Subject: Re: CCL:ToPMod: have questions and need a little help!

From: "Pablo Vitoria" <[email-masked]>
Date: Tue, 23 Apr 2002 10:07:18 +0200

Hi Harald,

I started recently using TopMoD, and since I have been a user of Molekel for
a while now, I am using it to visualize the ELF basins.

First, I generate the compid_elf.sbf file with top_grid (using a coarse
grid, otherwise the final cube file may be quite large), and compid_ebas.sbf
with top_bas (compid=name of the compound). If simmetry is used in top_grid,
run top_sym on both compid_elf.sbf and compid_ebas.sbf. Then, run
bas_to_syn, which will generate compid_esyn.sbf.

To get the Gaussian cube files (to be used as input to Mlekel) of both
compid_elf.sbf and compid_esyn.sbf, run sbf_to_cube with them as input
files, to generate compid_elf.cube and compid_esyn.cube.

In Molekel, load (as Gaussian cube) compid_elf.cube. This will only get the
coordinates of your molecule, that will be visible now in the window. From
the Surface menu, Load (Gaussian cube) compid_elf.cube, and Create Surface
choosing an appropriate cutoff (usually between 0.7 and 0.8). You will see
now all the basins with the same color. Load (Gaussian cube)
compid_esyn.cube. Choose Grid Value button (to map the syn cube on the elf
cube), and on the window that shows up, choose 1.0 as Vmax and 5.0 as Vmin
(they seem to be reversed, at least in my version of Molekel). And you
should see now the basins colored according to their type (core,
monosynaptic, disynaptic,...). If you donŽt like the default colors, you can
change them in the Texture menu.

I hope this helps you.
Best regards

Pablo

--------------------------------------------------------
Pablo Vitoria Garcia
Dpto. Química Inorgánica, Facultad de Ciencias
Universidad del País Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)

Tfno. 94 6012579
Fax. 94 4648500
----- Original Message -----
From: "Harald Bock" <[email-masked]>
To: <[email-masked]>
Sent: Monday, April 15, 2002 2:02 AM
Subject: CCL:ToPMod: have questions and need a little help!

| Ladies and Gentlemen,
| has anyone experience with the program-package ToPMod of Silvi et al. for
| calculating ELF?
| I've got everything set up and running, but I'm in need of some help with
| visualisation of the output.
| I would like to use Molekel but didn't succeed in assigning different
colors
| to the different basins types by using bat_to_syn due to a lack of
| documentation (if it is possible at all).
|
| If there is anyone out there, able and willing to help me, I would be very
| thankfull.
| Harald Bock
| University of Cologne
|
|
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