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Re: [ccp4bb]: Additional capability needed for CIF generation inmtz2various



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Hi there,

> I am trying to deposit structure factors with the PDB, but I've
> hit a snag.  I'd like a general pathway that lets me produce an
> acceptable CIF file containing any arbitrary subset of the 
> information in an mtz file.  In particular I'd like to be able
> to include the measured I and sig(I).

    The program 'mtz2various', as far I understand, is *the*
    program widely used for converting a binary 'MTZ' reflection
    file to an ASCII (CIF) formatted file. (may be there are other
    programs, which I am not aware of.. so, apologies fot that!).

> So far as I can determine, the mtz2various utility would be the
> way to go, except that it basically ignores all entries other
> than FP, SIGFP, FC, and PHIC.

     I don't think so...

    When using mtz2various & for the case of a 'CIF' output option.. 
    the program will 'only' accept the following list of input labels:

    H, K, L, FP, SIGFP, DP, SIGDP, FC, PHIC, FOM, I+, SIGI+, I-, 
    SIGI-, FPART_BULK_S, PHIPART_BULK_S and FREE 
 
    Therefore, if you have measured the analomous data, you may be
    finding a way to incorporate IMEAN and SIGIMEAN (though you have
    options for I+, I-, SIGI+ and SIGI- columns to dump) in the
    output CIF file.

    For example, if you have an MTZ file, say inputref.mtz (which also
    has the anamolous data), with the following column labels:

    * Column Labels :

     H K L FO SIGFO DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN
     I(+) SIGI(+) I(-) SIGI(-) ISYM FreeR_flag

    A simple example script is:

    mtz2various   \
    HKLIN inputref.mtz \
    HKLOUT outputref.cif <<E
    OUTPUT CIF data_sf
    LABI I(+)=IMEAN   SIGI(+)=SIGIMEAN  FREE=FreeR_flag
    END
    E

   Then the output CIF file will look something like this:

loop_
_refln.index_h
_refln.index_k
_refln.index_l
_refln.status
_refln.intensity_meas
_refln.intensity_sigma
    1    0   14 o     0.1161E+05     472.8
    1    0   15 o      5359.         194.7
    1    0   16 o      777.8         35.88
    1    0   17 f      26.54         5.872
    1    0   18 o      242.2         21.03
etc..

Hope this helps..

Cheers,
Ravi.

======================================================================
|S.Ravichandran (Graduate student)  |E-mail: ravi@cmb2.saha.ernet.in |
|Crystallogr. & Mol. Biology Div.   |FAX:    (91)(033)-337-4637      |
|Saha Institute of Nuclear Physics  |                                |
|I/AF, Bidhan Nagar, Calcutta 700064|                                | 
|INDIA.      URL:- http://www-bsg.saha.ernet.in/ravi.html            |
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