[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Re: [ccp4bb]: problems with cif2mtz
*** 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/