Re: [ccp4bb] test data sets part II...

- Protein crystallography

Main steps:

- Protein purification
- Crystallisation

Special:

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: resuspending precipitated protein
From: "Uitdehaag, J {- dot -} C {- dot -} M {- dot -} (Joost)" joost {- dot -} uitdehaag {- at -} SPCORP {- dot -} COM
Date: 2008-10-02

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Subject: Re: test data sets part II...
From: Ashley Buckle ashley {- dot -} buckle {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2008-10-02

Subject: Re: test data sets part II...
From: "Mark J {- dot -} van Raaij" mark {- dot -} vanraaij {- at -} USC {- dot -} ES
Date: 2008-10-02

Dear All,

with regards to diffraction images storage (see also Androulakis et
al., Acta Cryst. (2008). D64, 810–814: "Federated repositories of X-
ray diffraction images"), I am all for it - one to be able to catch
fraud, but more importantly so structures can be improved in the
future and better data processing programs can be developed.

However, I would welcome a central repository or at least a central
organisation of local nodes, because I can see no local solution where
I am (probably other small macromolecular crystallography groups would
have the same problem). In fact, if someone would agree to "host" our
data I would be happy to upload datasets. For some datasets it would
even be useful if I could send the digital tapes, we don't have a
reader for them anymore and in that way we ourselves can have access
to our own data...

Greetings,

Mark

Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
http://web.usc.es/~vanraaij/

On 24 Sep 2008, at 02:43, Ashley Buckle wrote:

> We put our raw data, plus metadata here: http://www.tardis.edu.au
> JCSG also make data available, but I think its just an archive, with
> little or no annotation
> cheers
> Ashley
>
> On 24/09/2008, at 7:02 AM, afyfe wrote:
>
>> Dear Tommi,
>> I'm not sure whether 'test data sets part I' relates to the query
>> I mailed the other day but, in light of the recent posts
>> regarding fundamental literature, your suggestion seems an
>> excellent one.
>>
>> Perhaps I'm not looking in the right places, but finding examples
>> of image sets exhibiting e.g., radiation damage, crystal slippage,
>> autoindexing failures or any of the aberrations shown in Phil
>> Evans' excellent scala tutorial seems difficult. Likewise for
>> examples of good and bad final-refinement maps. Making primary/
>> intermediate data available would benefit both students and
>> algorithm comparison/validation (e.g. measuring performance on
>> standard data sets is routine in data-visualization/image-
>> processing papers).
>>
>> Tommi Kajander wrote:
>>
>>> Also, i think that would be nice if this type of info could be put
>>> on the web, part of the wiki for instance..
>>> if there is some consensus to what works + the typical proteins
>>> easily available.
>>>
>>> Tommi Kajander, Ph.D.
>>> Structural Biology and Biophysics
>>> Institute of Biotechnology
>>> University of Helsinki
>>> Viikinkaari 1
>>> (P.O. Box 65)
>>> 00014 Helsinki
>>> Finland
>>> p. +358-9-19158903
>>> tommi.kajander@helsinki.fi
>>
>>
>>
>> --
>> Alastair Fyfe
>> Graduate Student
>> Biomolecular Engineering Dept.
>> University of California, Santa Cruz
>
>
>
> Associate Professor Ashley M Buckle
> NHMRC Senior Research Fellow
> The Department of Biochemistry and Molecular Biology
> School of Biomedical Sciences, Faculty of Medicine &
> Victorian Bioinformatics Consortium (VBC)
> Monash University, Clayton, Vic 3800
> Australia
>
> http://www.med.monash.edu.au/biochem/staff/abuckle.html
> iChat/AIM: blindcaptaincat
> skype: ashley.buckle
> Tel: (613) 9902 0269 (office)
> Tel: (613) 9905 1653 (lab)
>
> Fax : (613) 9905 4699
>
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Next message:
Subject: Re: test data sets part II...
From: Ashley Buckle ashley {- dot -} buckle {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU
Date: 2008-10-02