Hi Sonali, regarding isotropic vs anisotropic parameterization of your individual ADPs: apart from common sense and theoretical considerations, this is also in great part software dependent.
I can't speak for other programs, but for phenix.refine I would say the rule of thumb is: - higher than 1.5A: refine macromolecule with individual anisotropic ADPs (the rest - isotropic); - higher than 1.2A: all anisotropic (macromolelcule, water, ligands) - lower than 1.7A: all isotropic; - 1.5-1.7A is a grey area where there is only one single way to know for sure: try both (isotropic and anisotropic) and see which one works best. I realize "works best" is a broad term, but I would say Rwork, Rfree, Rfree-Rwork and values of refined anisotropic ADPs should be enough to make a decision. If it's not a neutron data, H atoms should be always isotropic (kind of obvious, but mentioning it just in case..). Good luck, Pavel On Sun, Mar 17, 2013 at 1:06 AM, sonali dhindwal < [email protected]> wrote: > Dear All, > > We want little suggestion and knowledge regarding refinement of data in > Refmac. We have a data with resolution upto 1.5A. Overall redundancy of 5.5 > and 3.7 in high resolution bin. and I over Sigma is also 21 overall and > 2.2 in last resolution bin. > > When we first did isotropic refinement we used automatic weighing term, > which gave good Rfree and Rfactor of 18.4 and 16.9 but high rmsBond and > rmsAngle of 0.027 and 2.5 respectively. We were able to improve rmsBond and > rmsAngle values by decreasing weighing term to 0.5. > > But when we do anisotropic refinement with weighing term of 0.5 it gives > Rfree, Rfactor and FOM of 16.8, 15.0 and 90.7 respectively. And rmsAngle > and rmsBond of 0.0074 and 1.25. > > Now, we want to know what should be the ideal values for rmsAngle and > rmsBond at such resolution. Secondly, if we can use anisotropic refinement > with such data. > > All your suggestions will be highly valuable. > Thanks in advance. > > -- > Sonali Dhindwal > > “Live as if you were to die tomorrow. Learn as if you were to live > forever.” >
