Thank you very much Elaine. The authors of the paper have deposited the normalised/filtered maps. So Vop command was helpful. Cheers, Neha On 28 October 2014 00:33, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>
I hope this helps, Elaine ---------- 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@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
-- Regards, Dr. Neha S. Gandhi, Curtin Research Fellow, School of Biomedical Sciences, Curtin University, Perth GPO U1987 Australia LinkedIn Research Gate