Just to add a minor comment to what Dave said: the mdv2map.sh script does
not exist anymore but there is an option in md2map.sh that let's you
provide the CRYST1 card directly (if your simulation was run at constant
volume). Also, the script MakePdgb4Map.py (same directory) simplifies
making the PDB files with CRYST1 cards (if your simulation was run at
constant pressure). Please feel free to provide us with any feedback or
issues you may encounter that can help us improve these tools.
The other relatively easy way of doing what you want would be to use cctbx
modules and make your own python script, but that option also requires
creating multiple PDB files first.
Pawel
On Sat, Nov 15, 2014 at 9:58 AM, Jose Borreguero <borreguero.gmail.com>
wrote:
> This is a lot of helpful information, I'll go over the scripts you wrote
> about. Thanks a ton!
> -Jose
>
> On Fri, Nov 14, 2014 at 9:31 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
> > 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 "md2map.sh" 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
> > mdv2map.sh script in the same directory.
> >
> > ...hope this helps...note that "support" for these scripts may be weaker
> > than
> > for other parts of Amber...so 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 md2map.sh.
> >
> > [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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Mon Nov 24 2014 - 15:00:02 PST
