Nat Echols wrote:
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
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