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Re: [ccp4bb]: problems with cif2mtz
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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:
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> *** 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/