Re: [PyMOL] Is there or should there be a pymol annotation server?
indeed, the SITE records could easily be parsed and made available as named selections. Similar: http://pymolwiki.org/index.php/Uniprot_features - makes named selections from uniprot annotations Cheers, Thomas Nat Echols wrote, On 07/13/12 23:24: On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: It would be nice if publishers required a common CSV format for specifying contacts and annotations. Then we could easily pull the data from reliable resources. But, alas, this doesn't exist. One possible (albeit incomplete) way to do this is with the SITE records in PDB files: http://www.wwpdb.org/procedure.html#toc_10 For instance, trypsin (http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES): SITE 1 CAT 3 HIS A 57 ASP A 102 SER A 195 SITE 1 AC1 6 ASP A 165 ALA A 177A GLU A 180 GLU A 230 SITE 2 AC1 6 HOH A 259 HOH A 261 Obviously this still requires that the authors actually perform the annotation. It's a poor substitute for having (for instance) entire PyMOL sessions accompanying a PDB deposition, but I've learned to keep my expectations low. -Nat -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there or should there be a pymol annotation server?
Dear Pymolers. Thanks for all the suggestions. :-) I definitely think that http://jolecule.appspot.com can become handy for a teaching situation or sending a colleague a question to a protein. Thanks! And I am all in for interactive publications, which I hope could use one day. The Uniprot_features http://pymolwiki.org/index.php/Uniprot_features is probably what I am looking for. So I will try that out. Best Troels Emtekær Linnet 2012/7/14 Thomas Holder spel...@users.sourceforge.net indeed, the SITE records could easily be parsed and made available as named selections. Similar: http://pymolwiki.org/index.php/Uniprot_features - makes named selections from uniprot annotations Cheers, Thomas Nat Echols wrote, On 07/13/12 23:24: On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: It would be nice if publishers required a common CSV format for specifying contacts and annotations. Then we could easily pull the data from reliable resources. But, alas, this doesn't exist. One possible (albeit incomplete) way to do this is with the SITE records in PDB files: http://www.wwpdb.org/procedure.html#toc_10 For instance, trypsin ( http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES): SITE 1 CAT 3 HIS A 57 ASP A 102 SER A 195 SITE 1 AC1 6 ASP A 165 ALA A 177A GLU A 180 GLU A 230 SITE 2 AC1 6 HOH A 259 HOH A 261 Obviously this still requires that the authors actually perform the annotation. It's a poor substitute for having (for instance) entire PyMOL sessions accompanying a PDB deposition, but I've learned to keep my expectations low. -Nat -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there or should there be a pymol annotation server?
Once again Thomas Holder have done a very nice work, and made a solution. Check it out here: http://www.pymolwiki.org/index.php/Select_sites fetch 1sgt, async=0import select_sites select_sites It works really brilliant. Best Troels Emtekær Linnet 2012/7/14 Troels Emtekær Linnet tlin...@gmail.com Dear Pymolers. Thanks for all the suggestions. :-) I definitely think that http://jolecule.appspot.com can become handy for a teaching situation or sending a colleague a question to a protein. Thanks! And I am all in for interactive publications, which I hope could use one day. The Uniprot_features http://pymolwiki.org/index.php/Uniprot_features is probably what I am looking for. So I will try that out. Best Troels Emtekær Linnet 2012/7/14 Thomas Holder spel...@users.sourceforge.net indeed, the SITE records could easily be parsed and made available as named selections. Similar: http://pymolwiki.org/index.php/Uniprot_features - makes named selections from uniprot annotations Cheers, Thomas Nat Echols wrote, On 07/13/12 23:24: On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: It would be nice if publishers required a common CSV format for specifying contacts and annotations. Then we could easily pull the data from reliable resources. But, alas, this doesn't exist. One possible (albeit incomplete) way to do this is with the SITE records in PDB files: http://www.wwpdb.org/procedure.html#toc_10 For instance, trypsin ( http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES): SITE 1 CAT 3 HIS A 57 ASP A 102 SER A 195 SITE 1 AC1 6 ASP A 165 ALA A 177A GLU A 180 GLU A 230 SITE 2 AC1 6 HOH A 259 HOH A 261 Obviously this still requires that the authors actually perform the annotation. It's a poor substitute for having (for instance) entire PyMOL sessions accompanying a PDB deposition, but I've learned to keep my expectations low. -Nat -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Is there or should there be a pymol annotation server?
