Just to clarify, with coot do not identify the ligand you mean

a) your ligand could not be read by coot 
b) Coot did not place it anywhere ?

if a, then run phenix.elbow to fix your ligand
If b, then select to difference density map as the map where the ligand is supposed to be found

Hope that helps,

Jürgen
......................
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:      +1-410-614-4894
Fax:      +1-410-955-2926
http://lupo.jhsph.edu

On Mar 30, 2013, at 3:58 PM, <[email protected]> wrote:

Hi all,

I tried to fit the ligand using the coot -> calculate-> other modeling tools->
Find ligands. I have imported cif to coot and also opened the pdb file of my
ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I
can see the density for my ligand. Could anyone suggest me what could be the
problem or if I am missing anything here.

Best regards.

Bishwa


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......................
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:      +1-410-614-4894
Fax:      +1-410-955-2926
http://lupo.jhsph.edu