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Hi,
You can try the "Ligand Fit" wizard/module in the PHENIX suite
(input mtz, pdb file with no ligand and ask it to do ligand fitting
using a difference map). This is automated and convenient and will use a
database of ligands to try to fit to the density.
You can also use COOT and try to manually fit ligands from the CCP4
ligand library one at a time (starting with what you think may be most
probable based on biochemical function of the protein or chemical
components used during
expression/purification/crystallization/cryoprotection.). For doing
this, you have to just click in the electron density and look up the
ligand/monomer 3 letter code in the library and use the "Get monomer"
function in COOT to read it in.
Hope this helps.
Thanks,
Debanu.
--
Debanu Das,
University of California,
Berkeley.
[EMAIL PROTECTED] wrote:
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Hello,
Does anybody have an idea how to identify a small molecule based on
density map? I have solved a structure at 1.7A and found a
mysterious fo-fc map at 3sigma. I believe it is the ligand
copurified with my protein. Is there a way to identify it in
addition to guess and try? I have done a lot of guessing and trying
without success.
Thanks.
Zhen
