Hi Jude,
thank you for your effort to desposit the untouched data.
I was actually wondering how to do this myself as I am getting close to
the deposition stage with my anisotropic data. Thank you for sharing
your concerns, it will be useful to other users.
Since Randy is asking for user's experience, what I've done in the past
was to dialog with the PDB and ask them to also include the original
data in the cif format. If I recall correctly, I've sent them the
original mtz file in the validation stage of the deposition, as the web
site only allows for one mtz file. Also, depending on how strong your
anisotropy is..., there was some "dialog" about data quality according
to standards, and other various concerns that we addressed in the
publication, but couldn't be accounted for in the deposition. So they
ended up accepting the data, with Author's comments.
What I was planning on doing for the current dataset, was to ask
staraniso to also include the original data in the final output. There
is a box to tick on the website, unticked by default. You can also
modify the labels there, asking for the modified data to be called
I_SA/SIGI_SA for example for StarAniso.
Hope it helps
Vincent
On 27/09/2018 09:56, Randy Read wrote:
Dear Kevin,
I’ve just been working through the issue myself of how to deposit both the pruned
data needed to reproduce the refinement and the unmassaged data. The advice I got
from the people at PDBe was to prepare an mmCIF file with two reflection loops.
The validation pipeline expects the first one to contain the data actually used in
refinement, so I prepared one in which the second loop contained the full set of
intensities. It should also be possible to have a third loop containing unmerged
original-index (but probably scaled) intensity data, and this would be a good
intermediate ground between the worst option of just depositing French & Wilson
(truncate) amplitudes and the ideal-world case of depositing the raw diffraction
images.
Like you, I used the sf-tool at wwPDB, but I’ve just double-checked and the
mmCIF file I got has the same free flags for both reflection loops. In case
this helps to narrow down why you had a problem and I didn’t, the data I
submitted were in a single MTZ file, and the R-free flags had been prepared
with the CCP4 convention, with values from 0 to 19, and not a binary convention
with just values of 0 and 1.
I’ve also been wondering about when you get to label the different intensity
sets! The mmCIF standard doesn’t have data types that distinguish different
kinds of observed intensities. We haven’t yet deposited the structure with the
data, and I’ve been hoping that you’re asked to provide labels during the
deposition process. Perhaps someone from one of the wwPDB sites, or someone
who has gotten as far as depositing such data, can comment!
Best wishes,
Randy Read
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail:
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.
www-structmed.cimr.cam.ac.uk
On 26 Sep 2018, at 19:34, Kevin Jude <kj...@stanford.edu> wrote:
I am preparing to deposit several structures that I refined against anisotropic
data that I truncated with STARANISO. I will of course be depositing the
original data with spherical resolution limits, but it seems that I should also
deposit the ellipsoidally truncated data that I actually refined against. To be
clear, these are the same dataset but in the second case the unmerged
reflections have been rescaled and I/SIGIs that fall outside the ellipsoid are
set to empty values. I have a technical problem with preparing the mmcif and a
broader question about presenting the data.
I've tried to create an mmcif file from my mtz using http://sf-tool.wwpdb.org, treating
the two sets of I/sigI as two datasets. For some reason, in the output file the test set
flags are reversed for the second "dataset" (whichever I choose to be second);
ie, o becomes f and f becomes o. This is a technical problem that I can correct with a
text editor, but still irritating.
More importantly, is there a way to distinguish in the file between the
spherically complete dataset and the truncated dataset that was used in
refinement in a way that is useful to future users? I have not worked with
mmcif before and am not sure what column names are permissible, nor what would
be recognizable to other users or software. I'm interested to hear the thoughts
and experiences of the community on this.
Best wishes
Kevin
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
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--
Vincent Chaptal, PhD
MMSB -UMR5086
Drug Resistance and Membrane Proteins Laboratory
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
http://mmsb.cnrs.fr/en/
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