[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
[PyMOL] Dynamic Bonds based on connection table ?
Dear PyMOL users, I´m looking for an option to generate animations with changing bonds. So far: cmd.load(testm.pqr) cmd.load(testm1.pqr) = 2 objects with correct bonding from conect entries load testm.pqr, mov load testm1.pqr, mov = trajectory, but only connection table from 1st frame seems to be used small test structures (only 1 bond removed) are attached, overall simulations consists of larger structures with substitution reactions and a large number of time steps - therefore a loop for loading the files should be possible. The conect entries per time frame are calculated in the simulation, the pqr files are generated using this information, either as single file/time step or as one file holding all time steps. Connection table reads are not necessary every single time step, but would be nice every n iterations based on typical structures changes in the simulations. I'm rather new to PyMOL, so hopefully you can guide me to a solution. Kind regards, Thomas testm.pqr Description: Binary data testm1.pqr Description: Binary data -- 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] movie in pymol
Dear users, I would like to create a movie using Pymol between two different conformations (structures) of a protein 1NL3_coli and 1MN6coli. I read this can be done with rigimol. I am giving the following commands and getting an error when giving the following command rigimol.morph ( m_in, m_out, refinement=5, async=1) What do I have to do for this? I am pasting the sequence of all the commands P.S. I also aligned the two structures. Thank you in advance very much Georgios Gkouridis Post-doc RUG/Single molecule microscopy The Netherlands PyMOLcreate m_in, 1NL3_coli, 1, 1 Selector: found 13230 atoms. Executive: object m_in created. PyMOLcreate m_in, 1MN6coli, 1, 2 Selector: found 13296 atoms. PyMOLrigimol.morph ( m_in, m_out, refinement=5, async=1) Traceback (most recent call last): File C:\Program Files\PyMOL\PyMOL/modules\pymol\parser.py, line 464, in parse exec(layer.com2+\n,self.pymol_names,self.pymol_names) File string, line 1, in module NameError: name 'rigimol' is not defined This message was sent using IMBB - WebMail. -- 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
