how to obtain electron density map of a particular cryo EM structure? And how to analyze it? Is it posiible to see a particular amino acid side chain interaction using cryo EM data? If yes, How? Since the resolution is generally low above 3-5 angstrom.
I'm not clear what you are asking. Is it 'How to I solve a structure by cryoEM?' or 'How do I view a structure solved by cryoEM?'
If the latter, the density can be deposited in EMDB and a fitted model in the PDB.
The model and the density can be viewed online at the PDBe website, eg http://www.ebi.ac.uk/pdbe/entry/pdb/5k12 and click on '3D visualisation' on the right. The model and the density map will be displayed.
At relatively low resolution, particular sidechains can generally not be seen and caution should be used in interpreting fitted models. The authors may have docked existing structures (high res) into a low res map simply to indicate which part of the map is which part of the complex, not to model the interaction between them.
Thanks Matthew for your reply and sorry for the inconvenience?
Actually I want to visualize , already solved structure (5lj3), using pymol, Its opening but the structure is not visualized.
If i want to download the electron map density, How can I download?
Please suggest
the map is viewable online at http://www.ebi.ac.uk/pdbe/entry/pdb/5lj3 in the '3D visualisation'
The density map (nb not electron density for EM) is deposited in EMDB at http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-4055/ and also viewable there
Chimera will load the map from EMDB and the model from PDB easily, its a little more tricky in pymol
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