[PyMOL] about running pymol on Linux

Dear everyone: I've installed pymol on Redhat 9.0.When I type pymol,it give the message like : >freeglut (/data13/gzhu/NP2/pymol/pymol.exe): Unable to create direct context rendering for window 'PyMOL Viewer' the viewer interface window also appears and I can load pdb file.The pymol seems that it

[PyMOL] secondary structure to different states

Hi all, If I read in a two pdb-files in different states, only the first one read in got assigned secondary structures. Example: load p1.pdb ,state=1 load p2.pdb ,state=2 hide all show cartoon only p1 has arrows and helixes the p2 has fat tubes. I also tried define it explicitly

[PyMOL] cgo objects and rotate/translate functions

Hello I just have a little question about cgo objects. Why is that cgo object can't move with rotate/translate function ? I know I may turn them with the camera view, but let's imagine I want to rotate two cgo objects relatively to each other, what would be the easiest way of doing that ? Thanks

[PyMOL] How to load volume density from python array?

Hi I have some data in the form of a python array which I would like to load as a volume density map in Pymol. Can this be done with the read_xplorstr, or is there another way? Can anyone shed any light on how I format the xplorstr? load_brick or load_map could be alternatives, but how do they wo

[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.

Hi there, I have written a little utility called apropos[1] (after a unix command of the same name) to help in locating commands that might do something you want done. It is like the grepset[2] command except this one looks up commands instead of settings. [1] http://www.pymolwiki.org/index.php/

Re: [PyMOL] secondary structure to different states

Hi Björn, Odd. I can't reproduce this. I load 1a2p and 1a12 into states one and two, hide, show cartoon, and bingo - I have two cartoons (in two different states). What happens if you load the first pdbfile twice? Or use another file instead of p2? Or a newer version (I'm using MacPyMol 1.0.0b03

Re: [PyMOL] Protein Surfaces in PyMol

Vijay, You can download the Global Protein Surface Survey (GPSS) PyMOL plugin at http://gpss.mcsg.anl.gov/GPSSpyMOL/ . The plugin allows you to visualize ligand, metal, dna and peptide binding surfaces as well as CASTp pockets and voids for all structures in the PDB. Feel free to email me if you

[PyMOL] load_brick broken?

Hi I dont know if my other post was sent to the mailinglist, but I want to load some volume density data from a python array I generate. I found the brick01.py example which seem to do exactly as I need, however it doesnt show any isosurfaces. I run brick01.py and it makes a brick object and so

[PyMOL] movie with 3 molecules

Dear Pymol uers, Sorry for this probably basic question but the "search" option for this mailing list seems to be out of order on the sourceforge website... I'm trying to make a movie with 3 molecules for each frame. As each molecule is in a separate pdb file, I would like to find a way to do s

[PyMOL] ANNOUNCE: apropos command to lookup commands matching a keyword.

Hi there, I have written a little utility called apropos[1] (after a unix command of the same name) to help in locating commands that might do something you want done. It is like the grepset[2] command except this one looks up commands instead of settings. [1] http://www.pymolwiki.org/index.php/

[PyMOL] GPSS Plugin Update

Hello, I would like to announce that there is an updated version of the Global Protein Surface Survey (GPSS) PyMOL plugin available for download at http://gpss.mcsg.anl.gov . The new version retains all the functionality of the original plugin with the ability to al