Re: [AMBER] Is there a tool to calculate electron density maps averaged over a trajectory?

From: David A Case <>
Date: Fri, 14 Nov 2014 21:31:54 -0500

On Fri, Nov 14, 2014, Jose Borreguero wrote:
> I want to calculate the electron density map (EDM) of a protein averaged
> over a trajectory generated with AMBER. The idea is to compare this map
> with the map derived from X-ray on a crystal. In particular, I want to
> compare those atoms that are mobile and whose positions are hard to assign
> from the EDM. Does anybody know of a tool that can help me compute this
> average EDM?

Here is the approach we use: run cpptraj with the "pdb multi" option on the
trajout line. This will create a set of PDB files. You then have to
add the "CRYST1" record from the experimental file at the top. Then you
can feed this pdb file to SFALL (from CCP4; other xray programs might work)
to create the electron density map for that snapshot. Do this for each
snapshot, and average all the resulting maps to get an averaged electron

This procedure is automated in the "" script which is in
$AMBERHOME/AmberTools/src/xtalutil/Analysis. Look at the comments at the top
of this file. It requires CCP4 programs to be in your PATH, and may require
some work to make things work (this is all pretty new, even to us.)

If your simulations is a constant volume one (using, presumably, the
experimental unit cell parameters), you can try the somewhat simpler script in the same directory.

...hope this helps...note that "support" for these scripts may be weaker than
for other parts of far as I know, only a very few people have used
these. We'll try to answer questions, but you may have to fiddle with things.

I'll bet there must be other approaches that take a set of PDB files and
compute electron density maps from them...doesn't have to have anything to do
with Amber. But I have to admit I didn't find anything with a simple Google
search. You might post a question on the CCP4 mailing list -- James Holton
might reply, but he is the main author of

[Aside: sander knows how to deal with electron density maps, and how to create
them from coordinates. But this is in the context of cryo-EM maps, and does
not know about crystal symmetry. So that seems not much help for you, but
just to point out to other readers an approach for the non-periodic problem.]

...good luck...dac

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Received on Fri Nov 14 2014 - 19:00:02 PST
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