[PyMOL] Resize window problem

Hello PYMOL users, I have problem when maximalizing PYMOL Viewer window. The window becomes black :(. I have never had this problem until I had to repair installation of Windows XP due to failure during installation of Servis Pack2. I managed to reinstall Windows XP and to install Servis Pack 2

RE: [PyMOL] paths in MacPyMol

FYI: Note that in MacPyMOL 0.99, if you "cd" into the application bundle "cd MacPyMOL.app" and run ./setup.sh, it will create a PyMOL startup script for you in the outer directory that you can then relocate to /usr/bin or wherever. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] saving coordinates of docked molecules in new orientation

Marilyn, Isn't that the default behavior already? I'm confused. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-87

Re: [PyMOL] output formats

Thank you Jerome. Do you know of any way to convert from .pov to any of the listed formats? More to the point, we're looking for an easy way to import molecules/surfaces/maps from pymol into our lab copy of 3D Studio, mostly for lighting effects (tinted-, omnidirectional-, volume-, object-sourc

Re: [PyMOL] SHARP map not opening in PyMOL

This brings up an minor issue I have with the way PyMOL deals with maps. As Sivaram has found out, file extension matters a lot in PyMOL. So if I have a normal ccp4-format map with the extension '.ccp4', PyMOL is happy and will display the map normally. However, if the extension is something els

[PyMOL] gui-programming

Hi everybody. I'm currently trying to create a pop-up GUI with Radiobuttons (e.g. checkboxes). I don't know why initial highlighting of a specific Checkbox won't work. Attribute .set() fails at this point (see below), although the GUI looks nice. from Tkinter import * root = Tk() def

[PyMOL] saving coordinates of docked molecules in new orientation

Hi all, After manually docking a molecule to another molecule (from a different .pdb file), is it possible to write out the coordinates of the moved and docked molecule with it's 'new' coordinates relative to the .pdb to which it was docked? Marilyn Marilyn D. Yoder Division of Cell Biology a

[PyMOL] SHARP map not opening in PyMOL

Hi all! I am trying to open a SHARP map (ccp4 format, i.e. .map format), but it does not open the map. According to the pymol users manual, it should open ccp4 format maps. Has anyone had this problem before, and what can I do to get around it? Thanks! Sivaram Mylavarapu.

Re: [PyMOL] output formats

Hi, I have work a little with .obj file. I've written a script that translates OBJ file to PDB file. It is quite simple to make the opposite. For more information on obj format, you can read this resume: http://www.fileformat.info/format/wavefrontobj/ You can also translate PyMOL CGO to OBJ fi

Re: [PyMOL] paths in MacPyMol

Hey Andrew, On my system, open launches Graphic Converter. In any case, I have an alias defined in ~/.bashrc to start pymol: alias pymol='/Applications/PyMOLX11Hybrid.app/Contents/MacOS/PyMOL' This way, pymol test.pdb opens the pdb file in pymol, and the path is set correctly. Andreas > I