VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 17 2012 - 10:37:43 CST

On Mon, Dec 17, 2012 at 5:19 PM, Bennion, Brian <Bennion1_at_llnl.gov> wrote:
>
> here is a mistake. for multimol anim you need to load
> each frame into a separate molecule. if you need to
> copy the choice of representations and selections,
> you can use the "Clone Representations" plugin.
>
> How will this help solve the problem? Now I will have X number of molecules that correspond to X number of frames of a protein simulation. I still have to find out a way to overlay the subsequent X number of mesh graphics objects (that were loaded as molecules) to the exact protein molecule from which it was calculated.

this is the basic assumption of the plugin. it
wasn't meant to deal with a setup that you have.

for anything else, it would have to be adapted.
it may not be too difficult tho. i can have a look
and send you a modified version, if needed.

>> mol new dir1/000000.mesh
>> ...
>> mol new dir999/000999.mesh
>
> and, of course you need to add the graphics
> to each molecule (=frame). loading them into
> separate frames may cause other viz problems
> later.
>
> I am confused by the comments above. Are you saying that the meshes that have been calculated should be added to each of the protein frames/molecules using the vmd graphics command language instead of loading them as separate molecules? I will look into how to do this in a frame independent manner. Thank you for the suggestion.

i've never dealt with this kind of direct mesh data before.
can't you just use them with "mol addfile" instead of "mol new"?
as i mentioned earlier, the plugin assumes that each frame
is a separate molecule and shows/hides them as needed.

axel. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.