Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

Sebastien, I cannot change the color for rendering modes I defined. I do not understand what you mean by this. Cheers, Warren I mean that the color, for cartoon view, is unchangeable when 'set cartoon_color' is defined in the $HOME/.pymolrc file. Thus, when I define 'set cartoon_color' in

[PyMOL] Re: New user needs help! (Michael Morbious)

Michael Morbious wrote: Dear All, I am a new pymol user. Does anyone know if it is possible to merge four units (all units are same) of a tetrameric assembly by using pymol? Each unit has the same Id and when I load each of them, they overlap. If you please help me, I will be really

[PyMOL] picking discrete coordinates

Hi all! I'm trying to pick a discrete coordinate outside of the loaded protein structure (something like create name, coord[x,y,z]) to which I can apply the around command. Creating an additional atom as a probe would be a makeshift solution. Is there a way to use the Fragment Builder

[PyMOL] How to raw_input() from windows Pymol?

Hello all, I am using the windows binaries for PyMol. Whereas in Python it is easy to do a: a=raw_input() When I use PyMol under windows it either gets crashed or halted while I am unable to input from keybord. I searched in this email list and I found some similar questions but no answer.

[PyMOL] automated H-bond computation visualization in pyMOL?

Hello everybody, I am new to PyMOL and I have a short question: In pyMOL - is it possible to automatically compute and visualize H-bonds in .PDB files as it is e.g. possible in SWISS-PDB-VIEWER? Maybe there is a pyMOL script for this purpose? I need such a function for my work with

[PyMOL] Geowall Testing

PyMOL Users: Regarding geowalls [also known as dual-projector passive stereo setups that use polarized lenses glasses to deliver low-cost stereo 3D to large audiences]... Does anyone have one set up right now who might be able to test a new PyMOL build with improved geowall stereo support?

Re: [PyMOL] [colors frozen for rendering modes defined in .pymolrc]

Sebastien, * Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-10-17 08:41] wrote: Sebastien, I cannot change the color for rendering modes I defined. I do not understand what you mean by this. Cheers, Warren I mean that the color, for cartoon view, is unchangeable when

RE: [PyMOL] automated H-bond computation visualization in pyMOL?

Michael d/l a recent build http://delsci.com/beta and use the find-polar contacts option under the objects Action A menu in the viewer window. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213

RE: [PyMOL] How to raw_input() from windows Pymol?

Evangelos, This is architecturally impossible in PyMOL due to clash between the asychronous nature of GUI event handling and the synchronous nature of script execution using the main thread. Right now, the best thing you can do is add a new command into the language which calls your function

RE: [PyMOL] picking discrete coordinates

The best way to approach this is simply to build a small molecular object on the fly. See examples/devel/chempy_model*.py Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San

RE: [PyMOL] Geowall Testing

I'll try it when I get back to work tomorrow - but I'm a bit confused :-) The features you mention, haven't they been part of PyMOL for some time already? We have active stereo glasses for our workstations, and use the same PyMOL version (0.99beta14) for those and the Geowall. Cheers,

RE: [PyMOL] Pharmacophore visualizations

Andrew, It's either-or for now. Either you can render pharmacophores using CGOs or you can represent them as molecules and thus align them. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213

RE: [PyMOL] Geowall Testing

Ah... That make things a bit clearer :-) We do have a geowall, but the Linux driver supplied by Nvidia directly supports sending the left and right images of the quad-buffered stereo to the two separate video heads on the card, which are then connected to the two projectors. This

RE: [PyMOL] Geowall Testing

Esben, Fantastic! I wasn't aware that nVidia quadro cards could do this. That provides a compelling reason to purchase nVidia Quadro cards for passive stereo under Linux. For the record: to configure passive stereo using the quadbuffer API with a Quadro card under Linux, XF86Config needs to

[PyMOL] set_dihedral

Hi, I'm trying to apply the command 'set_dihedral' to residue from a molecule object which contains only three non-consecutive residues from the original protein. The program complains with the following error message: GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex.