I would like to also add that depending on what you want to
use the test data for, you may find that the data JCSG has deposited
with the PDB is sufficient.
The JCSG crystal structures include the following data sections in
the structure factor file deposited with the PDB (since spring 2004).
1. First section -- loop over merged Fobs, (or Iobs), sigF (or sigI),
Fcalc, Phicalc, FreeR-flag (status)
2. For each wavelength of data used in phasing there is a separate loop
over the scaled, unmerged, original index intensities and sigI.
3. Then there is a data loop for the experimental phasing results listing
the HL-coefficients from the phasing program (usually autoSHARP or solve).
4. The last loop is over fom, pdbx_fom_weighted_fmap and phase from
density modification. The Fmap coefficient and the DM phase is the
starting map used for automated model building.
(For MR structures, the just the first 2 data sections are present).
If you are interested in testing MAD or SAD phasing, DM or autobuilding,
algorithms etc, then the data deposited with the PDB is probably sufficient
for your needs.
http://www.pdb.org/pdb/search/navbarsearch.do?newSearch=yes&isAuthorSearch=no&radioset=All&inputQuickSearch=JCSG%20crystal
If you wanted to reintegrate the data from the diffraction
images or if you wanted to compare your autotraced model with the
autotraced model we obtained, then these additional data (as well as
log files) are only available through the JCSG dataset archive. So
as Ashley mentioned, please request access to the archive if you are
still interested in this additional data.
Regards,
Mitch
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Deacon, Ashley
Sent: Thursday, June 12, 2008 9:41 AM
To: [log in to unmask]
Subject: [ccp4bb] JCSG dataset archive
All,
Thanks to everyone who has recently requested access to the
JCSG dataset archive. We have a large and growing number of users.
Your requests will be handled shortly and you will receive
notification via e-mail.
Our registered users fall into 3 main classes:
1) Methods developers who want access to a wide array of test data.
2) Students and postdocs who want datasets for training purposes.
3) Researchers interested in one of our structures, who want access
To all the data we have available, including datasets from different
constructs or crystal forms that didn't necessarily make it into our
final PDB deposition.
For those who may still be interested, the dataset archive can
be accessed through our structure gallery page:
http://www.jcsg.org/prod/scripts/structure_gallery/gallery.shtml
The datasets are available without restriction, most of them are Se MAD/SAD
or distant homology MR.
We do ask you to register and explain why you want access. This is largely
for tracking/statistics purposes (we won't be sending you a lot of junk mail).
Hopefully in the future we can improve the system to better serve our users.
Soon we will be adding diffraction image datasets for *all* our structures as
Soon as they are deposited.
In the meantime, if there is a dataset you would like that is not currently
available through the archive just drop me an e-mail.
Suggestions are always welcome.
Sincerely,
Ashley Deacon
Joint Center for Structural Genomics.
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