VMD-L Mailing List

From: Thomas C. Bishop (bishop_at_latech.edu)
Date: Mon Aug 11 2014 - 12:39:26 CDT

Thanks Axel and Maxim,

I had no frames in my molec so could not add coords.
an animate dup is needed. e.g.

set molid [mol new atoms 2]
animate dup $molid
set all [atomselect top "all"]
$all set x [list -5.0 5.0]

ref.

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22961.html



On 08/11/2014 12:36 PM, Axel Kohlmeyer wrote:
On Mon, Aug 11, 2014 at 12:59 PM, Thomas C. Bishop <bishop@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 >

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   Thomas C. Bishop
    Tel: 318-257-5209
    Fax: 318-257-3823
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