Actually for teaching I think the RAVE approach of exposing all the intermediate steps and results may be better.
Ideally the student will remember something like:
NCS averaging? Yeah, first we optimized the ncs operators based on density in the experimental map, then we used those operators to average density from all the asymmetric units into one reference ASU, then we expanded that average asu back up into the whole cell, while flattening density around the mask. Then we calculated new structure factors and and a new 2Fo-Fc map based on these and the Fobs. We repeated this over and over, optimizing the operators and mask every tenth cycle, until the process converged and the density was clearly interpretable.
With some more automated procedures it would be more like:
NCS averaging? Yeah we ran this program whatchamacallit and fed it our MTZ with Fobs and experimental phases, and it spit out a much better map that was clearly interpretable.
But maybe the former is a bit much for undergrads, given all the other steps in the overall process.
And I do agree, once a fairly complete model is available, refinement with NCS restraints is better than density averaging. Atomization is the most powerful form of density modification, like atomization > skeletonization > MC+NCS averaging > NCS averaging > solvent flattening.
eab
On 03/04/2016 08:44 AM, Zachary A. Wood wrote:
> Hello All,
>
> Does anyone know of any ‘newer’ programs that do what Kleywegt’s wonderful RAVE software package does?
>
> What is great about RAVE is that you generate a mask based on the coordinates of a protomer, you then optimize your NCS operators using the masked electron correlation coefficients of the other protomers, and then generate a nice, averaged electron density map for model building. The electron density based optimization of the NCS operators is the best feature in my opinion. I am hoping that someone has automated this process of electron density averaging. Don’t get me wrong, RAVE does a fantastic job, but it is a bit time consuming and seems ripe for some automation (especially when teaching undergrads how to do this stuff). Thanks in advance for any suggestions.
>
>
> Best regards,
>
> Z
>
>
> ***********************************************
> Zachary A. Wood, Ph.D.
> Associate Professor
> Department of Biochemistry & Molecular Biology
> University of Georgia
> Life Sciences Building, Rm A426B
> 120 Green Street
> Athens, GA 30602-7229
> Office: 706-583-0304
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