VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 21 2015 - 12:18:50 CST

On Wed, Jan 21, 2015 at 12:38 PM, George Patargias <gpat_at_bioacademy.gr> wrote:
> Thanks for this.
>
> I run the command topo getdihedrallist on a pdb containing only backbone
> atoms. Apart from the phi/psi, the omega angles are also reported.
>
> Is it possible to include the topo deldihedral id1 id2 id3 id4
> command in a Tcl script so I can delete all the omega dihedrals from the
> list?

of course!

that is what i already told you in my previous email. there even isn't
really a need to doctor up a special pdb file, but just use a proper
atom selection. please refer to the canonical Tcl and VMD script
command documentation and tutorials for more details.

axel.

>
> Thanks again.
>
>
>> On Wed, Dec 10, 2014 at 9:12 AM, George Patargias <gpat_at_bioacademy.gr>
>> wrote:
>>> Hello,
>>>
>>> Is there any way to select only the phi and psi dihedrals with
>>> TopoTools?
>>
>> no.
>>
>>>
>>> The commands:
>>>
>>> topo guessdihedrals
>>> topo getdihedrallist
>>>
>>> select all the dihedrals.
>>
>> but you should be able to restrict getdihedrallist with a selection to
>> the backbone and then postprocess that list further based on the usual
>> naming conventions for backbone atom types/names.
>>
>>
>>>
>>>
>>> Many thanks.
>>>
>>> George
>>>
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>>
>
>
> Dr. George Patargias
> Postdoctoral Research Fellow
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.