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. Cheers, Warren -----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? J _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 913 Dunedin 9054 New Zealand Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of X-raylab info 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; gnu-darwin-po...@lists.sourceforge.net; blueobelisk-disc...@lists.sourceforge.net; ccp...@jiscmail.ac.uk; gnu-darwin-distribut...@lists.sourceforge.net; corecifc...@iucr.org; vm...@ks.uiuc.edu 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. http://molecules.gnu-darwin.org/mod/Bisphenol-more.html 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 welcome. Regards, -- 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 Interoffice Mail: 608B WBSB, SoM office: 410-614-2267 lab: 410-614-3179 fax: 410-502-6910 cell: 443-824-3451 http://www.gnu-darwin.org/ Visit proclus realm! http://proclus.tripod.com/ -----BEGIN GEEK CODE BLOCK----- Version: 3.1 GMU/S d+@ s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++ h--- r+++ y++++ ------END GEEK CODE BLOCK------ ==================================================================== Auto Generated Mail Footer If this email is requesting your password then it is a HOAX. DO NOT reply to the email. Validate this footer at the Otago University web site keyword search: information security phish ==================================================================== ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
