Phil,
> If I "colour by chain" (my preferred option), metal ions disappear
I see, but not all metals disappear (only your favourite ones I guess,
e.g. PT is there). Not sure if feature or bug (I guess the latter).
> also is there any way of refining a zone around a metal ion without the sidechains vanishing into the metal density? I know the refine-by-sphere ("R") option works better, but then I have no control over what I'm refining
There are two ways how to do this:
- mask your map (Extensions->Maps->Mask Map by Atom Selection)
- define your own residues to be included in the refinement (as done in
sphere_refinement, i.e refine_residues; see e.g. fitting.py)
I can elaborate more on these if needed.
Hope this helps,
B
--
***************************************************
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]
