VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 04 2003 - 13:52:49 CDT

Dear Suzanne,
  I assume that the VMD output you got from Situs is a script containing
VMD 'draw' commands right? An alternative way to load your CCP4 map
would be to try out the latest test version of VMD 1.8.1 and load your
CCP4 map directly into VMD. The new version of VMD includes several new
plugins for reading electron density maps, one of which is a CCP4 plugin.

Alternately, we'd be happy if you could send us a copy of the CCP4 map
you're working with, along the Situs output and any other files you're
loading into VMD so we can test it here. If you'd like to do this but
the files are too large for email, let me know and we can arrange an
incoming FTP area for you.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 04, 2003 at 03:22:23PM +0100, Suzanne Brewerton wrote:
>
> I am trying to use vmd with Situs (for docking models into electron
> microscopy data). I have a CCP4 format map and I have converted it to the
> situs format using conformat and then to vmd format so that I can view it.
> However the conversion is not working as the map looks extremely peculiar
> when I open it. Does anyone have any experience in this?
>
> Thanks
> Suzanne
>
> **---------------------------------**
>
> Suzanne Brewerton
> PhD Candidate
>
> Department of Biochemistry
> University of Cambridge
> Old Addenbrookes site
> 80 Tennis Court Road
> Cambridge CB2 1GA
> United Kingdom
>
> Tel: 01223 766030
> Email: suzanne_at_cryst.bioc.cam.ac.uk
>
> **---------------------------------**
> 

-- 
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