Re: [PyMOL] Ray tracing max_threads

Hi all, Quick summary after off-line discussion with Jesper: The max of 32 threads was hard coded in PyMOL. The latest SVN update increases this limit to 125. If you ever need a higher limit, look for PYMOL_MAX_THREADS in the code. Cheers, Thomas On 22 Jan 2016, at 03:27, Jesper Lykkegaard

Re: [PyMOL] auto_show_cartoon or similar

Hi Ivan and Carsten, I can take "auto_show_cartoon" as a feature request. It's trivial to implement. What also would be nice: automatically showing sticks for ligands. e.g. corresponding to the "not polymer" or the "organic" selection. Thoughts? Cheers, Thomas On 08 Feb 2016, at 09:07,

Re: [PyMOL] auto_show_cartoon or similar

Hi Ivan, you could either try to overload the “load” function in Pymol (not sure this is supported) or write your own custom load function under a different name, which loads the protein, assigns the name of the object, hides lines and shows the cartoon. Sorry, this is a rather generic answer

[PyMOL] auto_show_cartoon or similar

Hello Is there a way to make cartoon the default representation, something akin to "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 (link below) but I haven't found anything more recent that does what I'd like.

Re: [PyMOL] auto_show_cartoon or similar

Showing metal ions (and FES clusters etc) as spheres would also be useful. Thanks, Abhinav Abhinav Kumar, PhD Senior Scientist, Bioinformatics Intrexon, Inc. 329 Oyster Point Blvd., South San Francisco, CA 94080 (650) 597-4072 | aku...@intrexon.com

Re: [PyMOL] auto_show_cartoon or similar

Every year I teach students PyMOL, and the look on their faces when they first open a pdb in PyMOL and get a cluster of green sticks… yikes! YES!!! to the default being secondary structure, ligands as sticks, and metal ions as spheres! Add - nucleic acids as cartoon. > On Feb 8, 2016, at

Re: [PyMOL] auto_show_cartoon or similar

My thoughts exactly! Dave Bourgaize On 2/8/16, 9:54 AM, "H. Adam Steinberg" wrote: >Every year I teach students PyMOL, and the look on their faces when they >first open a pdb in PyMOL and get a cluster of green sticksŠ yikes! > >YES!!! to the default being secondary

Re: [PyMOL] auto_show_cartoon or similar

That would be great, my standard is open file, cartoon, ligand sticks Great idea -Original Message- From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] Sent: Tuesday, 9 February 2016 5:52 AM To: Ivan Vulovic ; Schubert, Carsten [JRDUS] Cc: