VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 12 2007 - 22:28:21 CDT

Hi,
  Can you provide me with a copy of your density map and
structure? It's possible there's a bug in the X-PLOR map
reader plugin, if so it should be easy to correct. If the files
are too big for email, please deposit them in the VMD Public project
on biocore:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 12, 2007 at 05:14:01PM -0700, Gunnar Schroeder wrote:
> Hi All,
>
> I am looking at electron density maps with VMD
> and it seems to me that the map representation is
> slightly off. I do not know if someone noticed that
> before? It looks like the map is shifted by a small
> amount, possibly one grid unit, in all three dimensions
> away from the origin.
> It is more obvious for maps having a coarse grid-spacing.
>
> I am reading x-plor ascii maps, I do not know if it also
> occurs for other map formats.
>
> Is there a way to correct this shift?
>
> Thanks,
> Gunnar
>
>
> --
> _______________________________________________________________
> Gunnar F. Schroeder
> Levitt Lab - Brunger Lab
> Stanford University - School of Medicine
> TEL: +1-650-725-0754
> FAX: +1-650-723-8464
> http://csb.stanford.edu/~gschroe/ 

-- 
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