I think the Ramachandranplot should be used in the refinement and rebuilding process - a Ramachandran outlier is a flag that that region of the model needs a closer look, and the fix may be more complicated than simply rotating a peptide. Maybe a C-beta is pointing the wrong way, maybe there is a register error. The danger is that people will treat a Ramachandran outlier by moving a dot across a graph without addressing the underlying structural problem.
kmj On Wed, Feb 25, 2015 at 8:37 PM, Jeremy Tame < [email protected]> 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 >
