This is an idea I had for a while but never had the time to implement or
test (it's still on my list though). For now torsion angle refinement
and especially back-rub rotamer fitting of side chains (default for
lower resolution; 2.8A IIRC) should help to prevent side chains from
moving into the 'main' density.
B
this one is for Paul, but maybe it's worth discussing it on the list. If that
feature already exists, please let me know.
Would it make sense to down-weight the side chain atoms in real space
refinement? At low resolution I often find that the side chain atoms are dragged
into the density of where I suspect the main chain to run, and maybe this effect
could be avoided by downweighting the X-ray 'force' on the side chain atoms.
This might correspond to having different matrix values for main and side chain
atoms.
I am curious to hear comments about this idea.
Cheers, Tim
--
***************************************************
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: [email protected]
