Hi Jacob, In our experience using MODELLER<http://salilab.org/modeller/> for the homology modeling part, followed by refinement with CHARMM<http://www.charmm.org/> leads to structures with very reasonable high quality statistics as reported by MolProbity.
Both programs are integrated in our commercial suite Discovery Studio<http://accelrys.com/products/discovery-studio/>, but you can also access them directly from their respective labs. Kind regards, Francisco Francisco Hernandez-Guzman, PhD, MBA Sr. Product Manager Accelrys Software, Inc. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, February 20, 2013 12:40 PM 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<mailto:j-kell...@northwestern.edu> *******************************************
