Re: [PyMOL] mixing ray_shadows states

seem to have any effect. (This is with a very recent > beta.) Is it even possible in theory for the raytracer to support such an > option? > POVRay can, if you're itching to do it. Check out the no_shadow object modifier. -Tim -- ------

Re: [PyMOL] Quadro-based 3D Mac Feedback

, and therefore doesn't require my input/money/praises in order to understand why its necessary to support poor little ol' me. Which is linux/BSD! > So let me make clear: We are not saying, "Go Mac!" blindly and without > reservations. But you said: On Thu, Dec 08, 2005

Re: : [PyMOL] Surface Vertex Coordinates

t; Me too. With coloring and/or other "property" information as well. > povscript+ will do all of this, in a somewhat-standardized GTS (gts.sf.net) format that is easy to port to a number of other programs. It will also dump surfaces as vertex2 objects in povray. HTH, Tim -- ------

Re: [PyMOL] sporadic pymol/X-server freezes?

st send it a KILL (try an INT signal first, of course)? Anything in dmesg or the XOrg logs? Can you grab the XOrg pid with gdb and get a stack trace? Can you switch over to a console (ctrl-alt-f1, typically)? -Tim -- -

Re: [PyMOL] Algorithm for Mesh Generation

of GTS, if you're looking for some code and more references: http://gts.sourceforge.net/ along with other sources (google for Paul Bourke's websites for some more goodies). HTH, Tim -- ----- Tim Fenn f...@stanford.edu

Re: [PyMOL] Anisotropic b-value thermal ellipsoids

rself. However, pymol's raytracer also doesn't understand quadrics, so you won't be able to raytrace them unless the code has been added since I last checked, or unless you describe the surface via more simplified means that pymol's raytracer can understand. -Tim -- ---

[PyMOL] pymol for fedora

Just as a quick FYI, pymol is available in the official fedora 9 updates, and will be part of the fedora 10 release. If you have fedora 9 or will be installing fedora 10, you can just do yum install pymol and you should be all set. The rpm is based on the b11 branch, SVN tag 3468. -Tim -- CA

Re: [PyMOL] where to find a 64 bit Linux version?

ps, Tim p.s. warren - pymol is available under RHEL as of version 5. -- ----- Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -

Re: [PyMOL] Slightly off topic

On Tue, 15 Dec 2009 10:27:14 +0100 Marius Retegan wrote: > In my opinion CentOS is not made for a desktop environment. > If you are confortable with the rpm system package, try switching to > Fedora and install the rpmforge repository > (https://rpmrepo.org/RPMforge). Marius > CentOS5/RHEL5 is

[PyMOL] isoprobability ellipsoids

Anyway, its a start. ;) I've posted it here, with a few examples: http://www.stanford.edu/~fenn/scripts.html Regards, -Tim F. -- --------- Tim Fenn f...@stanford.edu Stanford University, School of Medicine

Re: [PyMOL] colouring surfaces according to molecular properties

there is a way to export it if you'd really like to save surfaces and the like, povscript+ allows you to export any surface in GTS (gts.sf.net) format. HTH, Tim -- ----- Tim Fenn f...@stanford.edu Stanford Universi

Re: [PyMOL] Generating a 3D Object in any position

ml I have a pymol script that spits out spheres/disks using glu for the purposes of seeing anisotropic ellipsoids (although passing them along to pymol's raytracer currently isn't possible, as you found out). HTH, Tim -- -----

Re: [PyMOL] Setting grid boundaries in APBS

he better... HTH, Tim -- ----- Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -

Re: [PyMOL] Saving a carved section of a map.

in GTS format (including vertex colors): http://gts.sf.net http://www.stanford.edu/~fenn/povscript/gts_fileformat.html HTH, Tim -- ----- Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H