Re: [PyMOL] Select crystal waters inside protein

2012-10-04 Thread Martin Hediger
Dear PyMOL Users I'm trying to remove water molecules from a crystal structure which are on the crystal surface while preserving the ones within the crystal interior. What I do is: select waters, resn HOH # cmd.select(waters, (waters extend 1), enable=1) get_area waters, load_b=1 remove waters

Re: [PyMOL] Select crystal waters inside protein

2012-10-04 Thread Folmer Fredslund
Hi Martin, 2012/10/4 Martin Hediger ma@bluewin.ch Dear PyMOL Users I'm trying to remove water molecules from a crystal structure which are on the crystal surface while preserving the ones within the crystal interior. What I do is: select waters, resn HOH # cmd.select(waters,

Re: [PyMOL] bond connection file

2012-10-04 Thread Thomas Holder
Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote,

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.

2012-10-04 Thread Mike Marchywka
fwiw, I never figured out why the out-of-the-box build hung  using the python approach but I went through the ./cogifure, make make install route and did get the test molecules to display. However, I ran into lots of problems with the ShaderMgr and ccealignmodule and then finally the link was

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.

2012-10-04 Thread Mike Marchywka
CC: pymol-users@lists.sourceforge.net From: li...@cowsandmilk.net Subject: Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb. Date: Thu, 4 Oct 2012 22:03:59 -0400 To: marchy...@hotmail.com You don't need a

Re: [PyMOL] I just built pymol, comes up but hangs on any attempt to view a test pdb.

2012-10-04 Thread David Hall
You don't need a license for the open source version. If you provided details on what OS/distribution you are building on, people may try to replicate and understand why the python version hung. In my experience, using setup.py generally worked out of the box. -David On Oct 4, 2012, at 9:22