Re: [PyMOL] Reset Default Carbon Color
Hi Wilson, interesting question and actually there is no command to control this. Howevery, it's possible, there is a setting which doesn't have a name. In the latest 1.6alpha, you can do: # reset color cycle cmd.set(239, 0) In older PyMOL versions, this should work: # reset color cycle _cmd.set(cmd._COb, 239, (2, (0,)), '', -1, 1, 0) Some related notes: - auto and current are color names which correspond to the cycle - You can also disable the color cycling: set auto_color, off Cheers, Thomas Wilson Omesiete wrote, On 04/10/13 09:03: I noticed that the default carbon color for loaded objects is set to cycle from green to pink and then repeat to differentiate models. I have a lot of models being loading and deleted within one session, and it would be very useful to be able to reset that cycle, So that the first model after a reset will have green carbons, the second will have cyan carbons, and so on. This way my coloring patterns would be consistent. The reset function does not affect the cba* cycle, and I know that I could manually call the cba* variants after every file is loaded to force this functionality, but I would rather avoid that if possible. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ 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] conect records?
Hi Boris, can you be more precise with your question? What file type did you load (pdb?), which connections (I assume you mean bonds) are wrong? Cheers, Thomas Boris Kheyfets wrote, On 04/09/13 19:30: Hello PyMOL users, I study system which has 160919 residues, and 217021 atoms (it is initially a gromacs' gro file). Is there a way I can display conections correctly in PyMOL? -- With great respect, Boris. -- Thomas Holder PyMOL Developer Schrödinger Contractor -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ 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] Reset Default Carbon Color
Thank you for your suggestion, Tsjerk Wassenaar, and thank you for your answer, Thomas Holder. Using _cmd.set(cmd._COb, 239, (2, (0,)), '', -1, 1, 0) ... Does exactly what I was looking for. On Thu, Apr 11, 2013 at 2:58 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Wilson, I don't know how to reset the color scheme, but maybe something along the following lines can help out: # set the colors (change to your liking): colors = (green,cyan,magenta,yellow) # create a color iterator: python def colit(): i = 0 while True: yield colors[i%len(colors)] i += 1 python end # initialize (or reset) colors c = colit() # load files and color them load file1.pdb cmd.color(c.next(), elem c) load file2.pdb cmd.color(c.next(), elem c) # ...etc Hope it helps, Tsjerk On Wed, Apr 10, 2013 at 9:03 AM, Wilson Omesiete womesi...@gmail.comwrote: I noticed that the default carbon color for loaded objects is set to cycle from green to pink and then repeat to differentiate models. I have a lot of models being loading and deleted within one session, and it would be very useful to be able to reset that cycle, So that the first model after a reset will have green carbons, the second will have cyan carbons, and so on. This way my coloring patterns would be consistent. The reset function does not affect the cba* cycle, and I know that I could manually call the cba* variants after every file is loaded to force this functionality, but I would rather avoid that if possible. -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter ___ 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 -- Tsjerk A. Wassenaar, Ph.D. -- Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter___ 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
