[Chimera-users] visualising electron density map

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 27 09:33:17 PDT 2014

Dear Dr. Gandhi,
The description in the paper  <http://www.nature.com/nature/journal/v504/n7478/full/nature12823.html> of this figure mentions filtering/normalizing with MAPMAN and subtracting the density map of the apo-protein from the density map of the liganded protein using another program (not Chimera).  Maybe the available maps already include this filtering/normalization, but I don't know for certain.  If they do, and those two maps are available, you could do the subtraction in Chimera with the "vop" command. Vop also has several filtering options, but they are probably different than what is in MAPMAN:


I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 27, 2014, at 2:39 AM, Neha Gandhi <n.gandhiau at gmail.com> wrote:

> 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 - http://www.nature.com/nature/journal/v504/n7478/fig_tab/nature12823_SF7.html). 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,
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia

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