Subject: Re: CCL:Open Visualization Data Explorer

From: Richard Gillilan <[email-masked]>
Date: Mon, 22 Nov 1999 09:15:36 -0500

Deepak Singh wrote:
> 
> Hi,
> 
> I have been looking into software (for IRIX) that will allow me to
> visualize MO's, charge densities etc.  I heard a lot about AVS but that
> seems to have disappeared.  I ran into IBM's 'Open Visualization Data
> Explorer' today and it seems to be similar to AVS.  I would like to know
> if people have used this a lot with G98/94, GAMESS and MOPAC?  Is the
> performance similar to AVS?

I have used DX and OpenDX to visualize both output of MOPAC
and experimental density files (XPLOR format) from time-resolved
xtallography. You'll probably want the m2dx filter written
by Tom Jackman (IBM). The current IRIX 6.5 executable for OpenDX
that can be downloaded from www.OpenDX.org seems to be stable
enough for most routine use, although there has been a lot
of activity among developers trying to track down some
aparent memory access violation problems. My chemistry
module suite gives DX the ability to combine conventional
ball-and-stick, ribbon, solvent surface, etc. with density
files sliced and diced in creative ways if you are willing to work at it.
When in graphics hardware mode, it takes advantage
of SGI graphics engines and can even do hardware (Crystal-Eyes) stereo now.

 Richard
 Cornell Theory Center

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From: Christian Pilger <[email-masked]>
Date: Mon, 22 Nov 1999 19:13:19 +0100

Dear CCLers,

	we plan to perform a Comparative Molecular Field Analysis (CoMFA)
on a dataset of compounds with known activities. As the X-ray structure 
of the receptor is known, we used an automated docking procedure to 
generate a reasonable alignment.

I have the following questions:

- Field geometry: does anyone have experience with different field 
  geometries, i.e. cubic arrangement of interaction points vs. spherical
  arrangement ?

- Would it be better to use an energetic cutoff value for the interaction
  energies (as in SYBYL) or should those grid points, that are located
  within the common volume of the aligned structures be omitted at all ? I
  can imagine a program that compares the distance of each grid point to
  each atom of the aligned structures. If this distance is smaller than
  the van-der-Waals radius of one of the considered atoms, the specified
  grid point is excluded. Would such an approach be resonable ?

- Which type of probes should be used/avoided ? I want to employ the
  program GRID by Peter Goodford.

I appreciate any comments. Furthermoe I'm interested in different
3D-methods, which might be suitable for my problem.

Regards,

Christan

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 Dipl.-Chem. Christian Pilger          Uni-GH Paderborn
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