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Dear All
I am making figures with pymol and wish to show electron density
around a ligand. When I put the distance around the object=0, I
still get density around other residues close to the ligand.
What do I have to do to get this work?
I am sorry this is not an answer to your question, but in case the
picture is intended for a scientific publication
and not for artistic use (ie fancy cover page for your thesis ...) I
would argue that you don't want to be doing that.
The danger is, that if you adjust carefully the radius and the sigma,
you can get perfect density for something that
is not there.
If you want to show something realistic and useful for your ligand,
calculate an omit map
and show the omit map for the whole region for which you show
residues. It should only then
show density for your ligand and would contain useful information.
Tassos
Thank you in advance
Veronica
---------------------------------------------
Tamu Dufe Veronica, PhD Student
Molecular Biophysics
Center for Chemistry and Chemical Engineering
Getingevagen 60
Lund University
P.O.B. 124
SE-22100 Lund
SWEDEN
Tel: +46462224513
