Comments on: Origin and Orientation http://www.P212121.com/2009/12/11/origin-and-orientation/ Protein Crystallography there is an Easier Way Wed, 18 Jan 2012 10:14:22 -0500 http://wordpress.org/?v=2.8.5 hourly 1 By: Pinko Punko http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1413 Pinko Punko Mon, 21 Dec 2009 15:16:10 +0000 http://www.P212121.com/?p=8074#comment-1413 I think the hardest things to fake would be plausible crystal contacts (not that I really know anything here). It does seem that discussions of the faked work have all mentioned that the structures tend to lack strong crystal contacts. I think the hardest things to fake would be plausible crystal contacts (not that I really know anything here). It does seem that discussions of the faked work have all mentioned that the structures tend to lack strong crystal contacts.

]]> By: Sean http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1377 Sean Tue, 15 Dec 2009 05:11:39 +0000 http://www.P212121.com/?p=8074#comment-1377 @Eric I believe that this idea accounts for all the anomalies seen in the structure. I have yet to find a template for the 2HR0 structure and as Pinko Punko notes there may not be one. @Artem I like you style. If you are going to fabricate data at least do a good job of it :) @Eric I believe that this idea accounts for all the anomalies seen in the structure. I have yet to find a template for the 2HR0 structure and as Pinko Punko notes there may not be one.

@Artem I like you style. If you are going to fabricate data at least do a good job of it :)

]]> By: Artem http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1372 Artem Mon, 14 Dec 2009 01:19:50 +0000 http://www.P212121.com/?p=8074#comment-1372 'Plausible packing' can be generated using molecular replacement programs that have packing function criteria. Give them a bogus dataset and relax solution criteria - and presto, you can get a 'properly packed' solution that can be further tweaked manually. Thing is though - why on earth would the fakers leave out 40A of empty space when they could have easily filled it in with something... ‘Plausible packing’ can be generated using molecular replacement programs that have packing function criteria. Give them a bogus dataset and relax solution criteria – and presto, you can get a ‘properly packed’ solution that can be further tweaked manually.

Thing is though – why on earth would the fakers leave out 40A of empty space when they could have easily filled it in with something…

]]> By: Pinko Punko http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1368 Pinko Punko Sat, 12 Dec 2009 15:58:13 +0000 http://www.P212121.com/?p=8074#comment-1368 I see no reason to assume that Krishna Murthy would use the same approach every time. I hypothesize that there will a few avenues among his different falsifications. I see no reason to assume that Krishna Murthy would use the same approach every time. I hypothesize that there will a few avenues among his different falsifications.

]]> By: Eric http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1367 Eric Sat, 12 Dec 2009 15:12:51 +0000 http://www.P212121.com/?p=8074#comment-1367 <blockquote>"I don’t have access to Scopus, but found the article that includes the authors you previously mentioned."</blockquote> I figured your university would give you access to Scopus, as mine does. Sorry. <blockquote>"My focus in this post is on the PDB entry 1BEF not 2HR0, which the correspondence addresses."</blockquote> I realize that. I referred to 2HR0 for two reasons (which I was too hurried to mention). 1) 2HR0 seems to be the model that got Murthy caught. 2) I figure he used similar methods on any falsified models. <blockquote>"The correspondence is also taking a different perspective on the issue. They are saying that we processed the data and have noted inconsistent features. This post is saying coming from the other side – here is the initial structure that they used to fabricate the data."</blockquote> As I read the correspondence, there seems to be a fair bit of implied "This is how he did it" (c.f. comments about protein in a vacuum). The last paragraph throws down the gauntlet by demanding to see the original diffraction data. Out of curiosity, does your proposed method account for the other anomalies mentioned by Janssen, et al.? Does it account for the missing bulk solvent and the strange B-factors and R-factors (see correspondence figures)? Lastly, have ideas what the template for 2HR0 might have been? Anyhow, thanks for humoring my ramblings. I'm an intelligent systems guy, not a structural biologist (though I work with one). I've picked up a lot, but there's still a lot I don't fully understand. ;)

“I don’t have access to Scopus, but found the article that includes the authors you previously mentioned.”

