VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Aug 11 2014 - 12:36:16 CDT

On Mon, Aug 11, 2014 at 12:59 PM, Thomas C. Bishop <bishop_at_latech.edu> wrote:
> Greetings VMD,
>
> I have a program that generates coordinate information.
> What's the recommended means of initializing a new molecule from memory
> rather than file?
> Below is my initial attempt/ideas.
> Thanks
> TOm
>
> a quick read of the html suggests (something like) the following is possible
> but it I"m missing something w/ the set command

you are missing coordinate frame storage. if you watch closely, you
should see that you create a molecule with no frames. for that you
need to insert.

animate dup top

axel.

>
> vmd > mol new atoms 2
> 0
> vmd > set all [atomselect top "all" ]
> atomselect0
> vmd > $all set { x } { { 1.0 } { 2.0} }
> vmd > $all get { x}
> 0.0 0.0
> vmd > $all get { x y z }
> {0.0 0.0 0.0} {0.0 0.0 0.0}
> vmd > $all get name
> X X
> vmd > $all set name { CA }
> vmd > $all get name
> CA CA
> vmd > $all set x { 1 }
> vmd > $all get x
> 0.0 0.0
> vmd >
>
> --
> *******************************
> Thomas C. Bishop
> Tel: 318-257-5209
> Fax: 318-257-3823
> www.latech.edu/~bishop
> ******************************** 

-- 
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.