Hi, Hear, hear! :) A suggestion might be to pass them through the PRODRG server (http://davapc1.bioch.dundee.ac.uk/prodrg/) which can be automated and is capable of providing an energy minimized structure (do mind the hydrogens/charges/valencies). It would also give you the opportunity to provide the public with a library including topological descriptions (in various formats) to be used for modeling. Although, truth be told, I commonly advice against blindly using the results from that server for modeling studies ;)
As a sidenote, it will also be more useful to have a 3D rotatable/scalable molecule (JMol) than a fancy rendered one. Cheers, Tsjerk On Thu, Sep 4, 2008 at 5:43 AM, DeLano Scientific <del...@delsci.info> wrote: > > 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 > > > ------------------------------------------------------------------------- > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
