VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 12 2005 - 10:55:56 CDT

Peter,
  I just loaded this structure and had no problems drawing
the backbone with a Tube representation, but I used the atom
selection "all", as VMD doesn't consider the disconnected CA
and P atoms as a complete structure. Try selecting "all", and
use "Tube" and see if that does what you need. Let me know if you
need more help getting this working.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 12, 2005 at 08:40:44AM +0200, Peter Schellenberg wrote:
> Hi all ,
>
> I have some trouble in displaying the RNA of a biomolecule in a
> trace, tube, or similar graphical representation. It concerns
> 1JGP.pdb, which displays the 30S ribosome subunit including t-
> RNA and m-RNA. The t and m-RNAs are displayed nicely as well
> as the protein backbone, but the 30S RNA backbone is not shown,
> despite that the Phosphors are defined. One can show the
> Phosphors in a atom presentation but not as a backbone. Strangely
> the analoge backbone structure for the corresponding 50S
> ribosome subunit ( 1GIY.pdb) does not cause problems although
> the pdb file is much more rudimentary than for 1JGP.pdb. Pymol
> seems to have the same problems with 1JGP, while Rasmol depicts
> the backbone structure well
> Is there any hint to a solution
>
> Many thanks in advance Peter
>
>
> Dr. Peter Schellenberg
> Institute for Physical High Technology Jena
> Dept. of Biotechnical Microsystems
> Albert -Einstein -Str. 9
> D-07745 Jena
> +49 -3641 -206 308 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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