Re: MDFF based on known EM maps

From: Ryan McGreevy (
Date: Tue Jun 28 2016 - 12:20:46 CDT

Yes, you can use experimental EM maps, such as those from EMDB, as your
target for MDFF. The tutorial uses a simulated map for simplicity's sake.
If your starting structure is not already aligned to the map, you can first
perform a rigid body docking, using a program like Situs, as discussed in
the tutorial.

On Tue, Jun 28, 2016 at 12:12 PM giulia palermo <>

> Dear all,
> I am new to MDFF and I am following the tutorial published on the web.
> From the tutoral one can generate the EM map, based on a PDB file and
> use this map for the refitting. My question is if it is possible with
> MDFF to use a published EM map as a target dtructure for the
> refinement of a structure coming from X-ray or MD simulations.
> It is possible to superpose the map downloaded from EM-data bank to
> the PDB structure with VMD?
> Thank you very much
> Giulia

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