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

From: Jose Borreguero <>
Date: Sat, 15 Nov 2014 09:58:23 -0500

This is a lot of helpful information, I'll go over the scripts you wrote
about. Thanks a ton!

On Fri, Nov 14, 2014 at 9:31 PM, David A Case <>

> 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
> density.
> 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
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Sat Nov 15 2014 - 07:00:02 PST
Custom Search