[Chimera-users] visualising electron density map

Neha Gandhi n.gandhiau at gmail.com
Mon Oct 27 02:39:36 PDT 2014

Dear Support,

I have downloaded pdb file 3j5r and also downloaded corresponding electron
density map from EMD (http://www.ebi.ac.uk/pdbe/entry/EMD-5777). The
microscopy structure was done in presence of the ligand and the original
paper reports electron density for the ligand (Extended figure 7 -
However,  the authors couldn't model the orientation of ligand in the
binding site.

I have docked the ligand in the binding site and I am trying to visualize
if the docked ligand fits well in the electron density or not. Is there a
way to visualise the electron density only for the ligand in UCSF chimera
as reported in the above nature paper?

Thank you for kind attention,

Awaiting your reply,

Dr. Neha S. Gandhi,
Curtin Research Fellow,
School of Biomedical Sciences,
Curtin University,
Perth GPO U1987
Research Gate
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