[Chimera-users] finding density maps

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 3 11:12:58 PST 2011

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: 

*** 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 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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