VMD-L Mailing List

From: Knapp Bernhard (bernhard.knapp_at_meduniwien.ac.at)
Date: Fri Nov 14 2014 - 10:24:32 CST

I do not want them to be connected but they are.
If I add a TER line then it is fine but I was wondering if there is an
easier way which does not require me to change all the input
trajectories.

Thank you very much,
Bernhard

Am 13.11.2014 17:31, schrieb John Stone:
> 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