Hi Yang, With PyMOL 2.1, "finish_launching" should not be necessary to use the PyMOL API in jupyter notebook. PyMOL will now automatically start a backend process (without the GUI, like with "-c") in the main thread if you call any pymol.cmd function. Check out this screenshot:
https://pymol.org/alpha/jupyter-notebook.png On the other hand, "finish_launching" will launch PyMOL in a new thread with an event loop, which will cause 100% CPU usage (at least with "-c"). Cheers, Thomas > On Mar 15, 2018, at 1:35 AM, Yang Su <s...@crystal.harvard.edu> wrote: > > Dear List, > > I would like to use some of the pymol capabilities with my other python code > in jupyter notebook. But after running > > import pymol > pymol.finish_launching(['pymol', '-qc']) > > CPU usage stays at 100% for the python process. After > > pymol.cmd.quit() > > CPU usage returns to normal. I see the same pattern when I run those > commands in an interactive python shell. Tried pymol 2.0/2.1 with both python > 2.7 and 3.6 on mac (anaconda) and linux. > > Did I do anything wrong or is it a bug in pymol? > > Thanks, > > Yang -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ 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
