VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Wed Dec 08 2004 - 12:22:50 CST

That's right - Tube will work with just CA atoms, as will Trace, but
the "anisotropic" reps like Ribbons need the whole protein backbone.
However, CA atoms are apparently not enough to identify residues as
protein residues.

If you want to show all the sidechains, in addition to a tube for the
entire chain, you could probably create two reps, one for "all" drawn
as Tube, and a second for "same residue as sidechain" drawn as
Licorice.

Cheers,
Justin

On Wed, 8 Dec 2004 00:53:05 -0700, Andrew Dalke
<dalke_at_dalkescientific.com> wrote:
> Matthew Thomas Geballe:
> > Thanks for your quick reply. It is interesting that if the only atoms
> > in
> > the pdb file are CA atoms and each residue only has a CA atom then the
> > tube representation works if the selected text is "all".
>
> Whew, you're tickling some unused brain cells. I *think* there's
> some code that special cases things if and only if all the atoms
> are CA, but no assurances. You'll need to get an answer with someone
> who has looked at the code in the last 6 years.
>
> > Do you know of any way to modify this?
>
> Modify the source code? :)
>
> Andrew
> dalke_at_dalkescientific.com
>
> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"