[PyMOL] Associating data structure with CGO object

Hi! Is there a way to associate data with an object and access it from a script? What I want to do is parse a file that has a bunch of coordinates and draw the spheres in PyMOL. But then I want to be able to adjust the cutoff for which points are to be drawn. What I was doing now was first to r

[PyMOL] GUIs interacting with PyMOL

Hi! I would like to create a GUI that interacts with PyMOL. What I'm thinking of doing is running PyMOL to visualize a molecule and then create a GUI that interacts with the visualization, such as draw new objects, add labels, etc. How would I go about extending PyMOL with new GUIs (using wxPyth

[PyMOL] ribbons or cartoons with Calpha coordinates

I would like to show ribbons and cartoons based upon Calpha coordinates. Is there a way this can be done short of generating the other mainchain atoms? Anthony -- Anthony Duff Postdoctoral Fellow School of Molecular and Mic

[PyMOL] parallel em code

Hi-- This sounds a bit offtopic, but it's related to a project that would probably be built off of PyMOL. Does anyone have any experience with protein dynamics software that runs on clusters and performs energy minimization? I've seen all sorts of pure MD packages that run on clusters (GROMACS,

RE: [PyMOL] 3D on linux

Naveen, We've had great results with the FireGL series, and the OpenGL performance of the FireGL X1 is excellent (http://www.spec.org/gpc/opc.data/vp7/summary.html). However, the trick with these cards is to allow ATI's binary driver compatibility to dictate your choice of Linux distribution

Re: [PyMOL] 3D on linux

Naveen, I recommend graphics cards with the nvidia quadro4 xgl chips. We several PNY Quadro4 700 XGL and they work great. The caveat is that if you have it configured for quad buffered Stereo then mono display (the usual) will be low performance. zac Naveen Michaud-Agrawal wrote: Hi, this is mor

Re: [PyMOL] 3D on linux

On Wed, 29 Jan 2003, Naveen Michaud-Agrawal wrote: > Hi, this is more a general question related to using pymol on linux, but > does anyone have any 3D graphics card recommendations for linux; ie good > driver support, supports more of OpenGL than is just required by games. Check out the VMD user

[PyMOL] 3D on linux

Hi, this is more a general question related to using pymol on linux, but does anyone have any 3D graphics card recommendations for linux; ie good driver support, supports more of OpenGL than is just required by games. I've looked around a bit on the web, but I figured since my primary use would be

[PyMOL] hbond from rTools 0.5.2.menu on Linux does not work

Hi all, I recently installed the very nice new rTools 0.5.2 with the latest release of Pymol (0.8.6) on a PC running SuSE-Linux 8.1. After setup of all external programs I tried to run HBExplore, but got an error from the pulldown-menu. When invoking hbond from the command-line, everything w