[Chimera-users] finding density maps

SURESH KUMAR sureshbioe at gmail.com
Mon Jan 3 19:54:19 PST 2011

dear Elaine,

           Thanks for your kind information.

On Tue, Jan 4, 2011 at 12:42 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Suresh,
> If you choose Chimera menu item "File... Fetch by ID"  and specify one of
> the "EDS" database choices and enter a 4-character PDB ID, you can get a
> density map for the structure with that same ID in the PDB database.
>  These density maps are obtained over the web from the Electron Density
> Server.  You can also go directly to that web server at:
> <http://eds.bmc.uu.se/eds/>
> *** However, it is important to realize that not all PDB structures have
> density maps available. ***  Chimera does not help you find which maps are
> available, but it simplifies getting the ones that are available.   You can
> simply try fetching the ones for the PDB files of interest; if they are not
> available, a message saying that will appear.
> Besides electron density maps for atomic structures in the PDB, there may
> also be lower-resolution maps available from the Electron Microscopy Data
> Bank (EMDB <http://www.ebi.ac.uk/pdbe/emdb/>), which is another choice in
> the Fetch by ID dialog.  If you specify one of the "EMDB" options in that
> dialog, you can also search by keyword.
> 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 Dec 31, 2010, at 4:40 AM, SURESH KUMAR wrote:
> > hello sir,
> >               I need to find electron density of protein, i am planning
> to use UCSF Chimera software for that... so please help me how to find
> protein electron density using UCSF Chimera
> >                      thank you
> > A.Suresh Kumar,
> > M.Tech Biomedical Engineering,
> > Amrita School of Engineering,
> > Ettimadai,
> > Coimbatore.
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