VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 06 2010 - 12:49:18 CST

Hi,
  I cannot say for sure what might be causing your problems without
looking at the actual the PDB file you generated. If you can send me
both a PDB of the original structure and the new modified structure, I
will have a look and give you suggestions based on what I find.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 05, 2010 at 11:09:16AM +0100, Kassem Ghaddar wrote:
> Hello,
>
> i have encountered a Problem after adding an molecule to an already exiting model created in VMD. When i save the coordinates of this molecule, the new cartoon representation shows only one alpha strand of the molecule (atoms 1 to 14) followed by the molecule that i added (tryptophan 601). it seems that the new model calculates the position of the C (alpha) atoms and apparently the position of the molecule that i added is closer to the carbon 14 than the normal C 15 that should follow. the other representations show the whole molecule, but still include my new molecule in the backbone of the chain, even though i precise in the PDB file that it should be considered as a separate chain.
>
> Where does the rest of my molecule disappear in the New Cartoon mode ?
>
> thank you
>
>
>
>
> GHADDAR Kassem
> PHD student
> Structure et Fonction des Membranes biologiques (SFMB)-Brussels
> Molecular Physiology of the Cell-Gosselies
> ULB-Brussels-Belgium 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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