[Chimera-users] visualising electron density map

[Neha Gandhi]

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 at 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 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
>
>


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