VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon May 17 2004 - 15:07:43 CDT

On Sun, 16 May 2004, John Stone wrote:

hi john,

thanks a lot for the tip. it is really embarrassing, as
i _have_ scanned the vmd script library some time ago for
inspiration. oh well.

JS>
JS> Hi Axel,
JS> I don't have a quick answer for 1) yet, but 2) is actually
JS> an easy one, there's an example script that does almost precisely what
JS> you have in mind, though one would need to write the appropriate code to
JS> feed it with the ramachandran histogram data you have in mind:

that code already existed <g>, i simply gave up on creating a
'properly formatted' cube file from within VMD (not much gain
over the (ugly) c++ code i already had).

anyway, the updated version is already on the web. since the code
now is pretty generic, i can send it to you for inclusion into
the VMD script library, if you want to have it.

JS> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/3Dgraph/
JS> If you can generate your histogram quickly enough in a script, then all of
JS> this can be done without the need for external binaries.

the time determining step is the loop over the trajectory
(especially for complicated selections), so this is no problem.

thanks a lot,
        axel.

JS>
JS> Let me think about what to do for 1) a bit more and I'll get back to you
JS> on that one.
JS>
JS> John
JS>
JS> On Sun, May 16, 2004 at 09:03:11PM +0200, Axel Kohlmeyer wrote:
JS> > hello everybody on VMD-L,
JS> >
JS> > there are currently two visualization problems for which i'd
JS> > like to find a better/cleaner solution. after banging my head
JS> > against the wall for quite some time, i thought that perhaps
JS> > the 'brain-pool' on VMD-L can provide some helpful suggestions.
JS> >
JS> > problem 1:
JS> >
JS> > check out
JS> > <http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part5.html#chap7_sect6>
JS> >
JS> > while this already works very nicely for creating animations from a script,
JS> > with a reasonably fast and large machine you can even work interactively.
JS> > in that case it would be nice to find a way, that changes in the Isosurface
JS> > representation are not overwritten every time a new frame is shown. this
JS> > would speed up the tuning of the parameters immensely, especially when using
JS> > multiple isosurface representations and/or volumeslices.
JS> >
JS> >
JS> > problem 2:
JS> >
JS> > check out
JS> > <http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part6.html#chap8_sect3>
JS> >
JS> > the challenge is, that i want to create a 3d 'rubbersheet' from within
JS> > VMD without using an external program (which has to be re-compiled and
JS> > installed at the proper place for each platform). since this is used in
JS> > an introductory MD exercise package for undergraduate students, i would
JS> > like to reduce the external dependencies as far as possible. also, the
JS> > way the cubefile/isosurface is used to emulate the rubbersheet, is somewhat
JS> > inelegant (to say the least). perhaps someone has a few ideas on how
JS> > to create a smooth 'rubbersheet' with VMD graphics primitives directly
JS> > from the protein backbone angle data.
JS> >
JS> > ...and it would be über-super-prima-cool, if the height of the peaks
JS> > could be color coded, but that is not really required.
JS> >
JS> > with the best wishes for the new week,
JS> > axel kohlmeyer.
JS> >
JS> >
JS> > --
JS> > =======================================================================
JS> > Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
JS> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
JS> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
JS> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
JS> > =======================================================================
JS> > If you make something idiot-proof, the universe creates a better idiot.
JS>
JS> 

-- 
=======================================================================
Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================