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Re: [ccp4bb]: problems with cif2mtz
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*** CCP4 home page http://www.ccp4.ac.uk ***
The code fix is simply:
354c354
< if (cdata.eq.'o') then
---
> if (cdata.eq.'o'.or.cdata.eq.'0') then
363c363
< elseif (cdata.eq.'f') then
---
> elseif (cdata.eq.'f'.or.cdata.eq.'1') then
in cif2mtz.f and re-compile.
However, this assumes the Xplor convention on 0s and 1s, and
will fail if the CIF was written with CCP4 convention.
That's the wonderful thing about standards ... so many to choose from.
Martyn
On Mon, 14 Apr 2003, Mark DePristo wrote:
> Hi Martyn,
>
> Thanks -- I've edited the cif files and it looks like its working.
> Funny, two of the four structures (1G35 and 1A3S) that I'm working with
> have 0, 1 instead of o and f. May be an non-standard convention 8)
>
> Just to clarify for everyone (and the googlebot), if you have problems
> converting the FREE R flags in your mmCIF file, and the _refln.status
> field contains 0 (for working set) and 1's (for free set), then you can
> fix the problem by changing the 0 to 'o' (that's little alphabetic o
> for observed) and 'f' (as in free), and rerunning cif2mtz.
>
> Mark
>
> On Monday, April 14, 2003, at 05:28 PM, M.D.Winn wrote:
>
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> >
> > 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
> > *
> > ***********************************************************************
> > ***
> >
>
> 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@dl.ac.uk (personal) *
* Fax: +44 1925 603124 E-mail: ccp4@dl.ac.uk (CCP4 problems) *
* URL: http://www.dl.ac.uk/CCP/CCP4/martyn/martyn.html *
**************************************************************************