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Re: [ccp4bb]: problems with cif2mtz
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Ah, I see the problem. cif2mtz was written to conform
to mmCIF dictionary where _refln.status has values
"o", "f" and others. See
http://www.iucr.ac.uk/iucr-top/cif/mmcif/ndb/dictionary/html-dic/Items/_refln.status.html
Entry 1g35 has 0's and 1's instead. No, the program can't
handle that. Well, I can and will change it.... Believe it or
not, no-one has asked before..
(I wanted to show example of conforming s.f. file, but it's
proving hard to find an entry that has not only structure
factors but free R flags as well ....)
Martyn
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> Hi Martyn,
>
> Sorry about that -- wrong directory. The structure factor file should
> be hiv-protease (1G35):
>
> ftp://ftp.rcsb.org/pub/pdb/data/structures/all/structure_factors/
> r1g35sf.ent.Z
>
> Mark
>
> On Monday, April 14, 2003, at 04:44 PM, M.D.Winn wrote:
>
> >
> >
> > As far as I can see, entry r1aacsf doesn't contain
> > a _refln.status column ?!
> >
> > Martyn
> >
> >>
> >> *** For details on how to be removed from this list visit the ***
> >> *** CCP4 home page http://www.ccp4.ac.uk ***
> >>
> >>
> >> --Apple-Mail-2--989291867
> >> Content-Transfer-Encoding: 7bit
> >> Content-Type: text/plain;
> >> delsp=yes;
> >> charset=US-ASCII;
> >> format=flowed
> >>
> >> 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
> > *
> > ***********************************************************************
> > ***
> >
>
> Mark DePristo
> Ph.D. Candidate
> Dept. of Biochemistry
> Cambridge University
> mdepristo@cryst.bioc.cam.ac.uk
> http://www-cryst.bioc.cam.ac.uk/~mdepristo/
>
>
--
**************************************************************************
* *
* 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 *
**************************************************************************