VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 09 2007 - 14:57:55 CDT

Gunnar,
  I finally had a chance to take care of this. If you let me know
what VMD platform you're using, I can provide you (and any other
interested users) with a new version of the X-PLOR map reader plugin
which cures the problem you encountered.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jul 13, 2007 at 09:13:19AM -0700, Gunnar Schroeder wrote:
> Hi,
>
> I just converted the xplor map to ccp4/mrc map format
> with mapman, and the ccp4 map looks fine. So, it is,
> as you said, likely a problem of the xplor reader plugin.
>
> I attached the files.
>
> Thanks,
> Gunnar
>
>
> John Stone wrote:
> >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/
> >
>
>
> --
> _______________________________________________________________
> 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