Re: [PyMOL] Font problem

On 22/11/13 01:02, Thomas Holder wrote: > Hi, > > this is fixed now in the sourceforge SVN repository. > > Cheers, > Thomas > Thanks for working quickly on it, but it isn't fixed here. There some things I observe, The font geometry changes according to the window geometry. That means a tall

Re: [PyMOL] Font problem

Hi, this is fixed now in the sourceforge SVN repository. Cheers, Thomas On 21 Nov 2013, at 15:36, Jason Vertrees wrote: > Justin, > > You're right, they are ugly! We're fixing that ASAP. > > Thanks for bringing this up. > > Cheers, > > -- Jason > > On Thu, Nov 21, 2013 at 8:10 AM, Justin

Re: [PyMOL] Pymol sas

Neshat, Warren wrote the surfacing algorithm years ago. A little more discussion on the algorithm can be found here ( http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg07124.html) and here (http://www.pymolwiki.org/index.php/Get_Area). Cheers, -- Jason On Tue, Nov 12, 2013 at 2:

Re: [PyMOL] Font problem

Justin, You're right, they are ugly! We're fixing that ASAP. Thanks for bringing this up. Cheers, -- Jason On Thu, Nov 21, 2013 at 8:10 AM, Justin Lecher wrote: > Hi, > > label fonts look ugly here with use_shaders=1. When switching on > use_display_lists=1 it looks good again. But the two o

Re: [PyMOL] UCSD pymol workshop

Hi Spencer, We're happy to help. Please email me offline and I'll see how we can assist. Cheers, -- Jason On Wed, Nov 20, 2013 at 5:30 PM, Spencer Bliven wrote: > We've been discussing putting together a PyMol workshop for the UCSD > undergrad bioinformatics club (http://ubic.ucsd.edu/). I w

[PyMOL] VanderWaal strain number and showbumps

New to the forum but have been uisng Pymol for about a year. I have a ? Re using the showbumps.py script and the vanderwaal strain number given after the run. The vanderwaal strain number that pymol gives after you run showbumps, is that in J/mol? kJ/mol? I am trying to get a handle on how dest

Re: [PyMOL] UCSD pymol workshop

Hi Spencer - You may already be aware of this, but the PyMOL Wiki is a great resource. Depending on the scope of what you want to cover and the experience levels of your members, there are several tutorials that may be helpful. I'd recommend Practical PyMOL for Beg

[PyMOL] 2 new plugins, and a bit more :-)

Dear all, I develop goChem, an open source library for computational chemistry written in the Go language. I have incorporated a couple of Python functions that allow easily writing PyMOL plugins with goChem, using JSON and pipes for data transfer. As a proof of concept, I wrote two (also open so

[PyMOL] Font problem

Hi, label fonts look ugly here with use_shaders=1. When switching on use_display_lists=1 it looks good again. But the two options are exclusive so I get a performance penalty for the gain of good looking fonts. After ray tracing the fonts look great in both cases. Is there a way to improve the fo

[PyMOL] RMSD calculation for the pdb ensemble

Dear PyMol users! I'm looking for python script which would perform the 1- loading ensemble of the pdbs to the pymol (assuming that it could be done by loadDir script) 2- Perform structural alighnemnt of all loaded structures against reference 0.pdb by means of buit-in TMalighn module this coul