Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

2012-06-15 Thread James Starlight
Thomas, thanks this works perfect. Jason, I've tested this script on my system ( this is the membrane protein inserted in the bilayer surrounded by two water layers ( up and down ). During simulation individual water mollecules move into the protein interiour ( in that case protein like a

[PyMOL] clipping planes

2012-06-15 Thread Christian Roth
Dear all, it is nice to set via mouse wheel the clipping. Is it possible to get this values somewhere out of pymol that one could use the actual values in a script? I find it a bit complicated and time consuming to play always a few times with the values in a script, to find values which looks

[PyMOL] Script to calculate Fab elbow angle

2012-06-15 Thread Sampson, Jared
Hello all - I'd like to share with you this script that I recently added (with Troels' help) to the PyMOL Wiki. http://www.pymolwiki.org/index.php/Elbow_angle Given a PyMOL object containing an antibody Fab fragment complex, light and heavy chain IDs for the Fab, and residue numbers for the

Re: [PyMOL] clipping planes

2012-06-15 Thread Schubert, Carsten [JRDUS]
Christian, you should be able to get the values from the tuple returned by get_view(). Looking into this would be a good starting point. from my old notes (origin unknown...): 0-8 is the 3x3 rotation matrix 9-11 is the camera location (I think -- been a while...) 12-14 is the origin of rotation

Re: [PyMOL] Script to calculate Fab elbow angle

2012-06-15 Thread Jason Vertrees
Jared, Very cool script -- and beautiful visualizations. It's good to note that since it's in git-repo the new Plugin Manager can access it (just be sure to install COM and transformations, first). What used to take 3--5 minutes (downloading each script and putting them somewhere after cleaning

Re: [PyMOL] GLSL Shaders

2012-06-15 Thread Jason Vertrees
Hi Shiven, Thought some of you may be interested in this: http://pymolwiki.org/index.php/GLSL_Shaders Very nice work! Flexibility of representation and speed were the two main reasons we advanced to GLSL shaders over immediate mode rendering and display lists for PyMOL. Shaders offer powerful

Re: [PyMOL] 60-mer virus capsid (need computing power!)

2012-06-15 Thread Jason Vertrees
Hi Shane, With PyMOL v1.5 and later, and a reasonable machine you should be able to use large systems (250,000, and upward of 1,000,000+ atoms) without much of a problem. Using the following simple test script: fetch 2xpj, type=pdb1, async=0 split_states 2xpj delete 2xpj orient For these

Re: [PyMOL] 60-mer virus capsid (need computing power!)

2012-06-15 Thread Shane Neeley
Hi Jason, Thanks a lot for the performance info. I think that a full capsid would be around 300,000 atoms, so your info is very helpful. We will probably invest in the newest version of pymol when we purchase the computer. On Fri, Jun 15, 2012 at 12:19 PM, Jason Vertrees