so perhaps the problem indeed is sending different wavelengths as one
file...in our case there is only one crystal, one wavelength, i.e. one
loop, while I clearly submitted all three wavelengths.
Quoting "Miller, Mitchell D.":
We (JCSG) too have been depositing multiple data sets (including unmerged
original index intensities for each wavelength and even for multiple crystals
when one was used for phasing and another for refinement, and MAD phases
and DM modified map coefficients) since 2004 without problems. These
are all in separate data loops of a single structure factor file.
Regards,
Mitch
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Of Jens Kaiser
Sent: Friday, April 27, 2012 11:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Off-topic: PDB deposition of multiple
structure factor files
It might be a portal issue. But the pdb staff is very helpful in getting
this deposited. We deposited data of I think 4 "crystals" and 3
wavelengths with different phase sets in 2008. (The data was
anisotropic, 3.5/4.2 A resolution, model building was not straight
forward, so we wanted to preserve as much information as possible. If
memory serves right, we have experimental fobs, anisotropy corrected
fobs, a derivative and a semet dataset; if you're interested, pdb code
is 3dhw, have a look at the sf-file)
hth,
Jens
On Fri, 2012-04-27 at 20:35 +0200, 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
>
>
>
>
>
>
>
>
>
>
>
>
Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoléculas
Centro Nacional de Biotecnología - CSIC
c/Darwin 3, Campus Cantoblanco
28049 Madrid
tel. 91 585 4616
email: mjvanra...@cnb.csic.es