I figured your university would give you access to Scopus, as mine does. Sorry.

“My focus in this post is on the PDB entry 1BEF not 2HR0, which the correspondence addresses.”

I realize that. I referred to 2HR0 for two reasons (which I was too hurried to mention).

1) 2HR0 seems to be the model that got Murthy caught.
2) I figure he used similar methods on any falsified models.

“The correspondence is also taking a different perspective on the issue. They are saying that we processed the data and have noted inconsistent features. This post is saying coming from the other side – here is the initial structure that they used to fabricate the data.”

As I read the correspondence, there seems to be a fair bit of implied “This is how he did it” (c.f. comments about protein in a vacuum). The last paragraph throws down the gauntlet by demanding to see the original diffraction data. Out of curiosity, does your proposed method account for the other anomalies mentioned by Janssen, et al.? Does it account for the missing bulk solvent and the strange B-factors and R-factors (see correspondence figures)? Lastly, have ideas what the template for 2HR0 might have been?

Anyhow, thanks for humoring my ramblings. I’m an intelligent systems guy, not a structural biologist (though I work with one). I’ve picked up a lot, but there’s still a lot I don’t fully understand. ;)

]]> By: Sean http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1366 Sean Sat, 12 Dec 2009 04:55:22 +0000 http://www.P212121.com/?p=8074#comment-1366 Hi Eric, I don't have access to Scopus, but found the <a href="http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html" rel="nofollow">article</a> that includes the authors you previously mentioned. My focus in this post is on the PDB entry 1BEF not 2HR0, which the correspondence addresses. The method that is proposed here of fitting a certain structure (or part of one) then placing that structure in a different space group could result in 30-40 Angstrom slabs that were mentioned in the correspondence. The slabs of missing density would appear as a result of falsifying the space group. This would be the challenging part of fabricating the data - generating reasonable crystal contacts and packing that fit your desired space group. The correspondence is also taking a different perspective on the issue. They are saying that we processed the data and have noted inconsistent features. This post is saying coming from the other side - here is the initial structure that they used to fabricate the data. Hi Eric,

I don’t have access to Scopus, but found the article that includes the authors you previously mentioned.

My focus in this post is on the PDB entry 1BEF not 2HR0, which the correspondence addresses.

The method that is proposed here of fitting a certain structure (or part of one) then placing that structure in a different space group could result in 30-40 Angstrom slabs that were mentioned in the correspondence.

The slabs of missing density would appear as a result of falsifying the space group. This would be the challenging part of fabricating the data – generating reasonable crystal contacts and packing that fit your desired space group.

The correspondence is also taking a different perspective on the issue. They are saying that we processed the data and have noted inconsistent features. This post is saying coming from the other side – here is the initial structure that they used to fabricate the data.

]]> By: Eric http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1365 Eric Sat, 12 Dec 2009 02:54:03 +0000 http://www.P212121.com/?p=8074#comment-1365 It's the correspondence to the Nature article. http://bit.ly/4Um0KZ It’s the correspondence to the Nature article.

http://bit.ly/4Um0KZ

]]> By: Sean http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1363 Sean Fri, 11 Dec 2009 23:19:46 +0000 http://www.P212121.com/?p=8074#comment-1363 I would love to hear another explanation. Could you link to the comments that you are referring too? I would love to hear another explanation. Could you link to the comments that you are referring too?

]]> By: Eric http://www.P212121.com/2009/12/11/origin-and-orientation/comment-page-1/#comment-1362 Eric Fri, 11 Dec 2009 22:50:49 +0000 http://www.P212121.com/?p=8074#comment-1362 Your explanation seems to disagree with the comment from Janssen, Read, Brunger, and Gros. Your explanation seems to disagree with the comment from Janssen, Read, Brunger, and Gros.

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