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Re: [ccp4bb]: problems with cif2mtz
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As far as I can see, entry r1aacsf doesn't contain
a _refln.status column ?!
Martyn
>
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> Hello all,
>
> I'm having some problems with cif2mtz. The program seems to ignore the
> _refln.status line in my cif file, producing an mtz file with the
> following description:
>
> Col Sort Min Max Num % Mean Mean Resolution
> Type Column
> num order Missing complete abs. Low High
> label
>
> 1 ASC 0 32 0 100.00 11.6 11.6 24.62 1.80
> H H
> 2 NONE 0 48 0 100.00 18.9 18.9 24.62 1.80
> H K
> 3 NONE 0 25 0 100.00 9.6 9.6 24.62 1.80
> H L
> 4 BOTH ? ? 19059 0.00 ? ? -999.00 0.00
> I FREE
> 5 NONE 14.9 2513.0 0 100.00 317.66 317.66 24.62 1.80
> F FP
> 6 NONE 2.4 207.7 0 100.00 18.95 18.95 24.62 1.80
> Q SIGFP
>
> The _refln.status fields of the .cif file are either 0 (working set) or
> 1 (free set), which appears to be a CIF file format standard. I've
> only noticed this because I hand-checked the .mtz file produced by
> running the "convert to mtz and standardize" set of programs in CCP4i
> 4.2.2. Although I stated to "keep existing rfree data", it actually
> generated a completely new set of rfree flagged reflections. It
> appears that this problem resulted from the original importing error of
> cif2mtz. I've been working with the CIF file for amicyanin (1AAC) at:
>
> ftp://ftp.rcsb.org/pub/pdb/data/structures/all/structure_factors/
> r1aacsf.ent.Z
>
> And can be reproduced by the command:
>
> uncompress r1aacsf.ent.Z
> mv r1aacsf.ent r1aacsf.cif
>
> then
>
> cif2mtz hklin r1aacsf.cif hklout foo.mtz << EOF
> CELL 58.500 86.900 46.900 90.00 90.00 90.00
> SYMM P21212
> END
> EOF
>
> Has anyone experienced this problem before? Or know a work around?
>
> Mark
>
> Mark DePristo
> Ph.D. Candidate
> Dept. of Biochemistry
> Cambridge University
> mdepristo@cryst.bioc.cam.ac.uk
> http://www-cryst.bioc.cam.ac.uk/~mdepristo/
> --Apple-Mail-2--989291867
> Content-Transfer-Encoding: 7bit
> Content-Type: text/enriched;
> charset=US-ASCII
>
> Hello all,
>
>
> I'm having some problems with cif2mtz. The program seems to ignore
> the _refln.status line in my cif file, producing an mtz file with the
> following description:
>
>
> <fontfamily><param>Courier</param> Col Sort Min Max Num
> % Mean Mean Resolution Type Column
>
> num order Missing complete abs. Low High
> label
>
>
> 1 ASC 0 32 0 100.00 11.6 11.6 24.62 1.80
> H H
>
> 2 NONE 0 48 0 100.00 18.9 18.9 24.62 1.80
> H K
>
> 3 NONE 0 25 0 100.00 9.6 9.6 24.62 1.80
> H L
>
> 4 BOTH ? ? 19059 0.00 ? ? -999.00 0.00
> I FREE
>
> 5 NONE 14.9 2513.0 0 100.00 317.66 317.66 24.62 1.80
> F FP
>
> 6 NONE 2.4 207.7 0 100.00 18.95 18.95 24.62 1.80
> Q SIGFP</fontfamily>
>
>
> The _refln.status fields of the .cif file are either 0 (working set)
> or 1 (free set), which appears to be a CIF file format standard. I've
> only noticed this because I hand-checked the .mtz file produced by
> running the "convert to mtz and standardize" set of programs in CCP4i
> 4.2.2. Although I stated to "keep existing rfree data", it actually
> generated a completely new set of rfree flagged reflections. It
> appears that this problem resulted from the original importing error
> of cif2mtz. I've been working with the CIF file for amicyanin (1AAC)
> at:
>
>
> ftp://ftp.rcsb.org/pub/pdb/data/structures/all/structure_factors/r1aacsf.ent.Z
>
>
> And can be reproduced by the command:
>
>
> uncompress r1aacsf.ent.Z
>
> mv r1aacsf.ent r1aacsf.cif
>
>
> then
>
>
> cif2mtz hklin r1aacsf.cif hklout foo.mtz <<<< EOF
>
> CELL 58.500 86.900 46.900 90.00 90.00 90.00
>
> SYMM P21212
>
> END
>
> EOF
>
>
> Has anyone experienced this problem before? Or know a work around?
>
>
> Mark
>
>
> Mark DePristo
>
> Ph.D. Candidate
>
> Dept. of Biochemistry
>
> Cambridge University
>
> mdepristo@cryst.bioc.cam.ac.uk
>
> http://www-cryst.bioc.cam.ac.uk/~mdepristo/
> --Apple-Mail-2--989291867--
>
>
--
**************************************************************************
* *
* Dr. Martyn Winn *
* *
* Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND *
* Tel: +44 1925 603455 E-mail: m.d.winn@ccp4.ac.uk (personal) *
* Fax: +44 1925 603825 E-mail: ccp4@ccp4.ac.uk (CCP4 problems) *
* URL: http://www.ccp4.ac.uk/martyn/martyn.html *
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