VMD-L Mailing List

From: Eric Johnson (johnson_at_scripps.edu)
Date: Mon Nov 07 2005 - 14:51:57 CST

We generally use CNS (X-plro) to calculate maps. I have not used the
server you indicated to generate maps. Maps may differ based on parameters
used to calculate them. We generally us O to view maps and build proteins
models, and Pymol to generate figures that incorporate maps. The latter
lacks many of the controls found in O for viewing and contouring maps. I
have no experience with viewing maps in VMD. The problem maybe in reading
the map file or in telling VMD about the space group or unit cell
parameters.

Another program for viewing in maps is MIFit from www.molecularimages.com.
This is a Windows version of Duncan McRee's XtalView program.

Eric

On Mon, 7 Nov 2005, Vlad Cojocaru wrote:

> Date: Mon, 07 Nov 2005 18:44:00 +0100
> From: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> To: VMD list <vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: visualizing CCP4 maps in VMD
>
> Dear vmd users,
> I downloaded a ccp4 map from the Electron Density Server (Uppsala)
> for a given pdb file and I loaded it into vmd. I changed the
> representation to Isosurface with an isovalue of 1.0. However the
> visualized map does not overlap with the atoms in the respective pdb
> file and changing the isovalue does not help.
> I tried the same with PyMOL and it worked well. However since I am
> much more familiar with VMD I was wondering if any of you has
> encountered such a problem and has any idea how to fix this.
> Cheers
> vlad
>
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Villa Bosch
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
>
>
>