VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Mar 10 2015 - 07:38:34 CDT

Dear Albert and John,
I apologize in advance for giving out cheap advices but I though about
it for a moment and maybe my thoughts are useful to share...

Since the trajectories are supported in VMD with all bells and whistles
for atoms, why not to treat the mesh vertices as atoms?
To make this idea usable it would be needed to patch the core VMD code
to provide "just" another graphical representation for mesh.
I do not know how involved this would be but if comparable to writing a
new plugin, it may be worth considering.
I see many avantages, lets assume that a specific "element symbol" is
used for vertices, say "Vx", and one could even load arbitrary meshes
from easily prepared XYZ or PDB files, color them using atom specific or
frame specific (e.g. User) properties, divide them into segments or
"residues", select parts of the mesh to show using selections, use
labels etc.
Just my two cents.
Pawel

W dniu 10.03.2015 o 11:53, Albert Solernou pisze:
> Hi John,
> thanks for the answer. Although it is not the ideal solution, and
> although I don't know tcl... I could give it a go. Could you point me
> to the right documentation?
>
> In addition I have a few extra questions:
> - Will I be able to define/label different bodies or parts so that I
> can click on them, change colors, and show/hide?
> - In that case how will that integrate with the next timestep given
> that it is a "different" molecule?
> - I have currently a Tkinter interface that I plan to port to, and I
> read that you support it. Could you point me to the right
> documentation site to do so? Do you have any suggestion?
>
> Cheers,
> Albert
>
> On 03/09/2015 06:00 PM, John Stone wrote:
>> Hi,
>> At present, VMD doesn't provide for time-varying mesh data.
>> In the short term, you could overcome this limitation by loading
>> different trajectory timesteps into separate molecules. Once loaded
>> you can animate the mesh trajectory using the multimolanim plugin.
>> Let us know if you need help to get this working.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Mon, Mar 09, 2015 at 03:11:26PM +0000, Albert Solernou wrote:
>>> Dear all,
>>> I am writing a new plugin that should enable VMD to work with Finite
>>> Element Trajectories. Currently, my plugin reads correctly the input
>>> file, through:
>>> plugin.open_file_read
>>> then loads and displays the surface triangles through:
>>> plugin.read_rawgraphics
>>> and finally releases my handler:
>>> plugin.close_file_read
>>>
>>> The next step should be to load the whole trajectory, and this is
>>> where I need some advice. I understand that this should be done
>>> through:
>>> plugin.read_next_timestep
>>> but, will it update the vertices of the triangles? How can I do so
>>> using molfile_timestep_t? Is there an easy workaround?
>>>
>>> Thanks in advance,
>>> Albert
>>>
>>> --
>>> ---------------------------------
>>> Dr Albert Solernou
>>> EPSRC Research Fellow,
>>> Department of Physics and Astronomy,
>>> University of Leeds
>