Dear Mark,
This is interesting. I also had submitted my data via the PDBe
(European portal). While they allow deposition of multiple datasets,
only a single file can apparently be made available for download from
the site. In contrast to your case, for my deposition the second
deposited dataset is not explicitly listed though.
Cheers,
Florian
On Apr 27, 2012, at 2:35 PM, Mark J van Raaij wrote:
again, it looks like this is particular to the US portal.
We submit via the European www.pdbe.org and can submit multiple
datasets.
See 2XGF for an example.
Note: I think from www.rcsb.org only one file can be downloaded, but www.pdbe.org
clearly shows both.
Although you are in the US, you can use the pdbe deposition tool
AUTODEP - or the Japanese one, if you like.
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 27 Apr 2012, at 20:23, Florian Schmitzberger wrote:
Dear All,
With my most recent PDBe deposition, in addition to the native
data, I had intended to deposit the anomalous data, used for
structure determination, and make it available for download. This
turned out to be less straightforward than I had anticipated,
because the current PDB convention is to only allow a single
structure factor file for experimental data (usually the native
dataset), available for download from the PDB. In my case, the
anomalous data were concatenated with the native data into a single
cif file (this worked and made sense, because both for both
datasets the unit cell dimensions are virtually identical).
I imagine it would be beneficial to be able to make available more
than a single structure factor file, including the ones derived
from experimental phasing, in the PDB, along with the final
coordinates, without concatenating the data into a single file
(which may lead to confusion to users when downloaded). Is this
anything the PDB is already working to implement in the near future
(perhaps via the coming PDBx format)?
Best regards,
Florian
-----------------------------------------------------------
Florian Schmitzberger, PhD
Biological Chemistry and Molecular Pharmacology
Harvard Medical School
250 Longwood Avenue, Seeley G. Mudd 123
Boston, MA 02115, US
Tel: 001 617 432 5603
