VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 20 2006 - 13:56:33 CDT

Vlad,
  VMD 1.8.5 fixes a number of problems with display of various types of
nucleic acid structures, but this has resulted it in it being (presently)
far more picky about the atom names used in nucleic acid residues, and it's
particularly picky about terminal residues. I was already aware of the
problem with 1S72 and four or five other PDB structures, I hope to have
this addressed soon. For 1S72 specifically, I think I have a
workaround written down somewhere, but I'll have to get back to you on this.

  John

On Wed, Sep 20, 2006 at 04:06:43PM +0200, Vlad Cojocaru wrote:
> Dear vmd users,
>
> I noticed that the Ribbons (NewRibbons) representation for nucleic acids
> doesnt work anymore in vmd 1.8.5.
> I loaded the 1S72.pdb structure (ribosome from PDB) in vmd 1.8.5 and I
> couldnt see the ribbon representation of the RNA. I did the same in vmd
> 1.8.4 and everything was fine.
>
> Best wishes
> vlad
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
> 

-- 
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