Comments on: X-ray crystallography: Got validation methods? http://eric.diluccio.fr/blog/2009/07/x-ray-crystallography-got-validation-methods/ Stardust and other Intergalactic considerations Sun, 11 Jul 2010 20:06:38 +0000 hourly 1 http://wordpress.org/?v=3.0.1 By: Eric http://eric.diluccio.fr/blog/2009/07/x-ray-crystallography-got-validation-methods/comment-page-1/#comment-4402 Eric Mon, 21 Sep 2009 20:32:59 +0000 http://eric.diluccio.fr/?p=634#comment-4402 Well the overall quality of X-ray structures didn't really improve over the years despite having a better technology and better softwares/computers. One of the main reason is, as you said, that we are becoming more and more dependent on the ‘black box’ approach to solve structures. All the automatic/semi-automatic pipelines for structure determination are contributing to this and do no help raising the bar in term of structure quality. Solving an x-ray structure is like a fancy videogame with great looking 3D graphics...right? it is easy to forget all the physical and mathematical aspects of X-ray crystallography when working with a set of nice GUI programs that can do *pretty much* everything for you. I see it all the time in the lab with new students. However, if the dataset is real good, the use of the ‘black box’ approach won't lead to a wrong structure per say. It may lead to a lower quality structure, not polished as it should be. But you are right that we might see more retractions in the future as we tend to forget the fundamentals of X-ray crystallography... Well the overall quality of X-ray structures didn’t really improve over the years despite having a better technology and better softwares/computers. One of the main reason is, as you said, that we are becoming more and more dependent on the ‘black box’ approach to solve structures. All the automatic/semi-automatic pipelines for structure determination are contributing to this and do no help raising the bar in term of structure quality. Solving an x-ray structure is like a fancy videogame with great looking 3D graphics…right? it is easy to forget all the physical and mathematical aspects of X-ray crystallography when working with a set of nice GUI programs that can do *pretty much* everything for you. I see it all the time in the lab with new students. However, if the dataset is real good, the use of the ‘black box’ approach won’t lead to a wrong structure per say. It may lead to a lower quality structure, not polished as it should be. But you are right that we might see more retractions in the future as we tend to forget the fundamentals of X-ray crystallography…

]]> By: Sean http://eric.diluccio.fr/blog/2009/07/x-ray-crystallography-got-validation-methods/comment-page-1/#comment-4360 Sean Sat, 19 Sep 2009 03:33:52 +0000 http://eric.diluccio.fr/?p=634#comment-4360 Hi Eric, The error by Chang, et al. and subsequent retraction of papers was an unfortunate occurrence. My fear is that with the great strides in program development that the crystallographic community will become too dependent on the 'black box' approach. It will be interesting to see if there are more retractions in the future. Hi Eric,

The error by Chang, et al. and subsequent retraction of papers was an unfortunate occurrence. My fear is that with the great strides in program development that the crystallographic community will become too dependent on the ‘black box’ approach. It will be interesting to see if there are more retractions in the future.

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