RE: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver

2005-03-29 Thread David A. Horita
Hi, I Haven't tried VMD yet, but Windows XP-pro pymol crashes upon file open under the 71.84 drivers, but not the 70.78 drivers. (Quadro 1300, XP-Pro servicepack 2) David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net

Re: [PyMOL] Problem with pml script and png command

2005-03-29 Thread Jacob Corn
Hi Gregori, If you are just saving an image without rendering it (eg - png without ray) then the raw OpenGL output is sent to the file. Meaning, if you have the command line/menu window open in front of the graphics window, your images will be cut off where they overlap. This might or might

RE: [PyMOL] G5 and pymol flashing

2005-03-29 Thread Warren DeLano
MacPyMOL users: I believe that I have worked around the bugs in the latest nVidia drivers hardware. Beta at http://delsci.com/macbeta Flickering specular reflections and periodic multicolored flashes should no longer be a problem. Cheers, Warren -- Warren L. DeLano, Ph.D.

RE: [PyMOL] psw files and powerpoint

2005-03-29 Thread Warren DeLano
The new pymol beta has been fun to play with. I like the scenes function but am having trouble importing the .psw file into PowerPoint. I can make a hyperlink as was suggested in the mail list, but this is not ideal. I need to go through two windows warnings about evil hyperlinks, the

Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver

2005-03-29 Thread Sabuj Pattanayek
Hi, Unfortunately I can't get pymol-0.97 0.98beta29/27 to open a pdb without crashing instantly. I also tested Chimera (1.2105), O v9.0.7, and rasmol and these seem to work ok but I guess they aren't using quads/quad strips. Thanks for your insight, I'll email nvidia with the contents of

Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver

2005-03-29 Thread John Stone
Sabuj, Yeah, it could be that Chimera and O don't use as large of a variety of OpenGL primitives and VMD and Pymol do. Last I checked, Rasmol didn't use OpenGL at all, it renders using its own algorithm and displays using Xlib calls. Do you have any other OpenGL programs to try, I suspect

[PyMOL] Fitting/alignment of non-identical sequences

2005-03-29 Thread Robert Campbell
Dear Folks, I know a number of people have stumbled over the difficulty of calculating RMSD values for structures of non-identical sequences. While teaching a class that introduced students to the use of PyMOL to look at protein structures and to the study of certain structurally homologous

Re: [PyMOL] pymol crashes with new [7167] nvidia driver

2005-03-29 Thread lieven
On Tuesday 29 March 2005 19:55, Sabuj Pattanayek wrote: Unfortunately I can't get pymol-0.97 0.98beta29/27 to open a pdb without crashing instantly. I also tested Chimera (1.2105), O v9.0.7, and rasmol and these seem to work ok but I guess they aren't using quads/quad strips. Thanks for your