Dear Tim,
Thanks for your advice.
I am refining my structure anisotropically.
If, as you suggested, I did something wrong converting
files to use in SHELXL I would expect that the whole
structure to have problems or am I wrong?
And how can I assign a free variable to the whole ligand?
I've just started using SHELXL.
Best,
Fátima
Em Mon, 7 Jun 2010 20:54:07 +0200
Tim Gruene <t...@shelx.uni-ac.gwdg.de> escreveu:
Dear Fatima,
just a couple of things you may consider:
- you can let shelxl refine the occupancy by assigning a
free variable to the
whole ligand
- did you refine the structure anisotropically? At this
resolution you certainly
should.
- maybe you made a mistake converting the files from
refmac to shelxl, e.g. you
might have used amplitudes where shelxl expects
intensities or vice versa.
Good luck, Tim
On Mon, Jun 07, 2010 at 05:46:01PM +0100, Fatima Fonseca
wrote:
Dear all,
I solved the structure of an enzyme at resolution of
1.1A with a bound substrate using Refmac5 and Coot for
refinement/building. I have a very nice density for my
ligand and a very good structure, as judged by Molprobity
analysis.
Now I'm using SHELXL to finish refinement but most of
the density for my ligand disappears when I put it in,
and it gets very high B factors. I though it could be
some problem with the occupancy so I did a set of runs
with different occupancies ranging from 0.2 to 1 and I
got the best R factors when using 0.4/0.5 for the
occupancy.
However, I still have most of the ligand outside
electron density… In Coot I get no ligand with “Find
ligand” even when I reduce the cluster sigma level to
0.8.
What am I missing here?
Just another question, how to reduce the acceptable fit
fraction in Coot “Find ligand”?
Thanks for any advice,
Fátima
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
---------------------------
Maria Fátima da Fonseca
PhD student
CESAM & Dep. Biologia
Campus Universitário de Santiago, Universidade de Aveiro
3810-Aveiro, Portugal
Fax: 234 372 587
E-mail: ffons...@ua.pt
