Andy, you should probably direct this question to the mentor first. What is her explanation?
What do you mean by "refinement messes up a conformation"? Sometimes with poor quality data refinement might lead to poor Ramachandran map. You fix it manually, only to see it deteriorating again. You may try to play with the weight of geometry restraints. Since polypeptide backbone conformation is forced to occupy certain areas of (phi,psi) space because of steric clashes, one would expect that increasing contribution of van der Waals repulsion term may help. I heard an opinion (which I share to some degree) that it is never a good idea to enforce Ramachandran directly, by setting (phi,psi) restraints, but you may try, for instance, restraining the hydrogen bonds that stabilize the secondary structure. What this means ideologically is that your data is not of good enough quality, so you incorporate the knowledge of secondary structure. Think of it as incorporating additional experimental data to boost your data/parameter ratio. If I understand correctly, what you want to do is to fix the model manually and then just do rigid body to tidy things up a bit. Alternative could be to fix/restrain the problematic parts of the structure and do refine the rest. HTH, Ed. On Fri, 2009-02-06 at 06:58 -0800, Andy Millston wrote: > I am told by a mentor that rigid body refinement should never be the > last refinement before submission to pdb. Any idea why? Structures in > which every round of retrained refinement messes up a conformation, is > there any alternative to not using rigid body refinement? > > Andy > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
