I'll second that.  

While applying PyMOL to generate millions of molecular renderings in an
automated fashion may be a cool demonstration of open-source databases &
technology, using 2D molecules as inputs kind of misses the point:  

PyMOL is a 3D viewer, optimized for depicting 3D representations of small
and large molecules.  Thus I would strongly recommending passaging those
structures through one of the open-source 2D to 3D converters before sending
them to PyMOL for rendering.


-----Original Message-----
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Joel Tyndall
Sent: Wednesday, September 03, 2008 6:49 PM
To: X-raylab info
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Molecule galleries

Hi there,

The gallery is currently in 2D format. Any plans to generate 3D galleries?



Joel Tyndall, PhD

Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 913 Dunedin 9054
New Zealand

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-----Original Message-----
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of X-raylab
Sent: Thursday, 4 September 2008 3:54 a.m.
To: x-ray...@spider.med.jhmi.edu
Cc: scit...@lists.apple.com; x-ray...@spider.med.jhmi.edu;
o-i...@origo.imsb.au.dk; objcryst-de...@lists.sourceforge.net;
comc...@iucr.org; pymol-users@lists.sourceforge.net; cn...@yahoogroups.com;
blueobelisk-disc...@lists.sourceforge.net; ccp...@jiscmail.ac.uk;
gnu-darwin-distribut...@lists.sourceforge.net; corecifc...@iucr.org;
Subject: [PyMOL] Molecule galleries

I have automated the process to make molecule galleries, which I am finding
very useful to my research, so I thought that I would share the opportunity
and take requests.  It is quick and easy.  I did a bisphenol search today,
and as I expected, the search turned up a few stilbenes, which is the same
molecular family as resveratrol.  Strikingly, Bisphenol A is a noted
teratogen, which shows that care must be taken when using such molecules
during development.  Here is a link to the bisphenol gallery.


If you would find it useful, I am definitely interested in taking
requests for molecule galleries.   Just send me the name of your
favorite molecule.  As you may be able to tell, we have access for galleries
to about 1% or 0.5 million structures, in the total archive thus far, but it
is already quite useful. The automated jobs are underway to fill in the
rest.  The next milestone is the capability to index and make galleries for
the remaining millions of molecules for which we have pdb files already,
which would be 5-10% complete.  Any comments or suggestions are also


Michael L. Love Ph.D
Department of Biophysics and Biophysical Chemistry School of Medicine Johns
Hopkins University
725 N. Wolfe Street
Room 608B WBSB
Baltimore MD 21205-2185

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