My collaborators used MDFF (http://www.ks.uiuc.edu/Research/mdff/) for this: Article Adenoviral vector with shield and adapter increases tumor sp...
Rosetta has a good methodology for fitting maps, especially large protein complexes like a virus. The paper detailing this is: Article Automated structure refinement of macromolecular assemblies ...
and a tutorial for fitting this is https://www.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement.
MDFF is good though should be monitored closely so may be more hands-on than rosetta. High enough res you can always fit it in Coot.
Apart from MDFF as mentioned above, please take a look at the following:
https://mmtsb.org/software/nmff.html
It uses normal mode, so should be simpler.
Another is SMOG, which also implements MDFF. See here:
http://smog-server.org/SBMextension.html
Last one to mention is IMP:
https://integrativemodeling.org/
This one requires you to write python code, if what you wanted to do is not there already
Hi Govindasamy Lakshmanan . First of all, cryo-EM map represent coulombic potential map and not electron density map (provided by X-ray crystallography).
Why dont you try Phenix? It is fast and has all fitting and real space refinement setup integrated with lot of restrained parameters.
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