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.
http://www.mail-archive.com/pymol-users%40lists.sourceforg
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
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 K
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, Schub
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
From
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 10:57
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 structure, ligands as sticks
Adam, Abhinav, Dave,
thanks for the very useful feedback.
To keep it simple, I propose a "auto_show_classified" setting (will depend on
"auto_classify_atoms", on by default) which will be equivalent to:
show cartoon, polymer
show sticks, organic
show spheres, inorganic
Question: should this aut
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: pymol-users@lists.sourceforge.net
Subjec
