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Re: [ccp4bb] practical limits of MR? |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007Subject: Re: practical limits of MR? From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA Date: 2007-03-05 > I had a debate with a coworker about using MR in desperation and I'm > curious what the most extreme case is where a very different model was > used to solve a structure. This could be highest RMSD, lowest % > identity, or most incomplete model. I'm also curious whether homology > modelling has ever been useful for this. (I'm pretty sure I've come > across papers discussing this last concept.) > > thanks, > Nat > > Hi Nat, I once had a situation of a search model with about 20-25% sequence identity, but the model had not been deposited. A stereo image of a C-alpha trace in a nature paper was the only data I had. I picked the coordinates of left and right eye images and used some program to reconstruct the 3D Calpha trace (playing with image angle and distance settings to get proper helices). I use that for MR and got what I remember was a recently convincing solution. However, as is often the case in these desperate situations, the model-derived phases where too poor to bootstrap the refinement. After solving the structure I never went back to check if the original MR solution was correct and am not sure the files are still on a disk somewhere. Anyway, with the improvements in software we may have reached a stage where the limitation of the search model is not whether or not you can find a MR solution, but whether or not that solution is going to help you determine the structure. What you can and can't get away with depends on the resolution of your native dataset and the power of density modification, in particular the presence/absence of NCS. It's always worth a try but if finding a MR solution is a challenge you should consider how useful a solution, if found, is going to be. Bart ============================================================================== Bart Hazes (Assistant Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================== CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 05 March 2007 |
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