On Tue, Jul 23, 2013 at 8:35 AM, Felix Frolow
Were Ramachandran restraints in PHENIX reside now in the recent GUI's ? Once there were immediately visible as well as rotamer restraints.
Yes, I took them off the main interface because we (Jeff and I) found that a) people were using them far too aggressively in circumstances where they really shouldn't, and b) they tended to screw up local structure and almost always result in chemically insensible Ramachandran plots. I really don't think there's any excuse to use except in absolute desperation, and I actually think it would be better to deposit a structure with 1% outliers than to use the restraints. Usually if the overall weight on the geometry restraints is sufficiently high, the Ramachandran statistics will naturally get better. You can still find the parameter either by clicking the "Model interpretation" button, or by using the parameter search (in the Settings menu). But I would exhaust every other possible option before resorting to this. We never had rotamer restraints (although I guess the new RSR method uses them internally), just the fix_rotamers option, but that is now merged with the RSR code.
According to your mail from yesterday I wonder how can I treat Ramachandran outliers in very large molecules (close to 9000 residues).
Turn on weight optimization - this will almost always reduce both the number of Ramachandran outliers and the clashscore. The alternative is to set wxc_scale much lower, but I've always found that manual adjustment of the weights ends up taking far more manual effort and just about the same amount of time as the automatic optimization. -Nat