VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 06 2006 - 17:26:32 CST

Vlad,
  I have a preliminary fix for the problems with unusual nucleic
acid terminal residues etc. This new test version of VMD is less sensitive
to atom names and certain structural elements that VMD 1.8.4 and 1.8.5
demanded, and so it should correctly handle the 1S72 structure, along with
several other new ribosome and other nucleic acid structures.

Due to short-term machine outages caused by a local problem with our
computer room chilled water supply, I'm only able to build a
64-bit Linux test version at present. Let me know if you're
able to try out this version and whether or not it cures the problems
you've had with some of the new ribosome and nucleic acid structures.
  http://www.ks.uiuc.edu/Research/vmd/alpha/nucfix/

I hope to have test versions built for other platforms shortly after
we regain air conditioning in our machine rooms, hopefully tomorrow or
in the next couple days.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 20, 2006 at 01:56:33PM -0500, John Stone wrote:
>
> 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 

-- 
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