Subject: Re: CCL:viewing SDfiles

From: Achim Herwig <[email-masked]>
Date: Thu, 11 Jan 2001 10:47:05 +0100

Hi,

a possibility (though I'm not sure about cheap for commercial applications) 
is the CACTVS system which covers all three of your problems and is even 
developed on a SGI (runs on other OSes, too):

http://www2.ccc.uni-erlangen.de/software/cactvs/index.html

HTH,
Achim Herwig.

Am Mittwoch, 10. Januar 2001 11:09 schrieben Sie:
> does anyone know of a free/cheap tool for looking at MDL SDfiles ?  It
> would be good to be able to be able to rapidly examine the structures.
> A web-based system would be ideal.
> Alternatively, are there tools for turning a structure into a gif format ?
> (It would bve good if it would run on an SGI machine.)

--
  Achim Herwig   | [email-masked], [email-masked]
+49 9131 8526574 | http://www2.ccc.uni-erlangen.de/people/Achim_Herwig/
PGP-Fingerprint16 = 17 9A 42 C5 E8 72 A8 3F  96 27 7B A0 48 0B 88 F3

---

From: John Wintersteen <[email-masked]>
Date: Thu, 11 Jan 2001 08:06:11 -0800

In reading Michael Charlton's message I thought it might be helpful to 
point out that in MSI's WebLab Viewers, there are is an alternate view, 
called the Hierarchy Window that provides a tool for viewing molecules one 
at a time in a multiple molecule file.

The Hierarchy window will present a list of the molecules in the file. The 
Hierarchy Window and the 3D Window are presented side-by-side. While in the 
Hierarchy Window, using the Display Tool, you can show/hide molecules 
individually or in groups. Once the Display Tool has been engaged, you can 
also use the up and down arrows keys to scroll through the list of 
molecules. For files containing only a few molecules, the Tile Molecules in 
Window Command can be used to automatically space out the molecules in the 
3D Window.

The WebLab Viewer also has exporters for writing out image files in several 
file formats including gif, jpeg, and bmp.

Regards,

John Wintersteen
Product Manager, Experimental Chemistry
Molecular Simulations Inc.

>From:	"Charlton, Michael" <[email-masked]>
>To:	"[email-masked]'" <[email-masked]>
>Subject:	CCL:viewing SDfiles
>Date:	Wed, 10 Jan 2001 15:31:59 -0000
>X-Mailer:	Internet Mail Service (5.5.2650.21)
>Sender:	"Computational Chemistry List" <[email-masked]>
>
>Many thanks for all the replies (below) I received.
>I feel I ought to clarify what I want here.
>I can view structures in SDfiles already, using typical modelling packages
>(MOE, Cerius etc.), but I am after a program that will allow lots of
>chemists to browse them (hence the requirement for cheapness).  The idea 
is
>to be able to flick up and down, one at a time, or perhaps several
>structures tiled on a page at a time.  The pssmiles utility that comes 
with
>with ClogP does this kind of thing, except postscript output is not very
>convenient.
>A common proposed solution is MSI's weblab viewer.  However, whenever I 
open
>an SDfile, I get all the structures overlaid on one another - 3000
>structures looks like a pile of spaghetti!!  I have yet to find a use for
>this - has anyone else ? ;-)
>The program I dream of could be stand-alone (for distribution around 
company
>PCs) or web-based (my intranet pages are on an SGI, so the clever bits 
would
>need to be on that).  My preference would be for 2D Isis Draw/ ChemDraw
>style output rather than 3D, since most of the structures are only 2D.
>My (sadly lacking) web skills could probably patch in a "smiles-to-gif"
>utility to do what I want, if such a thing existed.  Whilst I have been
>composing this, a message from Marc Nicklaus just came in, and this could 
be
>what I am after for the gif generation.
>
>Thanks again,
>
>Michael Charlton.
>Replies :
>Michael,
>