VMD-L Mailing List

From: Knapp Bernhard (bernhard.knapp_at_meduniwien.ac.at)
Date: Thu Nov 13 2014 - 05:39:06 CST

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