Dear Peter, First a common misconception: your goal should be to get the best possible fit of your model to your electron density maps. Rfree is only an indicator, telling you whether you are moving in the right direction.
So in coot, you should look for places where your model does not fit the electron density very well and correct them. Things to look for are peaks (positive and negative) in the electron density maps. Here I use the default of +/- 3 sigma. You should also look for parts of your model with weak or bad electron density, as well as uninterpreted electron density. Good parts usually have density above the 1.5 sigma level, but for weak parts, you could go down to ~0.6 sigma. Below that, you get into the noise/artefact level. Things to do are fitting side chains in different orientations, flipping peptides, removing disordered loops with no or very bad density, fitting extra residues where there is extra density etc. In certain cases, you may have to rebuild complete loops. You are done with your refinement when you see nothing any more that could be improved. Good luck! Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von ?? Gesendet: Montag, 21. April 2014 02:34 An: [email protected] Betreff: [ccp4bb] coot problems to decrease R FREE Dear all, I'm a novice of coot and ccp4. Now I'm doing refinement using both refmac5 and coot.Here are some problems I'm facing. Really hope you can give me some suggestions. 1、THE RESOLUTION OF THE DATA IS 2.5 angstrom. After first refinement of refmac5 I got R factor which is 0.26 and R FREE which is 0.31. My question is what the final R factor and R FREE should be after several rounds of refinement by refmac5 and coot. 2、At which map level（e/A3 or rmsd）should I refine the data by coot? 3、Can you give me some tips and strategies about how to use coot to decrease R free? now I just use some basic tricks such as fit density and Ramachandran plot to refine the data. Best regards, Peter Chen
