VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 13 2014 - 11:31:45 CST

Bernhard,
  I'm not sure I understand what you're asking. Are you saying that
you want VMD to connect the separate chains, or are you saying that
you don't want it to, but it IS connecting them? Normally, I would not
expect them to be connected.

Cheers,
  John Stone

On Thu, Nov 13, 2014 at 11:39:06AM +0000, Knapp Bernhard wrote:
> Hi John,
>
> Okey thanks that should do as a workaround ... VMD is just connecting
> the chains now i.e. the last CA of chain A with a long straight line
> across the molecule to the first CA of chain B. In the pdb file it looks
> like below. Do I need to add TER lines between the chains or can I
> somehow tell this to VMD?
>
> ...
> ATOM 823 CA GLU A 275 20.231 14.612 11.662
> ATOM 826 CA MET B 276 -24.147 -8.692 14.871
> ...
>
>
> Thanks,
> Bernhard
>
>
>
> Am 12.11.2014 16:35, schrieb John Stone:
> >You could either use the Tube or Trace representations in VMD for
> >sure. I don't think Ribbon or NewRibbon would work with
> >only CA atoms, because they compute ribbon orientation.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Wed, Nov 12, 2014 at 02:00:27PM +0000, Knapp Bernhard wrote:
> >>Hi,
> >>
> >>Is there an easy way in VMD to get a cartoon representation of a
> >>molecule with CA atoms only?
> >>
> >>Like you would do it in pymol
> >>(http://www.pymolwiki.org/index.php/Cartoon, section "CA (Alpha
> >>Carbon)
> >>Trace")?
> >>set cartoon_trace,1
> >>show cartoon
> >>
> >>I haven't found such a command for VMD yet. Can anyone help with that?
> >>
> >>Cheers,
> >>Bernhard 

-- 
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