainly does not seem to require hkl unique
within the reflection data.
Like CIF the mmCIF formalism has been developed to allow a complete
description of a diffraction experiment and the data arising from it.
There is a full description at
http://mmcif.pdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/diffrn_refln.html
(I am grateful to Rachel Kramer Green at the RCSB for pointing out these
links to the dictionary and the papers describing its development).
Having chosen mmCIF for the archive and then not using its flexibility
seems a bit like having your cake and NOT eating it.
It is strange to hear on a discussion board that recently considered the
advantages of depositing complete image data, that a case will have to
be made for allowing the deposition of full unmerged datasets.
++Martyn
On 16/09/2013 14:03, Gerard DVD Kleywegt wrote:
Dear all,
At present, unmerged data cannot be handled properly as part of a PDB
deposition. One reason for this is that changes to the mmCIF/PDBx data
model will be required (at the moment, hkl must be unique within the
reflection data, which is logical for merged data but precludes
handling of unmerged data). There are other (easier to resolve) issues
to work out, e.g. having to do with file naming and distribution via
the wwPDB ftp archive.
The wwPDB partners are presently focusing all efforts on rolling out
the new joint deposition and annotation system. Once this system is
reasonably stable we will look into accepting/validating/distributing
new kinds of data. This concerns not only unmerged Is for X-ray but
also unassigned NOE peak lists for NMR. We will seek the advice of the
corresponding wwPDB VTFs (Validation Task Forces) to help define the
data items that need to be captured, how the data should be processed
by wwPDB, and what kind(s) of validation is/are required.
--Gerard
---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
On Thu, 5 Sep 2013, Raji Edayathumangalam wrote:
Hi Folks,
Sorry for the non-ccp4 post.
I am trying to determine what is the best form of unmerged reflection
data
to deposit to the PDB. I have single wavelength anomalous data for my
structure and I have two flavors of scaled files from the same exact
set of
diffraction images: (1) data indexed and scaled in p1, and (2) data
indexed
in p222, scaled in Scalepack using the "no merge original index"
option and
converted to .mtz since the unit cell in the header of the output
.sca file
was missing.
The space group for the dataset is p212121.
Please could you let me know what might be the best approach.
Many thanks and cheers,
Raji
--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
******************************************************************
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
******************************************************************
The opinions in this message are fictional. Any similarity
to actual opinions, living or dead, is purely coincidental.
******************************************************************
Little known gastromathematical curiosity: let "z" be the
radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
******************************************************************
