VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Mar 08 2005 - 10:33:32 CST

It's probably useful to define an atom selection macro to handle this
common case. By putting the following in your .vmdrc file:

  atomselect macro side {sidechain or name CA}

you can draw reps with connected side chains using the selection
  
  resid 1 2 3 and side

Note that "((not backbone) or name CA)" is not equivalent, as it will
also pick up the amide hydrogen, which you probably don't want since
it will appear as a disconnected atom.

Cheers,
Justin

On Mon, 7 Mar 2005 16:46:47 -0600, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Except that you'll have to use an "or" rather than "and" when
> combining "name CA" with the rest of that selection. I'd try
> something like:
> residue 47 45 44 40 and ((not backbone) or name CA)
>
> John
>
> On Mon, Mar 07, 2005 at 06:36:29PM -0500, Luis Rosales wrote:
> >
> > Mmmm, In order to display the ca-cb bond, I think that you should
> > replace the 2 selections with only one selection, something like:
> >
> > "name CA and residue 47 45 44 40 and not backbone"
> >
> > hope this helps,
> >
> > Ludwig
> >
> > ---------- Original Message -----------
> > From: Peter Holm <Peter.Holm_at_mbfys.lu.se>
> > To: vmd-l_at_ks.uiuc.edu
> > Sent: Mon, 07 Mar 2005 22:42:40 +0100
> > Subject: vmd-l: Display only side chains
> >
> > > Dear list-readers,
> > > I wish to display only a selected set of residues created as a
> > > separate selection where the side chains are sticking out from the
> > > "new ribbons" object without main chain CO and NH disturbing the
> > > view. So I did the following selections:
> > >
> > > "residue 47 45 44 40 and not backbone"
> > >
> > > "residue 47 45 44 40 and alpha"
> > >
> > > This results in the view I wish to have when visualising the
> > > selection with licorice except that the Ca-Cb bond is missing. Any
> > > hints on how I can get the side chain visualised from Ca and
> > > "outwards" are most welcome and appreciated?
> > >
> > > Regards
> > >
> > > Peter
> > >
> > > ****************************************************
> > > Peter Holm, Ph.D. Student
> > > Molecular Biophysics
> > > Center for Chemistry and Chemical Engineering
> > > Lund University
> > > P.O.B. 124
> > > SE-22100 Lund
> > > SWEDEN
> > >
> > > Telephone numbers
> > > Office: +46-(0)46-2221448
> > > Mobile: +46-(0)709-625451
> > > Fax: +46-(0)46-2224692
> > > E-mail: peter.holm_at_mbfys.lu.se
> > > http://www.mbfys.lu.se
> > > ****************************************************
> > ------- End of Original Message -------
>
> --
> 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
> 

-- 
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"