Dear Ed,
I think I get your idea, however this is not a straight forward issue I
believe. What do you imagine happens for a loop then? You may end up
connecting a high B residue to a low one when closing it? Does that make
refmac happy? Or your last residue (since it is still well ordered) has
a low B, then you dont gain anything? More appropriate may be a
weighting and adjustment of B-factors based on e.g. real-space CC. But I
guess until we have tools in Coot to refine (or in the first instance
guess) B-factors you better adjust the Bs yourself. Your guess (knowing
the structure and seeing the map) is better than any approximation we
can easily come up with (at least for now).
My 50 Oere (just fazed out BTW),
Bernhard
> When adding residues to the N- or C-terminus, it may be desirable that
> the B-factors of the new residue match that of the previous terminal
> residue. Right now it uses defaults (20 for main chain, 30 for side
> chain) which are sensible fir a well-ordered model, but this causes
> problems with the subsequent refmac run for somewhat disordered regions
> where<B> may be significantly higher.
>
> The current workaround is to modify residue properties manually (or keep
> resetting the defaults). Naturally, the wisdom of adding extra residues
> with<B>~100 is questionable :)
>
> Cheers,
>
> Ed.
>
--
***************************************************
Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden
phone: (+46) 08-52487651
fax: (+46) 08-327626
email: [log in to unmask]
|