[BiO BB] bio game / bioinformatics game /fun

[Mike Marchywka]

Thanks. It doesn't have to have any features specialized to molecules but 
they
would be a plus as long as it could also function as a general rendering and 
interaction
engine. I started my search looking for some way to display 3D data and 
allow user
interaction ( rotate for example). Sure, it would be nice if certain 
artistic devices
similar to the stuff in Cn3D were available, but mostly I was looking for 
ways to
prototype analysis ideas ( imagine you are sitting on the interesting atom 
of
a complicated enzyme and want to "visually" verify some calculation you 
made?
How much room is there really at an active site? And do my metrics
for fitting a sqaure peg in a round hole really capture the situation?  ).

I guess what I may be  trying to determine are things like the following:
1) Are there any "holes" big enough for solvent or reactants to find me at 
oxidized
sulfur of my prior example?
2) If I used the coordinates of a pdb file as starting point, and made up 
some simple potentials,
could I write a perl script ( probably with some complied code :) ) to watch 
the molecular
dynamics in response to various things?

I don't have any immediate objectives I've set on- lots of ideas- but I 
would like to see
how easy it is to do the visualization part. If it is easy, perhaps I could 
do some
"screening" with scripts.


Thanks!



( note new address as of 10-06)
Mike Marchywka
586 Saint James Walk
Marietta GA 30067-7165r
( NOTE MORE NEWER  NUMBER )
404-788-1216 (C)<- leave message
989-348-4796 (P)<- emergency only





>From: Deepan <codeshepherd at gmail.com>
>Reply-To: codeshepherd at gmail.com
>To: Mike Marchywka <marchywka at hotmail.com>, viswanathanc at gmail.com
>CC: bio_bulletin_board at bioinformatics.org
>Subject: Re: [BiO BB] bio game / bioinformatics game /fun
>Date: Tue, 26 Dec 2006 11:19:10 +0800
>
>Hi Mike,
>  you may want to work with Vishwanath, He has wrote molecule viewers
>like Rasmol, in C using OpenGL, He calls it as Vismol.
>
>
>
>On Fri, 2006-12-22 at 10:56 -0500, Mike Marchywka wrote:
> > Actually, does someone know of an opensource or free graphics rendering
> > program
> > that can be used with scripts for prototyping these kinds of ideas?
> >
> > I downloaded this thing:
> > http://www.csim.com/models/vpt/viewer/format2.html
> > and wrote some perl to take the pdb file for a
> >
> > COMPND    Ptp1b With The Catalytic Cysteine Oxidized To A
> > COMPND   2 Sulfenyl-Amide Bond
> >
> > and display selected atoms using the above viewer. It worked ok- I could
> > put the viewpoint at the oxidized cysteine and see what other things
> > could still get to the residue. However, before investing a lot of time
> > in scripts to support this viewer, I thought someone here may have
> > some better suggestions. It doesn't have to be fancy but transparency 
>and
> > shadows would be nice ( being able to move lightsources and view point
> > interactively with tolerable CPU usage a big plus ).
> >
> >
> > Thanks.
> >
> >
> >
> >
> > ( note new address as of 10-06)
> > Mike Marchywka
> > 586 Saint James Walk
> > Marietta GA 30067-7165r
> > ( NOTE MORE NEWER  NUMBER )
> > 404-788-1216 (C)<- leave message
> > 989-348-4796 (P)<- emergency only
> >
> >
> >
>
> > >Deepan wrote:
> > >>Does anyone have any interesting ideas about games wrt to
> > >>biology/bioinformatics ? If you have any good ideas, or pointers I 
>would
> > >>like to create a web
> > >>game just for fun. I was thinking about some kind of game to program a
> > >>vector and infect a culture or designing of vectors or bacterial 
>genome
> > >>blah blah blah..
> > >>
> > >>
> > >
> > >Sim 'virus' or Sim 'bug' - that would be really great!
> > >
> > >How about a 'first person perspective' view of protein structure? Take 
>Doom
> > >/ Quake and map the floor of the game onto the surface of your favorite
> > >structure. Then you could explore the active site 'on foot' and carry a
> > >ligand into the receptor to get to level 2. (Watch out for the slippery
> > >hydrophobic cluster!)
> > >
> > >
> > >
>
> >
> > -----------------------------------------------
> > Regards
> > Deepan Chakravarthy N
> > http://www.codeshepherd.com/
> > http://sudoku-solver.net/
>

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