Re: [PyMOL] loading a cube file from the API
Hi Thomas, I am using the build that comes with Fedora. One could think they skipped the plugin when compiled, as the error I get is: load something.cube ObjectMolecule: plugin 'cube' cannot open 'kim-dense.cube'. Nevertheless, it does load it correctly when I use Open from the gui. Thanks! Raul On Mon, Feb 17, 2014 at 11:41 PM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Raul, there should be no difference between loading from the GUI or using the load (not Load) command. The cube file needs to have a .cube extension. Cheers, Thomas On 16 Feb 2014, at 19:45, Raúl Mera Adasme rme...@gmail.com wrote: Hi all, I am trying to code a little script that needs to load Guassian cube files (to later create some isusurfaces). The cube format is supported, and one can easily use the TK interface (file-open) to load the file into PyMOL. I have been looking for the command to do it automatically in a script, but have not found it. Load is unable to open the files. Any ideas? Cheers, Raul -- Thomas Holder PyMOL Developer Schrödinger, Inc. -- Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121054471iu=/4140/ostg.clktrk ___ 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] loading a cube file from the API
Hi all, I am trying to code a little script that needs to load Guassian cube files (to later create some isusurfaces). The cube format is supported, and one can easily use the TK interface (file-open) to load the file into PyMOL. I have been looking for the command to do it automatically in a script, but have not found it. Load is unable to open the files. Any ideas? Cheers, Raul -- Android apps run on BlackBerry 10 Introducing the new BlackBerry 10.2.1 Runtime for Android apps. Now with support for Jelly Bean, Bluetooth, Mapview and more. Get your Android app in front of a whole new audience. Start now. http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk ___ 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] 2 new plugins, and a bit more :-)
Dear all, I develop goChem, an open source library for computational chemistry written in the Go language. I have incorporated a couple of Python functions that allow easily writing PyMOL plugins with goChem, using JSON and pipes for data transfer. As a proof of concept, I wrote two (also open source) plugins that I hope are useful. Both deal with proteins: 1) goQM: You pass it one or more selections, it will cut only the side chain, or the backbone depending on your choice (you can have only the sidechain for one selection and include the backbone for another). It will saturate the cut bonds in a sensible way, run a QM calculation of your choice and display the optimized structure back in PyMOL, and/or print the energy. (Requires MOPAC2012, ORCA 3.0 and/or TURBOMOLE. The first 2 are free for academic use). 2) goRama: Given one or more selections, it will generate a Ramachandran plot for it/them. If one selection is chosen, the color of each point in the graphic will change from red to violet with the number of the residue in the sequence. If several selections are chosen, each will be assigned a color. Links: The goChem library, the sources and binaries for the plugins for some architectures (Linux 32, Linux 64 and MacOS 64) can be found at gochem.org Just write me to de...@gochem.org, for instance, if you have suggestions for future plugins. Cheers! Raul -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ 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] Guessing bonds for a chempy model.
Hi all, I want to load a chempy model into PyMOL. Unfortunately, the model has all the coordinate information, but not bonds defined. I know PyMOL can guess the bonds from the distances, but it does not do it if I just use cmd.load_model, and I could not find a way of doing it. Does anyone know how can I achieve this? Thanks! Raul -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ 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
