Sampath Natarajan wrote:
Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting term, then I didn't find any splits. At the same time I noticed that figure of merits is not increasing after model fitting. But the correlation coefficient is more than 80%. Also while refining with auto weighting term, the figure of merit goes down about 25% than previous.Finally I find that some of the residues show high B factor. Could anyone give suggestions to reduce the B-factor? Thanks in advance! Yours sincerely, Sampath
There are several Qs here but you must remember that initial refinement protocols straight from an MR solution are somewhat different to those you would use later. High B factors may be useful - they often indicate where something is wrong, and ditto poor geometry.
These are the regions you will probably need to rebuild. Eleanor , to the
