From: Jim Nettles (
Date: Sat Dec 18 2004 - 18:20:39 CST

Dear Armarda,

Although fabulous for other things, (unless John has done something in
this newest version?) VMD isn't your best tool for dealing with maps.

"O" is the classic tool and is free to academics. It runs well on Linux
as well as MacOSX. is the
link to get you to the distributioninformation and you then just need
to send Alwyn your system information to get keys.

As far as the actual comparisons, that is an involved discussion and
not really suited for this list. If you write to me directly, I'll do
what I can to help.

Good luck,

Jim Nettles

On Dec 18, 2004, at 4:29 PM, Amarda Shehu wrote:

> Hello everyone,
> does anyone have any experience with visualization and/or comparison of
> electron density map files?
> I want to be able to compare a pdb file with a .map file I got from
> somewhere. I can create an electron density map from the pdb file in a
> .mrc file, but do not know how to visualize it or compare it to the
> .map
> file (which I am assuming also contains an electron density map - just
> in
> some weird format).
> I have been looking at chimera and swiss pdb viewer but cannot
> understand
> whether they have what I am looking for. Plus, if there is any software
> that does visualization and/or comparison of EM files, I need it to
> run on
> a linux platform.
> I would appreciate any idea, because I am clueless when it comes to
> electron density maps.
> Thank you,
> Amarda Shehu.
> ***********************************
> Amarda Shehu,
> Graduate Student, Computer Science,
> Rice University.
> ***********************************
Jim Nettles, Scientific Consultant
Liotta/Snyder Group, Modeling Division, Department of Chemistry
Emory University 1515 Pierce Dr. Atlanta, Ga. 30322
TEL: (404)966-4617 FAX: (404)728-0991