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I was surprised to hear that others have had so much trouble with
the deposition of phases at the RCSB site. At JCSG, we have been
depositing experimental phases since Dec 2003/Jan 2004 without
any problems from the RCSB.
Our standard for MAD/SAD structures is to have several data
sections that are defined in the structure factor file.
1- loop over merged refinement data / results Fobs, SigFobs, Fcalc, PhiCalc,
status
2- loop over scaled but unmerged intensities for the refinement wavelength
3- loop over scaled but unmerged intensities for 2nd wavelength
4- continue with similar loops over all wavelengths
.....
5- loop over HL-coefs for the experimental phases
6- loop over DM modified phases (before including partial
models from iterative building) phase, fom and _refln.pdbx_fom_weighted_fmap
The last item is a pre-weighted amplitude that can be used with the
DM phases to calculate the MAP that was used for the start of
auto-building.
In cases were we have MAD phases from one crystal and our final
refinement is against a second higher resolution crystal, we include
the scaled, unmerged original index intensity from both crystals / all
wavelengths. We use the refln.crystal_id value to identify which data
comes from which crystal in the file.
Regards,
Mitch
P.S. for those that are interested in the mmCIF format details
for our structure factor files, the file structure starts with
data_rxxxsf for the refinement data (where xxxx is the PDB ID).
Then subsequent data values of the form data_rxxxxAsf,
data_rxxxxBsf, etc... By having them in separate data_ section
we can have slightly different unit cells for the different
wavelengths / crystals.
Here are a few examples....
2AML is a standard 2-wavelength MAD case
http://www.pdb.org/pdb/explore/explore.do?structureId=2AML
and 2HUJ is an example of a case with 2 crystals. One for
3-wavelength MAD and the second for refinement.
http://www.pdb.org/pdb/explore/explore.do?structureId=2HUJ
________________________________
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Erik Vogan
Sent: Friday, December 15, 2006 7:34 AM
To: William Scott
Cc: [email protected]
Subject: Re: [ccp4bb]: PDB and phases ...
Bill (and list),
When I initially deposited the diffraction data for structure I solved as a
graduate student, I met with the same "they won't take them" attitude regarding
my experimental phasing data (full MAD/MIR data sets, not phases). It was
after some encouragement from people at the 2004 Diffraction Methods GRC that I
decided to take the attitude "they bloody will take them." After all, the PDB
works for _us_, not the other way around.
In any case, after writing a couple of very strongly worded emails, the
RCSB did, in fact, accept my experimental phasing data sets.
Although this does not in any way specifically address your attempt to
contribute phases, the mmCIF format contains both _refln.phase_meas and
_refln.phase_calc items, so there should be no reason for the fine folk at the
PDB to refuse your (very reasonable) request that they accept phases along with
the amplitudes.
Finally, for what it is worth, the EBI seemed much more willing to accept
heavy atom data sets. They did not even raise a tiny fuss about the issue.
However, if you have already contributed a structure to a specific site (say,
RCSB for instance), then you will need to take the issue up with that site, as
they are the only ones who can update the initial deposition.
Erik Vogan, Ph.D.
Structural Biology and Computational Chemistry
Wyeth Research
200 Cambridgepark Drive, T6011E
Cambridge, MA 02140
(617) 665-5501
>>> "William Scott" <[EMAIL PROTECTED]> 12/15/2006 10:05:00 AM >>>
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I've tried to give them phases. They won't take them. I think it would
be really helpful to have the experimental map (or a composite-omit map in
the case of MR). I don't think there is a way of representing the latter
as phases, so the option to submit phases and/or map should be available.
Peter Adrian Meyer wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk
> <http://www.ccp4.ac.uk > ***
>
>
>> I agree that more information to referees is desirable, & I've often
> wanted to see the coordinates and the structure factors to check things.
> But to follow up after publication, there are still a lot of structures
> deposited without structure factors - why is deposition of structure
> factors not compulsory? And who can change things so that
>
> This is probably an idiot newbie question, but the vast majority of
> structures I've seen in the PDB w\ "structure factors" only have
> amplitudes. Granted, you could calculate phases from the model; but
> shouldn't a structure factor be a complex number instead of a real number?
>
> I'd think there should be the experimental phases, or at least model
> phases with the weighting scheme the authors used for their final maps for
> it to be called a structure factor...but evidentally I'm wrong.
>
>
> Pete
>
>
> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
>
>
>
>
