Re: [PyMOL] Stucked...

2012-10-08 Thread Mike Marchywka
> Date: Tue, 9 Oct 2012 03:07:08 +0200 > From: ivan...@gmail.com > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Stucked... > > Dear PyMol users, > > I'm facing very unusual runtime problem. After successful compiling of > PyMol 1.5.0.1 on Sl

Re: [PyMOL] Make sure zoom is viewed from surface

2012-10-08 Thread Edward A. Berry
Jason Vertrees wrote: > Hi Troels, > > I've run into this problem a few times, too, but never took the time > to solve it correctly. > > A quick plan might look like: >* cmd.orient on the selection >* store the view vector (http://www.pymolwiki.org/index.php/Get_View) >* let C1 = count

Re: [PyMOL] Make sure zoom is viewed from surface

2012-10-08 Thread Jason Vertrees
Hi Troels, I've run into this problem a few times, too, but never took the time to solve it correctly. A quick plan might look like: * cmd.orient on the selection * store the view vector (http://www.pymolwiki.org/index.php/Get_View) * let C1 = count the number of atoms behind the view vecto

Re: [PyMOL] Mutation script

2012-10-08 Thread Jason Vertrees
Hi Martin, > I use the following script to prepare small side chain fragment PDB > files of mutants in PyMOL: > http://pastebin.com/nDTZApHP > I use the PyMOL built-in mutagenesis wizard and the sculpting wizard to > locally optimize the side chains within the environment of the protein. > For lar

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

2012-10-08 Thread Jason Vertrees
Hi Ben, We read the shaders from $PYMOL_PATH/data/shaders. We should be reading them from $PYMOL_DATA/shaders. If you'd like to change this on your own compiled PyMOL you'll need to change lines 411 and 418 of pymol/layer0/ShaderMgr.c and rebuild. If you're a paying PyMOL subscriber this should be