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Re: [ccp4bb] The importance of USING our validation tools |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: The importance of USING our validation tools From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK Date: 2007-08-16 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 CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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