VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 07 2005 - 15:22:40 CST

Vlad,
  If you haven't updated your VMD 1.8.3 plugins yet, we fixed an
alignment bug in the CCP4 plugin back in March which may be causing
the particular alignment problem you're experiencing. You can also
try one of the VMD 1.8.4 test versions if you prefer.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 07, 2005 at 06:44:00PM +0100, Vlad Cojocaru wrote:
> 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
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078