Re: [PyMOL] Pymol Mobile viewer?

Hi, Sorry to dig up such an old thread, but now development time has been found for an iPad version of Pymol, can we hope for an Android version to appear at any point in the future? cheers, Doug > > Re: [PyMOL] Pymol Mobile viewer? > > Jason Vertrees Sun, 17 Jan 2010 06:48:31 -0800 > > Tsj

Re: [PyMOL] Pymol Mobile viewer?

Did you only install it because > it's for free or would you be willing to pay for it? Would you pay > for an Android version? Does the limited interface and reduced > functionality (compared to desktop PyMOL) satisfy your needs? If > not, which critical features are m

[PyMOL] Access API without the GUI

Hi all, Does anyone know if there's a way of accessing Pymol's API without the GUI? There are some useful functions in there and my loops would iterate a lot faster if the GUI didn't fire up every time. cheers, Doug _ Dr. Douglas R. Houston

Re: [PyMOL] Access API without the GUI

import pymol > > # Call the function below before using any PyMOL modules. > pymol.finish_launching() > > from pymol import cmd > > #now your commands > cmd.fetch('1YCR') > > # > > > You may also want to check out these pages on scripting: >

[PyMOL] Optimize plugin throws "NameError: global name 'ob' is not defined"

Hi all, I installed Optimize.py, now when I start Pymol I see: "Optimize plug-in needs openbabel to be installed in your system, please follow the instructions at http://openbabel.org/wiki/Get_Open_Babel"; If I try to use any optimize commands I get: "PyMOL>minimize all, nsteps 2 Traceback (m

Re: [PyMOL] Optimize plugin throws "NameError: global name 'ob' is not defined"

.so] Error 1 make[1]: *** [scripts/CMakeFiles/bindings_python.dir/all] Error 2 make: *** [all] Error 2 Quoting Matthew Baumgartner on Wed, 12 Nov 2014 08:55:27 -0500: > Hi, > Can you check to see if the python bindings are compiled openbabel? > > On the bash command line, run t

Re: [PyMOL] Access API without the GUI

Surely there must be a way to run Pymol in a mode that does not fire up the GUI but still allows it access to OpenGL?? > Michael, > > The "-c" option forces PyMOL to run in command-line-only mode which means it > doesn't have access to the OpenGL hardware (used by cmd.draw and interactive > gra

Re: [PyMOL] best way to rotate molecular bonds without dihedral context?

Hi John, Does the 'torsion' command work? Cheers, Doug Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 01:06:04 -0700: > Hello, PyMOL users! > > I am trying to figure out within the Python interface how to rotate the > parts of a molecule on one side of a bond about that bond's axis, given

Re: [PyMOL] best way to rotate molecular bonds without dihedral context?

That's alright, I only discovered the "Volume" feature yesterday and that's been around since v1.4 ... Quoting johnbax...@cs.unm.edu on Thu, 20 Nov 2014 11:06:39 -0700: > It does! Thank you very much; I don't know how I missed that command. > >> Hi John, >> >> Does the 'torsion' command work?

Re: [PyMOL] Detecting holes/cavities in surface

Hi Daniel, If you don't HAVE to use Pymol, something like fPocket, HOLE or PocketDepth from this list might do what you want: http://www.vls3d.com/links/bioinformatics/binding-pockets You might find this list interesting too: http://www.vls3d.com/links/bioinformatics/peptides-antibodies-epito