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
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