Subject: Summary: two visualisation questions

From: "Jeremy R. Greenwood" <[email-masked]>
Date: Thu, 12 Dec 2002 16:54:54 +0100

Hi CCList,

Summary of responses to 
Subject: CCL:Two visualisation questions
Date: Fri, 6 Dec 2002 17:49:15 +0100

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My first question concerned software for visualising molecular
data P(X,Y,Z) calculated at a set of abitrary (non-grid) points.

Thanks to Jim Kress who listed:
gOpenMol (http://www.csc.fi/gopenmol/), 
Molden (http://www.caos.kun.nl/~schaft/molden/molden.html), 
GaussView (www.gaussian.com), 
Molekel (http://www.cscs.ch/molekel/)

Of these, gOpenMol seems to be the most flexible/powerful, but it seems 
it would still require me to order and interpolate my data onto a cubical
grid in .plt format.

Thanks to Carsten Menke at Accelrys, who pointed out that Materials Studio
can visualise the .grd format, which though still a grid, need not be 
cubic: Accelrys software can also handle arbitrary rhombic grids 
(e.g. from solid phase unit cell).

Many thanks to Aldo Jongejan who put me onto Dino:
http://cobra.mih.unibas.ch/dino  
-- this nifty program is still intended for chemists (emphasis on
large molecules) yet it can handle a very wide variety of data 
and rendering. The install was also trivial, and the hardware stereo 
works straight out. I'll be using it first.

Thanks to Fred P. Arnold and Malcolm Gillies who recommended OpenDX.
http://www.opendx.org
-- this is an advanced, general visualisation suite, and is no doubt
the most powerful suggestion, offering spectacular rendering of 
multidimensional data sets. It's not specifically for chemists though, 
and may have a steeper learning curve than the above. I also 
found that it is not trivial at present to get it working under IRIX; 
there are compiler, library, and supporting software version issues.
Other platforms are probably better supported though, and it seems 
to be under quite rapid development.

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My second request was for a handy tool for processing QM spectral
predictions into convincing curves to show to spectroscopists.

Thanks to E. Lewars who gave me references to the use of both Gaussian
and Lorentzian functions in IR:
H. Lampert et. al., J. Phys. Chem. A, 1997, 101, 2254-2263. (Gaussians)
M. D. Haus, H. B. Schlegel, J. Chem. Phys, 1998, 109, 10587-10593. (Lorentzians)
Lorentzians are also used in VCD:
F.J. Devlin et al., J. Phys. Chem. A., 1997, 101, 6322-6333

Thanks again to Aldo Jongejan who pointed out Paul D. Soper's
spectrum.c in the CCL archives:
http://server.ccl.net/cca/software/SOURCES/C/IR-spectrum/README.shtml
-- in conjunction with a little scripting and some plotting software,
this little program does the job, not only for IR, but pretty
much any spectroscopic data from QM, including signed spectra
such as ECD and VCD. 

E. Lewars requests (and so do I) feedback on which curve shape
(Gaussian or Lorentzian) better reproduces experimental spectra
for various kinds of spectroscopy (e.g. IR, NMR, UV/Vis, VCD, ECD).

--Jeremy
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Jeremy Greenwood                                  [email-masked]
Department of Medicinal Chemistry                      bh +45 35306117
Royal Danish School of Pharmacy                        fx +45 35306040
Universitetsparken 2, DK-2100 Copenhagen, Denmark      ah +45 32598030
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