Dear PyMolers. Reading crystallographic papers, and feeling the need for seing a papers annotation and explanation of important residues, I often have pymol at my hand. fetching the protein, and typing in commands to see the mentioned residues. That is time-consuming, but okay. Inspired by John Amraph's need for a preset.ligand_cartoon, when loadning a paper, I would wish there were a: preset.as_article or a fetch 1SVN, as_article. Simply a pymol script file that fetch the protein, shows it as cartoon, and selecting/labelling/showing the mentioned important residues in the article. Or the catalytic triad, the substrate channels... etc. You get the point. :-) So, does anyone know there already exist such a databank/annotation server? If it exist, could one make a script that can fetch and convert these annotations to a pymol script? Or if doesnt exist, would it be a interesting project to pursue? Best Troels Emtekær Linnet PhD student SBiNLab, Copenhagen University -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there or should there be a pymol annotation server?
Hi. Not too long ago, Bosco Ho put together something like that in HTML5 http://jolecule.appspot.com/ cheers, wlad On Jul 13, 2012, at 6:41 AM, Troels Emtekær Linnet wrote: Dear PyMolers. Reading crystallographic papers, and feeling the need for seing a papers annotation and explanation of important residues, I often have pymol at my hand. fetching the protein, and typing in commands to see the mentioned residues. That is time-consuming, but okay. Inspired by John Amraph's need for a preset.ligand_cartoon, when loadning a paper, I would wish there were a: preset.as_article or a fetch 1SVN, as_article. Simply a pymol script file that fetch the protein, shows it as cartoon, and selecting/labelling/showing the mentioned important residues in the article. Or the catalytic triad, the substrate channels... etc. You get the point. :-) So, does anyone know there already exist such a databank/annotation server? If it exist, could one make a script that can fetch and convert these annotations to a pymol script? Or if doesnt exist, would it be a interesting project to pursue? Best Troels Emtekær Linnet PhD student SBiNLab, Copenhagen University -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there or should there be a pymol annotation server?
Troels, It would be nice if publishers required a common CSV format for specifying contacts and annotations. Then we could easily pull the data from reliable resources. But, alas, this doesn't exist. Cheers, -- Jason On Fri, Jul 13, 2012 at 5:41 AM, Troels Emtekær Linnet tlin...@gmail.com wrote: Dear PyMolers. Reading crystallographic papers, and feeling the need for seing a papers annotation and explanation of important residues, I often have pymol at my hand. fetching the protein, and typing in commands to see the mentioned residues. That is time-consuming, but okay. Inspired by John Amraph's need for a preset.ligand_cartoon, when loadning a paper, I would wish there were a: preset.as_article or a fetch 1SVN, as_article. Simply a pymol script file that fetch the protein, shows it as cartoon, and selecting/labelling/showing the mentioned important residues in the article. Or the catalytic triad, the substrate channels... etc. You get the point. :-) So, does anyone know there already exist such a databank/annotation server? If it exist, could one make a script that can fetch and convert these annotations to a pymol script? Or if doesnt exist, would it be a interesting project to pursue? Best Troels Emtekær Linnet PhD student SBiNLab, Copenhagen University -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there or should there be a pymol annotation server?
On Fri, Jul 13, 2012 at 2:12 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: It would be nice if publishers required a common CSV format for specifying contacts and annotations. Then we could easily pull the data from reliable resources. But, alas, this doesn't exist. One possible (albeit incomplete) way to do this is with the SITE records in PDB files: http://www.wwpdb.org/procedure.html#toc_10 For instance, trypsin (http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES): SITE 1 CAT 3 HIS A 57 ASP A 102 SER A 195 SITE 1 AC1 6 ASP A 165 ALA A 177A GLU A 180 GLU A 230 SITE 2 AC1 6 HOH A 259 HOH A 261 Obviously this still requires that the authors actually perform the annotation. It's a poor substitute for having (for instance) entire PyMOL sessions accompanying a PDB deposition, but I've learned to keep my expectations low. -Nat -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Is there or should there be a pymol annotation server?
The main technology I've seen used for interactive publications is ActiveICM (see http://www.molsoft.com/activeicm.html#aipub ). In my lab, we regularly include pymol sessions as supplementary material to help people understand our results. -David On Friday, July 13, 2012 at 6:41 AM, Troels Emtekær Linnet wrote: Dear PyMolers. Reading crystallographic papers, and feeling the need for seing a papers annotation and explanation of important residues, I often have pymol at my hand. fetching the protein, and typing in commands to see the mentioned residues. That is time-consuming, but okay. Inspired by John Amraph's need for a preset.ligand_cartoon, when loadning a paper, I would wish there were a: preset.as_article or a fetch 1SVN, as_article. Simply a pymol script file that fetch the protein, shows it as cartoon, and selecting/labelling/showing the mentioned important residues in the article. Or the catalytic triad, the substrate channels... etc. You get the point. :-) So, does anyone know there already exist such a databank/annotation server? If it exist, could one make a script that can fetch and convert these annotations to a pymol script? Or if doesnt exist, would it be a interesting project to pursue? Best Troels Emtekær Linnet PhD student SBiNLab, Copenhagen University -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net (mailto:PyMOL-users@lists.sourceforge.net)) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
