In Coot, you can "beam in an xxx" where xxx in this case is an
"acetate" using
File -> Search Monomer Library
Text: "acetate"
Click Search
Click "ACT: Acetate ion"
You can then Use Copy Molecule on this monomer and "Move molecule" to
move the copies to where you want them and use "Merge Molecules" to add
the acetates to the main molecule.
You will have to delete your waters that are in the acetate densities.
Paul.
p.s. this presumes that you have a working CCP4 distribution, of course.
On 26 Feb 2007, at 23:05, Arti S. Pandey wrote:
Hi Sam,
Ideally, with the R factor you are at, you should be able to build
these
residues in, using Coot/Ono/xtalview and then refine with shelxl.
If you want to go to shelxl straightaway, you might want to refine res
9-86 as one chain and res 94-last residues as another.
I guess you could mutate a wate to an acetate ion. Or just read in a
pdb
for acetate and move it into the density where you think it should be.
The tutorial for Lysozyme actually gives tells you how to do this, but
it
is in xtalview. You could still get some hints from it. I believe
within
that there are some missing residues too, deliberately removed, but
kind
of like your situation.
Hope this helps.
Arti
Hi
I would appreciate few things for my protein structure. Data is 1.5A.
This protein is of 400 residues. 2 molecule in the asymm unit.
Missing residues are : N-terminal 8 residues, C-terminal 5 residues
and in
the middle residues 87-93.
Final R(working) = 21% after refmac refinement. Some (not all) waters
created into the structure.
I am taking this structure into Shelxl for further refinement and
building
the missing residues.
(1) During Shexl refinement how the missing residues I can fix. what
kind
of keyword I should use to fix the missing residues with a reasonable
Occunany and B value.
(2) In COOT how can I build acetate ions in place of waters. Or any
other
way I can call acetate ions.
Thanks
Sam
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Arti S. Pandey
Graduate Student
Chemistry and Biochemistry
Montana State University
Bozeman,MT 59717
--
http://www.ysbl.york.ac.uk/~emsley
Structural Biology Laboratory, University of York, York, YO10 5YW, UK
