Re: [PyMOL] Showing electric field lines
Dear Michael, With help of Andreas I got apbs plugin 2 working on my pymol and I must say that's beautiful and I believe it's a 'must have' functionality to add to your plugin, the ability to show field lines easily. Another suggestion I have is considering the use of apbs with mpi. Putting simply, e.g., apbs-mpi-openmpi in pymol apbs plugin configuration will not take advantages, e.g., of a dual-core computer. 'pdime' need to be setup properly in pymol-generated.in (see http://www.poissonboltzmann.org/documentation/parallel-electrostatics-calculations-actin-dimer ) I wonder if there would be a clever way of setting 'pdime' according to the number of cpus available. For a dual-core, 'pdime 2 1 1' should work. Many thanks for your plugin. Alan On Mon, Feb 15, 2010 at 10:42, Alan alanwil...@gmail.com wrote: Dear Michael, I am using Pymol 1.2r3pre and APBS 1.2, all installed via FINK in my Mac (10.6.2). I start pymol, build a TRP, call apbs plugin, set grid, run apbs and I can see surface and all, but when trying your commands below, pymol-generated doesn't exist for me. Either I am doing something wrong or I don't have the right version of Pymol and/or Apbs. May you clarify me here? This addition to the plugin would be very welcome. Thanks in advance, Alan On Sat, Feb 13, 2010 at 04:55, pymol-users-requ...@lists.sourceforge.netwrote: Message: 3 Date: Wed, 10 Feb 2010 20:26:47 -0500 From: Michael Lerner mgler...@gmail.com Subject: [PyMOL] Showing electric field lines To: pymol mailinglist pymol-users@lists.sourceforge.net Message-ID: e4c539ed1002101726k30ae7cbcm2482f11fe09dc...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi all, Someone recently asked me if there was a way to display field lines with PyMOL or with an external plugin. Here's what I wrote: It turns out that PyMOL recently grew the ability to display field lines. After you've run APBS, you'll have a map object called pymol-generated. Try this series of commands from the PyMOL prompt: gradient my_grad, pymol-generated ramp_new my_grad_ramp, pymol-generated color my_grad_ramp, my_grad -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- Alan Wilter Sousa da Silva, D.Sc. PDBe group, PiMS project http://www.pims-lims.org/ EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK +44 (0)1223 492 583 (office) -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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] Use of PyMOL for inspection and saving of docking results from Autodock
I already have the new plugin, and unfortunately only the part to view poses and export the results works for me, but it has a great potential if the bugs are fixed so great work DanieI. I make something useful when i converted the poses.pdb to poses.mol2 so thank you. If i may ask you one more off topic question maybe directly on your mail concerning Autodock, about some false results (results which aren't like we expect them to be), if you have some spare time to answer that? Thank you for the answer! Mark 2010/2/15 Daniel Seeliger dsee...@gwdg.de Hi Msev, if you download the latest version you'll find what you're looking for. On the Score/Rank-page you can export docking scores and also docking poses in pdb format. If you save a list containing different ligands it might indeed look weired when you reload the file into pymol since pymol makes the bonds only based on the first model. But you can convert the poses.pdb to a mol2 file with babel and load that into pymol. That should look nice. Cheers, Daniel On Monday 15 February 2010 08:05:35 pm Marko S wrote: Hello, I'm quite a novice user of PyMOL but I am already impressed at the speed and beauty of the rendering. But I have some questions regarding it's use for viewing results of Autodock. So I normally proceed as follows, i open the PDB molecule say fetch BLABLA and i get the pdb file...Then i have two options, one is to simply open the .dlg file then i get only one ligand results which i scrool with the play button to see all the results, but there is also an option (i use the autodock plugin, and with that i get all of the results on the screen), but the problem is how to save everything together in one pdb. file. I tried with the write complex.pdb but it made a strange mess when i look with other pdb viewers such as Viewerlite. What can you suggest me to do? Thank you for the answers! Msev -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ 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] Autodock plugin
Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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] Autodock plugin
Hi Sing, take a look into ~/.ADplugin/pymol_autodock_plugin.conf and set the path to the autodocktools scripts correctly. Then the plugin should find them. Cheers, Daniel On Tuesday 16 February 2010 08:06:40 pm Kin Sing Stephen Lee wrote: Dear all, This is the first time for me to use the autodock plugin and I have some simple questions. I'm using Macbook Pro (OS X v 10.5 - leopard). Autodock and autodock tools run fine in the X11 terminal. In the autodock plugin, I need to put in the autodock tool program path,so I put in the path where I installed the autodock tool (under applications folder). When I tried to prepare my receptor and ligand file, the plugin cannot find the autodock tools (prepare_receptor4.py as well as prepare_ligand4.py) so I am wondering where I can find the autodock tools program path or is it possible to use the plugin in mac? Thank you very much Sing --- --- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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 -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev ___ 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
