Comments on: Coot Tips http://www.P212121.com/2009/04/28/coot-tips/ 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: DrL http://www.P212121.com/2009/04/28/coot-tips/comment-page-1/#comment-314 DrL Thu, 07 May 2009 03:28:07 +0000 http://www.P212121.com/?p=1351#comment-314 I know they are working with the Phenix project to incorporate their analysis. I was under the impression that they were trying to work with Paul Emsley and incorporate it into coot. The issue is that the good old Ramachandran plot is based on very old data. I always put my final structure through Molprobity which gives much more satisfying result and analysis. I know they are working with the Phenix project to incorporate their analysis. I was under the impression that they were trying to work with Paul Emsley and incorporate it into coot. The issue is that the good old Ramachandran plot is based on very old data. I always put my final structure through Molprobity which gives much more satisfying result and analysis.

]]> By: Sean http://www.P212121.com/2009/04/28/coot-tips/comment-page-1/#comment-313 Sean Thu, 07 May 2009 02:02:22 +0000 http://www.P212121.com/?p=1351#comment-313 I assuming you are referring to MolProbity. I have not used MolProbity, does it have the ability to be updated as you adjust the amino acids? My guess the reasons for keeping the Ramachandran plot around is due to users being familiar with that type of output and that it can be updated on the fly. I assuming you are referring to MolProbity. I have not used MolProbity, does it have the ability to be updated as you adjust the amino acids?

My guess the reasons for keeping the Ramachandran plot around is due to users being familiar with that type of output and that it can be updated on the fly.

]]> By: DrL http://www.P212121.com/2009/04/28/coot-tips/comment-page-1/#comment-306 DrL Mon, 04 May 2009 19:28:02 +0000 http://www.P212121.com/?p=1351#comment-306 I still don't understand why Coot uses the old Ramachandran plots. Just integrate it with Richardson's validation tool. (or maybe I have an old version of coot) I still don’t understand why Coot uses the old Ramachandran plots. Just integrate it with Richardson’s validation tool. (or maybe I have an old version of coot)

]]> By: admin http://www.P212121.com/2009/04/28/coot-tips/comment-page-1/#comment-293 admin Tue, 28 Apr 2009 21:02:51 +0000 http://www.P212121.com/?p=1351#comment-293 We will keep our eyes open for the update, thanks for all your work with Coot it is truly appreciated! We will keep our eyes open for the update, thanks for all your work with Coot it is truly appreciated!

]]> By: Paul Emsley http://www.P212121.com/2009/04/28/coot-tips/comment-page-1/#comment-291 Paul Emsley Tue, 28 Apr 2009 17:11:35 +0000 http://www.P212121.com/?p=1351#comment-291 Ha, seeing them all like that, I see that there are some small typos. I've clarified things a touch. Thanks. Ha, seeing them all like that, I see that there are some small typos. I’ve clarified things a touch. Thanks.

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