[PyMOL] atom picking hooks

Let me help break the new mailing list in. I haven't been using pymol for very long, but I've been impressed with some of its features and with its potential. At the moment, I'm working on a program that could benefit by integrating pymol. Specifically, I need to be able to read in a molecule (m

[PyMOL] getting image sizes

Does anyone know how to get the size (pixels) of the viewer? I'd like to be able to write a python script that orients and colors a molecule and then renders it at whatever dpi I provide as a command-line argument. Best, Ben

Re: [PyMOL] ca-trace

But that's what you should get, since alpha carbons aren't bonded directly to other alpha carbons, right? Perhaps what you really want to do is draw the protein "backbone only"? Try this: hide all show (name ca,c,n,o) Cheers, Ben "Frank Vondelft" writes: > Hidy Pymollers > > I *think*

Re: [PyMOL] png output

Jason Yano writes: > Hi All, > I just wanted to know if there was a way to include resolution > and pixels per inch ie 150 or 300 rather than the default of 72 > pixles/inch in the .pml scritp ie > Just provide `ray' with an optional width and height. Ben

[PyMOL] autotools

Warren, Would you have any interest in an autoconf/automake build setup for pymol? I have done some preliminary work on such a system this week, mostly to learn how to use the GNU autotools. The code is still pretty rough, but if you think that you might be interested in incorporating it, I will

[PyMOL] ccp4 map?

Can anyone offer some advice on how to convert a ccp4 map to an XPLOR map for import into pymol? I know next to nothing about crystallography, so perhaps the question is not even meaningful. Thanks, Ben

Re: [PyMOL] ccp4 map?

Thanks to all who replied. I was going by the html manual, which said that pymol only reads XPLOR/CNS maps. I know that the manual is out-of-date --- I should have dug harder. Thanks, Ben

Re: [PyMOL] PyMOL gentoo package

On Mon, Jun 17, 2002 at 03:43:56PM +0200, Eckhart Guthöhrlein wrote: > Hi all, > > just a short notice for debian users: there is a PyMOL deb-package > available as part of the unstable distribution. > > http://packages.debian.org/unstable/science/pymol.html > > It is currently version 0.80, but

Re: [PyMOL] picture size and resolution

David, Type 'help ray'. What you want is 'ray 3000,2400', followed by 'png foo.png'. Regards, Ben On Thursday, September 12, 2002, at 11:01 AM, David Guerra Aragao wrote: Dear all, Thanks to Gareth i solved my problem about SS prediction using rTools package. My Thanks to Kristian Rother a

[PyMOL] gentoo linux ebuild for 0.88

Gentoo linux users: You can find an ebuild for 0.88 here: http://bugs.gentoo.org/show_bug.cgi?id=22235 I imagine that this update will make its way into the portage tree at some point. Regards, Ben

[PyMOL] molcad surfaces

Does anyone know of a way to get a ray-traced image of a (sybyl) molcad surface? I've googled everything I can think of, but I can't find any information about the format of a molcad surface file (binary, .sld). Any help would be greatly appreciated. Best Regards, Ben

[PyMOL] gtk+ gui

I've put together a preliminary Gtk2 replacement for PyMol's usual Tk interface. Those interested can find screenshots, patches, and installation instructions at http://www.tuxbox.us Some things don't work, particularly items under the `File' menu. Most things are done, however, so I think you c

Re: [PyMOL] gtk+ gui

Thanks for giving it a look. I'm not much of a graphic artist, so I will probably stay away from creating any custom button pixmaps. I agree, however, that the ui could benefit from a little reorganization. For this first pass, I just stuck with mimicking the layout of the Tk interface, but I'm