Annealing before complete model building!
I have built an almost complete model with some refinement but I am
still unable to build two small loops (5-6 residues)using "coot" or
"O" even after some refinement.
I want to do annealing and energy minimization with CNS.I was
wondering that will it help if I use my current incomplete model for
annealing and minimization to get a better electron density for
further model building?
Or is it always required to build the complete model first and then
proceed with minimization and annealing to get the best/publishable model?
Thanks for your suggestions.
- Dear Subhendu --On 4 Aug 2008, at 06:44, i_m_subh wrote:It might help your modeling, but I quite sure it will not make the density of the loops appear, or at least not completely. Have you tried to add water molecules? You might try to refine further your model to have better phases, and then the density for those loops will appear. Also, what you might want to try is to add one residue only from each end of the missing loop, then run annealing, and check if any density appeared. If so, then repeat the process until your loop is completed. If not, it just means either it is unstructured completely, or that it has been cleaved somewhere in the purification process.just a short comment: you don't want to have a "publishable" data (well, you do want to publish, obviously...) but rather a "biological meaningful" data. If the fact to have the loops unbuilt is biologically meaningless, then I'd start to worry. But is it the case?...HTH