Am 22.11.10 10:49, schrieb Eleanor Dodson:
On 11/18/2010 05:45 PM, Phil Evans wrote:
On 16 Nov 2010, at 13:22, Paul Emsley wrote:
Dear Phil,
Sorry for the delay, I am only just back from somewhat extensive
travels.
On 01/11/10 12:26, Phil Evans wrote:
If I "colour by chain" (my preferred option), metal ions disappear
Thanks for the notification of this bug. It is fixed now, rev 3245.
thanks
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
Sphere refine is simply a thin layer around the refine-residues
function which takes a list of residue specs - that gives you enough
control, I hope. (You can also trivially change the "radius" in
sphere refine.)
Paul.
How do you change the radius?
I had a long chat to Bernhard about this. My feeling is that in order
to avoid "user consternation" ((c) George Sheldrick), RS refinement
in Coot should _never_ move something into space already occupied by
another part of the same molecule (zero occupancy excepted). I
realise there are implementation difficulties, but I do think this is
a major problem.
Phil
I absolutely agree with this. It is a disaster of curse when you have
a metal - all nearby side chains rush to take up the density..
Eleanor
This could be avoided by including geometrical restraints (VDW
distances, hydrogen bonds) with a shell of residues surrounding the
refined ones.
Hydrogen bonds would also stabilize secondary structure elements of the
refined part at low resolution.
Best regards,
Dirk.
--
*******************************************************
Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected]
WWW: www.genzentrum.lmu.de
*******************************************************
