Hi Jacob, I'm usually pretty happy with the automated modeling pipeline in YASARA. The various model building steps have different types of minimization and refinement to get rid of bumps as best as it can. Added bonus (and shameless plug): it uses PDB_REDO structures as input if those are better than the original PDB file. This may also help get better models.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Jacob Keller > Sent: Wednesday, February 20, 2013 21:40 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Improving Homology Models > > Dear Crystallographers, > > it has been my experience that homology modelling programs get folds > pretty well, but sometimes the details are pretty obviously bad, like too- > close contacts. One might think that the modelling software would put in a > sort of "polishing" step, but they don't seem to. Is there any way to trick the > CCP4 or other software to fix these things, such as by simulated annealing or > otherwise, I guess without any weight on the [non-existent] structure > factors? > > Thanks, > > Jacob > > > -- > ******************************************* > Jacob Pearson Keller, PhD > Postdoctoral Associate > HHMI Janelia Farms Research Campus > email: j-kell...@northwestern.edu > *******************************************
