Hi,

Sorry, can’t take the credit for that!  The names that come to mind are Gerard Kleywegt and Alwyn Jones.

I’ve actually said in the past that, the more criteria you add to optimising your model, the less likely that you can satisfy all the criteria and still have a wrong model!  But I agree with the point I think Gert was making, which is that the Ramachandran plot doesn’t lend itself to a simple gradient-driven optimisation strategy, i.e. the correct answer isn’t likely to simply be downhill in a potential function that includes some kind of Ramachandran restraints, because you will almost certainly have to do something more exhaustive that will involve jumping local barriers.

Randy

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K.                               www-structmed.cimr.cam.ac.uk

On 26 Feb 2015, at 04:37, Jeremy Tame <[log in to unmask]> wrote:

> I think Goodhart's Law applies here (see the Wikipedia page):
> When a measure becomes a target, it ceases to be a good measure.
> 
> From memory I believe Randy Read and George Sheldrick have commented that
> Ramachandran plots are a good measure of structure quality, and therefore should
> not be used explicitly at the modelling stage. Some residues may be difficult
> if they have more than one backbone conformation or are just mobile, but
> expressly holding them in favoured regions of the Ramachandran plot is not a good 
> idea. The most interesting proteins are of course enzymes, and the Ramachandran
> outliers are often among the most interesting active site residues. So you may be trying
> to eliminate something which is actually more important than a low Rfactor.
> 
> The idea of limiting data use may seem counter-intuitive, but to take another
> example from economics, John Cowperthwaite was in charge of Hong Kong's
> financial affairs in the 1960s. He attributed the success of the economy under his
> tenure to his adamant refusal to collect any economic data whatsoever!
> 
> 
> On Feb 26, 2015, at 2:08 AM, Michael Murphy wrote:
> 
>> Does anyone know of a way to adjust Ramachandran angles so that they fall within the preferred range? Either in Coot or possibly some online server? I have been trying to do it manually without much success, I was wondering whether there might another way to do it. -Thanks