Re: [PyMOL] Molecule galleries
Michael There are also some problems with the 2D files you supply. The SDF files have an extra line at the top that is not in the format specs. This causes problems with most pieces of software. The PDB are also a not correct. The atom names are simply the element name which can cause problems. Apart from the format errors, the bond lengths in the files are so far from ideal that determining the correct bond orders without hydrogens is impossible. As an example, benzene and cyclo-hexane are the same in 2D formats without hydrogens. Nigel --- bNigel W. Moriarty/b - Original Message From: X-raylab info x-raylab-i...@jhmi.edu To: x-ray...@spider.med.jhmi.edu Cc: Tsjerk Wassenaar tsje...@gmail.com; pymol-users@lists.sourceforge.net Sent: Thursday, September 4, 2008 6:41:14 AM Subject: Re: [PyMOL] Molecule galleries On 4 Sep, Tsjerk Wassenaar wrote: 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 ;) We have received many suggestions about how to get to improved structure pdb files sooner. Thank you for your kind suggestion. As a sidenote, it will also be more useful to have a 3D rotatable/scalable molecule (JMol) than a fancy rendered one. While this may seem obvious in practical terms, it is more efficient to attract users to the site with nice graphics, and they can optimize their own structures until the time that we are able to provide improved ones. As it has been pointed out on the main page, and in several fora, providing regularized or minimized structures is truly an obvious next step and definitely in the works. Also think big, as it is just the beginning. Meanwhile, PyMol happens to be an excellent piece of software for regularizing these structures by hand, so that they really are useful now. I am told that OpenBabel will do automatically this too. I had thought to try minimization with NAMD, and in fact there are many possible options. Regards, Michael L. Love 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
Re: [PyMOL] Molecule galleries
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
Re: [PyMOL] Molecule galleries
On 4 Sep, Tsjerk Wassenaar wrote: 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 ;) We have received many suggestions about how to get to improved structure pdb files sooner. Thank you for your kind suggestion. As a sidenote, it will also be more useful to have a 3D rotatable/scalable molecule (JMol) than a fancy rendered one. While this may seem obvious in practical terms, it is more efficient to attract users to the site with nice graphics, and they can optimize their own structures until the time that we are able to provide improved ones. As it has been pointed out on the main page, and in several fora, providing regularized or minimized structures is truly an obvious next step and definitely in the works. Also think big, as it is just the beginning. Meanwhile, PyMol happens to be an excellent piece of software for regularizing these structures by hand, so that they really are useful now. I am told that OpenBabel will do automatically this too. I had thought to try minimization with NAMD, and in fact there are many possible options. Regards, Michael L. Love 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
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
Re: [PyMOL] Molecule galleries
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=100url=/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
