Re: [PyMOL] Fuse gaps

Hi Alex, the gaps and the scrambled sequence view have the same reason, it's the internal ordering of atoms which is not consecutive. PyMOL does this based on atom identifiers (chain, resi, etc.). I suggest assigning ascending chain letters to the three parts before fusing. alter nterminus, chain

Re: [PyMOL] Pymol in command mode - no output

Hi Per If you're still having problems, you can try to install and run pymol under the X virtual frame buffer (xvfb). Cheers, Esben Best Regards Esben Peter Friis Science Manager Novozymes A/S Krogshoejvej 36 2880 Bagsvaerd Denmark Phone: +45 44461334 Mobile: +45 30771334 E-mail: e...@no

[PyMOL] ribbon trace, visualizing polymers (resent)

I use pymol to generate images of simple polymers by loading their coordinates as .pdb files. The 'polymer .pdb' files contain only alpha carbon coordinates. I connect them using the ribbon_trace option, and color them by varying b-factors in the .pdb file. I had created many different movies and

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

> From: jason.vertr...@schrodinger.com > Date: Mon, 26 Nov 2012 10:37:52 -0600 > Subject: Re: was: [PyMOL] Mobile PyMOL Problem and Solution/ Now: pdb or > related libraries > To: marchy...@hotmail.com > CC: pymol-users@lists.sourceforge.net > > Hi Mik

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

Mike, > Although I am curious now if I had a pdb that lacks hydrogens, like I did in > this case, > what pymol facilities are there for adding them? Apparently you have some > editing h_add object_name Type, "help h_add" or check out h_add on the PyMOLWiki (http://www.pymolwiki.org/index.php/H

Re: [PyMOL] ribbon trace, visualizing polymers (resent)

Hi Erik, Can you please send me a copy of one of the problematic sessions? Cheers, -- Jason On Tue, Nov 27, 2012 at 11:23 AM, Erik Nelson wrote: > > I use pymol to generate images of simple polymers by loading their > coordinates as > .pdb files. The 'polymer .pdb' files contain only alpha car

Re: [PyMOL] ribbon trace, visualizing polymers (resent)

Hi Erik, This is a known bug introduced in OS X 10.8 and some video cards. To fix this just type, set cylinder_shader_ff_workaround, 1 and all should be well. PyMOL uses an official rendering optimization but some systems have difficulty with it, hence our workaround. This is automatically fi

Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or related libraries

> From: jason.vertr...@schrodinger.com > Date: Tue, 27 Nov 2012 12:37:41 -0600 > Subject: Re: [PyMOL] was: Mobile PyMOL Problem and Solution/ Now: pdb or > related libraries > To: marchy...@hotmail.com > CC: pymol-users@lists.sourceforge.net > > Mike,