I'd expect imposing Ramachandran restraints to lower the Rfree or at least the gap between R and Free, otherwise I would not do it. If there were genuine Ramachandran outliers, the restrained model might not have these included, while these outliers could potentially be very interesting. Of course, if there were many, most would probably not be genuine and genuine ones difficult to identify.
For your second Q, I’d vote for: 2. authors/depositors have discretion to submit/publish the model they prefer so long as refinement protocol is accurately described and weaknesses such as poor Ramachandran statistics are evident in the presentation of the data and not concealed But referees should insist on them also providing the data so that whoever wants could re-refine the structure to their liking. Imposing Ramachandran constraints should also be clearly described and not concealed…and authors and users of models refined against low-resolution data should be realistic about the conclusions one can draw from them. Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://wwwuser.cnb.csic.es/~mjvanraaij > On 8 Mar 2017, at 15:29, Radisky, Evette S., Ph.D. <radisky.eve...@mayo.edu> > wrote: > > Dear all, > > I have two questions. I would like to find out the community consensus of > (1) best practices in refining against lower resolution data (~4 angstrom) > to achieve the best model, and also (2) what manuscript referees should ask > for in this regard. One might encounter a hypothetical situation where > standard refinement approaches gave a model with poor Ramachandran > statistics. Imposing Ramachandran restraints gave a model with improved > Ramachandran statistics but at the expense of higher Rfree. I would expect > that the model with better geometry is probably more reliable, and wonder if > this is the general consensus view? I also wonder should a referee be the > geometry police, or should authors/depositors have discretion to > submit/publish the model they prefer so long as refinement protocol is > accurately described and weaknesses such as poor Ramachandran statistics are > evident in the presentation of the data and not concealed? > > Thanks for your input! > > Evette > > Evette S. Radisky, Ph.D. > Associate Professor and Consultant > Department of Cancer Biology > Mayo Clinic Cancer Center > _________________________________________ > Griffin Cancer Research Building, Rm 310 > 4500 San Pablo Road > Jacksonville, FL 32224 > (904) 953-6372 > http://www.mayo.edu/research/faculty/radisky-evette-s-ph-d/bio-00094471 > <http://www.mayo.edu/research/faculty/radisky-evette-s-ph-d/bio-00094471>
