Regarding the riding hydrogens: They are obviously not visible, but your protein in solution is also not visible but still has those weird riding hydrogens:-) Use them, they are there. And ther was a recent compendium of neutron scattering in one of our favorite journals if you really want to see them.
Another rule to add: You are 98% done with refinement of your structure, does it really matter - I mean from a functional/ biological perspective ? Is it wrong to stop at some point ? This of course implies you've already passed rule 3-5 from Robbie. Just some Espresso-thoughts in the morning Jürgen ...................... Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Oct 27, 2010, at 1:29, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > 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 >> >> >>
