| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | Advert | | |
Re: [ccp4bb] The importance of USING our validation tools |
||
- Protein crystallographyMain steps:- Protein purification- Crystallisation Special:- Programs for crystallography- X-ray detectors Basic tutorials:- Chemistry- Protein - Peptide - Amino Acids Xtal community:- CCP4BB |
CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: The importance of USING our validation tools From: Ashley Buckle ashley {- dot -} buckle {- at -} MED {- dot -} MONASH {- dot -} EDU {- dot -} AU Date: 2007-08-16 Validation aside, access to raw data is also helpful for method development (eg integration and scaling algorithms), on which we all rely. Ashley On 17/08/2007, at 1:04 AM, Santarsiero, Bernard D. wrote: > Sorry, I think it's a waste of resources to store the raw images. I > think > we should trust people to be able to at least process their own > data set. > Besides, you would need to include beamline parameters, beam position, > detector distances, etc. that may or may not be correct in the image > headers. I'm all for storage and retrieval of a primary intensity data > file (I or F^2 with esds). > > Bernie Santarsiero > > > On Thu, August 16, 2007 9:46 am, Mischa Machius wrote: >> Hmm - I think I miscalculated, by a factor of 100 even!... need more >> coffee. In any case, I still think it would be doable. Best - MM >> >> >> On Aug 16, 2007, at 9:30 AM, Mischa Machius wrote: >> >>> I don't think archiving images would be that expensive. For one, I >>> have found that most formats can be compressed quite substantially >>> using simple, standard procedures like bzip2. If optimized, raw >>> images won't take up that much space. Also, initially, only those >>> images that have been used to obtain phases and to refine finally >>> deposited structures could be archived. If the average structure >>> takes up 20GB of space, 5,000 structures would be 1TB, which fits >>> on a single hard drive for less than $400. If the community thinks >>> this is a worthwhile endeavor, money should be available from >>> granting agencies to establish a central repository (e.g., at the >>> RCSB). Imagine what could be done with as little as $50,000. For >>> large detectors, binning could be used, but giving current hard >>> drive prices and future developments, that won't be necessary. Best >>> - MM >>> >>> >>> On Aug 16, 2007, at 9:13 AM, Phil Evans wrote: >>> >>>> What do you count as raw data? Rawest are the images - everything >>>> beyond that is modellling - but archiving images is _expensive_! >>>> Unmerged intensities are probably more manageable >>>> >>>> Phil >>>> >>>> >>>> On 16 Aug 2007, at 15:05, Ashley Buckle wrote: >>>> >>>>> Dear Randy >>>>> >>>>> These are very valid points, and I'm so glad you've taken the >>>>> important step of initiating this. For now I'd like to respond to >>>>> one of them, as it concerns something I and colleagues in >>>>> Australia are doing: >>>>>> >>>>>> The more information that is available, the easier it will be to >>>>>> detect fabrication (because it is harder to make up more >>>>>> information convincingly). For instance, if the diffraction data >>>>>> are deposited, we can check for consistency with the known >>>>>> properties of real macromolecular crystals, e.g. that they >>>>>> contain disordered solvent and not vacuum. As Tassos Perrakis >>>>>> has discovered, there are characteristic ways in which the >>>>>> standard deviations depend on the intensities and the >>>>>> resolution. If unmerged data are deposited, there will probably >>>>>> be evidence of radiation damage, weak effects from intrinsic >>>>>> anomalous scatterers, etc. Raw images are probably even harder >>>>>> to simulate convincingly. >>>>> >>>>> After the recent Science retractions we realised that its about >>>>> time raw data was made available. So, we have set about creating >>>>> the necessary IT and software to do this for our diffraction >>>>> data, and are encouraging Australian colleagues to do the same. >>>>> We are about a week away from launching a web-accessible >>>>> repository for our recently published (eg deposited in PDB) data, >>>>> and this should coincide with an upcoming publication describing >>>>> a new structure from our labs. The aim is that publication occurs >>>>> simultaneously with release in PDB as well as raw diffraction >>>>> data on our website. We hope to house as much of our data as >>>>> possible, as well as data from other Australian labs, but >>>>> obviously the potential dataset will be huge, so we are trying to >>>>> develop, and make available freely to the community, software >>>>> tools that allow others to easily setup their own repositories. >>>>> After brief discussion with PDB the plan is that PDB include >>>>> links from coordinates/SF's to the raw data using a simple handle >>>>> that can be incorporated into a URL. We would hope that we can >>>>> convince the journals that raw data must be made available at the >>>>> time of publication, in the same way as coordinates and structure >>>>> factors. Of course, we realise that there will be many hurdles >>>>> along the way but we are convinced that simply making the raw >>>>> data available ASAP is a 'good thing'. >>>>> >>>>> We are happy to share more details of our IT plans with the >>>>> CCP4BB, such that they can be improved, and look forward to >>>>> hearing feedback >>>>> >>>>> cheers >>> >>> >>> -------------------------------------------------------------------- >>> -- >>> ---------- >>> Mischa Machius, PhD >>> Associate Professor >>> UT Southwestern Medical Center at Dallas >>> 5323 Harry Hines Blvd.; ND10.214A >>> Dallas, TX 75390-8816; U.S.A. >>> Tel: +1 214 645 6381 >>> Fax: +1 214 645 6353 >> >> >> --------------------------------------------------------------------- >> --- >> -------- >> Mischa Machius, PhD >> Associate Professor >> UT Southwestern Medical Center at Dallas >> 5323 Harry Hines Blvd.; ND10.214A >> Dallas, TX 75390-8816; U.S.A. >> Tel: +1 214 645 6381 >> Fax: +1 214 645 6353 >> *NOTE* My new tel. no: (03) 9902 0269 Ashley Buckle Ph.D 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 navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
|
| ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd |