 |
 |
Dear Robbie, Rules 3-5 I found could be approached using my previous rule of thumb. If anisotropy reduced Rfree by more than half the reduction in R, then I liked it. It helped me decide to introduce anisotropy for xenon, iodine and chlorine atoms (supported by non-spherical omit electron density) but not for light atoms. My rule told me to always add riding hydrogens, they typically reduced R and Rfree similarly. Anthony Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 -----Original Message----- From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Robbie Joosten Sent: Wednesday, 27 October 2010 4:29 PM To: [log in to unmask] Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) Dear Anthony, That is an excellent question! I believe there are quite a lot of 'rules of thumb' going around. Some of them seem to lead to very dogmatic thinking and have caused (refereeing) trouble for good structures and lack of trouble for bad structures. A lot of them were discussed at the CCP4BB so it may be nice to try to list them all. Rule 1: If Rwork < 20%, you are done. Rule 2: If R-free - Rwork > 5%, your structure is wrong. Rule 3: At resolution X, the bond length rmsd should be < than Y (What is the rmsd thing people keep talking about?) Rule 4: If your resolution is lower than X, you should not use_anisotropic_Bs/riding_hydrogens Rule 5: You should not build waters/alternates at resolutions lower than X Rule 6: You should do the final refinement with ALL reflections Rule 7: No one cares about getting the carbohydrates right Obviously, this list is not complete. I may also have overstated some of the rules to get the discussion going. Any addidtions are welcome. Cheers, Robbie Joosten Netherlands Cancer Institute > Apologies if I have missed a recent relevant thread, but are lists of > rules of thumb for model building and refinement? > > > > > > Anthony > > > > Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 > > >