Re: [ccp4bb]: cif2mtz

["M.D.Winn" <M.D.Winn@dl.ac.uk>]

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First off, yes you do need to change the CIF names, as
you have done. I should add in more options some time,
although strictly speaking squared F is not the same
as intensity, so assigning _refln.F_squared_meas to
column I is dubious.

Now to your main problem. The simple answer is to leave
out the LABOUT line entirely. This is the cause of
the problem, and you are asking it to keep the default
names anyway. Without the LABOUT line, it works fine.

But this is a bug. There is a fixed cif2mtz.f on the
CCP4 prerelease directory:

ftp://ftp.ccp4.ac.uk/pub/prerelease/cif2mtz.f

Regards
Martyn


> I tried to convert a PDB reflection file from mmCIF format
> to MTZ using the following script:
> 
> cif2mtz  HKLIN r1d9ysf.cif HKLOUT test.mtz << eof > cif2mtz.out
> TITLE 
> CELL 40.58 111.01 140.42 90.0 90.0 90.0 
> SYMMETRY 20 
> LABOUT H=H  K=K L=L I=I SIGI=SIGI FC=FC PHIC=PHIC 
> END
> eof
> 
> The header of the CIF file is like:
> 
> data_r1d9ysf
> #
> loop_ 
> _refln.index_h 
> _refln.index_k 
> _refln.index_l 
> _refln.F_squared_meas 
> _refln.F_squared_sigma 
> _refln.F_calc 
> _refln.phase_calc 
> 4 4 0 60253.66 8600.38 412.70 180.0
> 6 4 0 895.29 10474.46 165.40 180.0
> ........
> 
> The output MTZ file had 5 columns with FC and PHIC only. I thought the
> item names in CIF file
> 
> _refln.F_squared_meas
> _refln.F_squared_sigma
> 
> might not be recognized by CIF2MTZ routine. Follow the documentation I
> modified them to 
> 
> _refln.intensity_meas
> _refln.intensity_sigma
> 
> but the program could not even generate an MTZ file, it gave the error
> 
>  ***  Error
>  From LWASSN : Duplicate column labels in output file, columns   4 and   7
> both have the label FC
> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
>  cif2mtz:  *** Program Terminated
>   
> Anything wrong in my CIF2MTZ script? Is there other way to achieve the
> format conversion, can I use F2MTZ treating CIF file as a free formatted
> ascii file?
> 
> Thanks for help,
> 
> Huiying
> --------------------------------------------------
> Huiying Li, Ph. D
> Department of Molecular Biology and Biochemistry
> University of California at Irvine
> Irvine, CA 92697, USA
> Tel: 949-824-4322(or -1797);  Fax: 949-824-3280
> email: hli@bragg.bio.uci.edu
> --------------------------------------------------
>  
> 
> 
> 


-- 


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*                                                                        *
*                  Dr. Martyn Winn                                       *
*                                                                        *
*      Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND     *
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