Re: PHASING categories and data names

• Messages sorted by: [ date ][ subject ][ author ]
• Previous message: Paula Fitzgerald: "PHASING categories and data names"
• Maybe in reply to: Paula Fitzgerald: "PHASING categories and data names"

Dear Paula,

Thank you very much for the responds and historical
information.  Since Joel asks me to deal with
the release of Structure Factors, I have to
clean up the differences between the mmCIF
and the PDB subset.  As you know, once the
SF data had been released, the changes
in the released SF data would cause problems
and would impact to the user community.
We will develop the policy for dealing with
such changes.

I will discuss your information with Joel
and collegues.  Hope we will work
more closely on the mmCIF for SF.

regards,
jiang.



On Feb 1, 10:22am, Paula Fitzgerald wrote:
> Subject: PHASING categories and data names
>
> Hello there -
>
> Jiansheng Jiang writes -
>
> > Still I could not find the PDB subset
> > cif for SF from mmCIF 0.9.0.
> >
> > >  _phasing_MIR_refln.der_id   . . . . . . . . . . . . . .    74
> > >  _phasing_MIR_refln.F_calc   . . . . . . . . . . . . . .    79
> > >  _phasing_MIR_refln.F_calc_au  . . . . . . . . . . . . .    85
> > >  _phasing_MIR_refln.F_meas   . . . . . . . . . . . . . .    91    99
  104
> > >  _phasing_MIR_refln.F_meas_au  . . . . . . . . . . . . .    95
> > >  _phasing_MIR_refln.F_meas_sigma   . . . . . . . . . . .    98
> > >  _phasing_MIR_refln.F_meas_sigma_au  . . . . . . . . . .   103
> > >  _phasing_MIR_refln.index_h  . . . . . . . . . . . . . .   108
> > >  _phasing_MIR_refln.index_k  . . . . . . . . . . . . . .   112
> > >  _phasing_MIR_refln.index_l  . . . . . . . . . . . . . .   116
> > >  _phasing_MIR_refln.phase_calc   . . . . . . . . . . . .   120
>
> Perhaps a little history would help clear up the mystery here.  Some years
> ago, the PDB needed a set of CIF definitions for their structure factor
> files.  Providing data items for the native data was a simple matter of
> added a few more data items to the REFLN category than were already present
> in the mmCIF draft.  But the PDB also asked us for data items for MIR data,
> and here we generated something based on the still (at that point) evolving
> PHASING categories in the mmCIF draft.
>
> Subsequent to that, the mmCIF draft dictionary went out for community review,
> and one of the changes that we were asked to make was to provide for storing
> all of the MIR (or MAD) data sets used in a phase determination within the
> same data block as the native data (the data against which the structure
> was eventually refined.)  This had not been our original data model - we had
> thought that users would store derivative data in separate data blocks.
>
> But people seemed to want them in the same data block as the native, so we
> redesigned the data model in the PHASING category to provide for this.  At
> present, the PHASING_SET categories are where the reflections are actually
> stored, and then the PHASING_MIR or PHASING_MAD categories can refer to those
> data sets by their set id.  This revised model for the PHASING categories was
> implemented in summer of 1995, and has been part of the mmCIF draft since
> that time.
>
> It seems that we have left some of the data names developed for the PDB
> structure factor files dangling in the process of responding to the desires
> of the community - I am sorry for that.  The question is how to fix the
> situation, and I see two paths.  The simplest would be for the PDB to switch
> to the data names in the current data model.  If for some reason that poses a
> difficulty, we would be happy to provide a compatability dictionary that
> aliases the old-style names to their current forms.  Please tell us which
> path you prefer to take, and we will act accordingly.
>
> Best wishes - Paula
>
> ********************************************************************************
>  Dr. Paula M. D. Fitzgerald  ______________ voice and FAX: (908) 594-5510
>    Merck Research Laboratories ______________ email:
paula_fitzgerald@merck.com
>      P.O. Box 2000, Ry50-105     ______________ or bean@merck.com
>        Rahway, NJ 07065  USA
>          (for express mail use 126 E. Lincoln Ave. instead of P. O. Box 2000)
> ********************************************************************************
>-- End of excerpt from Paula Fitzgerald



-- 
====================================================================
Jiansheng Jiang Ph.D.          | 
Protein Data Bank              | Phone: (516) 344-6388            
Biology Department, Bldg 463   | Fax:   (516) 344-5751
Brookhaven National Laboratory | mailto://jiang@bnl.gov
Upton NY 11973-5000, USA       | http://www.pdb.bnl.gov/~jiang  
====================================================================

• Previous message: Paula Fitzgerald: "PHASING categories and data names"
• Maybe in reply to: Paula Fitzgerald: "PHASING categories and data names"