[PyMOL] launching PyMOL on cygwin

Dear fellow PyMOL users, I have been trying to install PyMOL on a cygwin platform on my Windows XP computer. So far I have built and installed PyMOL using the commands python setup.py build python setup.py install python setup2.py in my pymol directory. This generated a script named "pymol" (no

Re: [PyMOL] Warning: Nvidia 6111 drivers for linux

Hi Peter, Just to provide report that 611 driver works without problem with: - pymol 0.97 - python 2.3.3 - 2.6.7-gentoo-r12 kernel - nvidia-kernel-1.0.6111 - nvidia-glx-1.0.6111 - xfree-4.3.0 - GeForce2 Go graphic card (as well as three other types of cards) Cheers, Stéphane

[PyMOL] showing apbs map from a script

HI everyone I'm pretty new to pymol and I'm trying to show an electrostatic surface. I have managed to use the apbs plugin to do this - however I REALLY want to be able to do this from a .pml script since this would make it easier to do some movies. Anyone have any ideas how to do this? Thanks i

[PyMOL] translating map/mesh

Hello, I loaded an Xplor map and created a mesh: load grid.xplor, map1 isomesh mesh1, map1, 30 Now I need to translate the mesh by 1.0A in all three directions (x,y,z). In other words, I need to shift the mesh object by some offset vector. Is there any way to do that in pymol? It seems like

Re: [PyMOL] Warning: Nvidia 6111 drivers for linux

Hi, Peter What Linux are you using? Seems it's not a problem on RedHat linux, I am running both 7.3 and EL-AS, with 2.4.20 and 2.4.21 kernel respectively, and the exact same NVIDIA version without any problem at all. Although we are using python2.2, looks like you are using python2.3, maybe th

[PyMOL] using package Scientific from within pymol on OS X-X11 hybrid

I guess this might seem obvious to some people, but I wanted to use Vectors and Objects3D from pymol scripts, but I couldn't see how. however, it turns out that if you copy the entire (python) source tree of Scientific - IE: "ScientificPython/Scientific/" into "/Applications/PyMolX11blahHyb

[PyMOL] Warning: Nvidia 6111 drivers for linux

Hello. I did a scan (albeit brief) of the mailing list for this issue, but didn't find it, so I decided to post it FYI. I wanted to mention a serious issue I just discovered after installing the new nvidia drivers for linux (specifically regarding the "NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver,

[PyMOL] molecular Mechanics calculations

Hi PyMolers Is it possible to make some basic molecular mechanics calculations in PyMOL, in fact I would like to measure the binding energy between a protein and various ligands? Thanks in advance Gabriel Gabriel PAËS PhD Student The Danish University of Pharmaceutical Sciences Depa

[PyMOL] rtools again (strange...)

Hi again, 1st of all thanks to Kristian -- the "time.sleep(1)" hint works fine. Maybe you can help me with this one also: calling a pdb file via pdb CODE usually checks if the file has already been downloaded and if yes, takes it from the local repository. however, calling this command from a

[PyMOL] apbs map size

Hi, I have a problem with apbs in pymol. I got it to work fine, if I cutted a 100 aminoacid stretch from my molecule and followed the instructions. However my protein is a bit bigger, ~800aa, and I cannot get the apbs map to cover my molecule. I get the whole surface, but only half of it is co

[PyMOL] PyMol and Virtual Reality

Hi! We are working on a project creating an OpenSource-library for a Virtual Reality gloves/positioning device-combination that is going to be integrated with a data analysis tool. However, the program is not in a state where we can integrate our work yet, so we will create a prototype to demonstr

Re: [PyMOL] 2 colors for transparent surface and cartoon

Hi Gabriel, You can set a specific color either for the surface or the cartoon with set surface_color, color set cartoon_color, color or if you want to have more control over the colors you can create a new object and show one in cartoon and the other in surface: create newobj, obj show surf