VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun May 16 2004 - 20:25:59 CDT

Hi Axel,
  I don't have a quick answer for 1) yet, but 2) is actually
an easy one, there's an example script that does almost precisely what
you have in mind, though one would need to write the appropriate code to
feed it with the ramachandran histogram data you have in mind:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/3Dgraph/
If you can generate your histogram quickly enough in a script, then all of
this can be done without the need for external binaries.

Let me think about what to do for 1) a bit more and I'll get back to you
on that one.

  John

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

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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