On Thursday 16 September 2010 09:56:14 am Dr. Mark Mayer wrote:
> Ethan wrote
>
> >I believe that deposition of Fc Phic FOM should be required.
> >Certainly it should be the recommended practice.
> >
>
> For the same series of structures I just deposited, which started the
> the riding H discussion, my mtz file had Fc Phic FOM + other data put
> out by Phenix - pavel can elaborate. rcsb stripped almost all of this
> and the processed file has only:
>
> HKL, Flag, Fc, SigmaF and FOC :{
Huh? That's not a cif fragment. What file are you looking at?
In my experience the PDB feeds back to you a cif format structure factor
file with a name like rcsb054058-sf.cif
Near the top of that file you should find a description of the data
columns. The columns present depend on what you fed it, of course.
loop_
_refln.crystal_id
_refln.wavelength_id
_refln.scale_group_code
_refln.status
_refln.index_h
_refln.index_k
_refln.index_l
_refln.F_meas_au
_refln.F_meas_sigma_au
_refln.intensity_meas
_refln.intensity_sigma
_refln.F_calc
_refln.fom
_refln.phase_meas
Caveat:
I have never tried to deposit a structure factor file from phenix;
maybe that triggers some other processing pathway. Does anyone here know?
I would say that the simple, and almost guaranteed to work, procedure
is to do the cif conversion yourself and deposit the cif file.
I noted in another message that the auto-conversion script on
the PDB deposition site has a tendency to lose columns.
That's why it is better to do the conversion yourself.
I can't say that they _never_ lose columns in an uploaded cif file.
I have had that happen, but only once and quite a while ago.
> What's a structural biologist to do?
The empiricist's approach.
Experiment till you find a procedure that works, then stick to it :-)
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
