Ed,
you did the right thing to 'refine' (x) the Ramachadran by setting:
(set-refine-ramachandran-angles 1)
This can be done from the GUI in various places as well, e.g.
Refine/Regularisation Control (R/RC) in the refinement toolbar or in
extensions: Extensions->Refinement->Refinement Control (*). The latter
has a few more option. You can check that the Ramachandran restraints
are used by looking at the traffic lights (you will get an extra one for
Ramachandran) and in the console output as well.
I just was wondering, maybe I am missing the point here and your 'zone'
is larger than my zone. My zone I can easily select with the mouse, if
you are after something more exotic then we need (more) function what
Judit mentioned.
B
(*) You can keep them open and tick the options on and off as you need
them, i.e. for one or the other zone e.g.
(x) The weighting of the Ramachandran plot is fairly low, so dont expect
miracles, all other restraints and maps (if used) are still included in
the refinement, so you may not see much of an 'improvement'.
Is there some way to do the Refine/Improve Ramachandran plot not on the
whole molecule? The underlying command stepped-refine-protein-for-rama
doesn't seem to have any other options but the imol, so obviously no
luck.
I also tried "set-refine-ramachandran-angles 1" which, afaiu, should
turn Ramachandran restraints on, but I don't see any difference (in
fact, when I refine a zone the residues move away from allowed angles).
I thought that this could be combined with stepped-refine-protein, but
that one would also tackle the whole thing, and one cannot narrow its
action to a zone.
I could, of course, delete the elements I don't want refined and later
reinsert them. Another workaround (maybe) is to fix the atoms I don't
want to move (in which case it'd be totally awesome if one could fix all
the atoms in a zone at once - is this possible?).
So, perhaps a future version may allow for all of these operations (e.g
fit-protein, stepped-refine-protein, stepped-refine-protein-for-rama) tp
be applied to a zone? Please?
Cheers,
Ed.
PS. Well, I was told long time ago that restraining "Ramachandran
angles" is a BAD idea because they should only be used for validation.
But this is 3A data.
--
***************************************************
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]
