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[PyMOL] PyMOL tips (was: Re: GNU-Darwin and Fink)
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From: proclus r. <pr...@in...> - 2002-01-10 07:35:45
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> Maybe the path where pymol expects other > packages is hardcoded into its source? GNU-Darwin has a unique PyMOL installation method, but it follows standards, and I'm expecting that it will be adopted by the other distributions eventually. The pymol executable is actually a shell script (pymol.com) that is installed in /usr/local/bin. I believe that you can edit this script to change the PYTHON_PATH variable to the Fink installation path. If you really want to use Python from the Fink with PyMOL, then you might consider copying this file to your home directory and editing it there, so that it does not get overwritten when you upgrade PyMOL. > > I also had to install py-pmw with pkg_add and I then moved it to the > site-packages directory from python. I'd be surprised if the Fink doesn't provide Megawidgets ;-}. Sorry, but I also find all of this a little amusing, because it seems like alot of work to use the Fink in this case, when GNU-Darwin was truly built as a PyMOL installer. You should note that the PyMOL developer, Warren Delano, intends to base his OSX development efforts on some of the GNU-Darwin tools. The situation is somewhat similar with CCP4, Raster3D, and many other major projects as well. http://www.ccp4.ac.uk/problems/ccp4onMacs.html http://www.ccp4.ac.uk/ccb/ http://www.bmsc.washington.edu/raster3d/r3d_FAQ.html#PC Although GNU-Darwin is a free software distribution, it was founded to build the infrastructure for molecular graphics and crystallographic computing. http://www.newsforge.com/article.pl?sid=00/12/01/2028254&mode=thread http://www.gnu.org/brave-gnu-world/issue-25.en.html PyMOL provided the impetus for GNU-Darwin to go Beta so that users would have a user friendly way to install PyMOL. I believe that our distribution will emerge as the primary free software distribution for biotechnology in general, and PyMOL support will be a crucial part of that emergence. I have the utmost respect for the Fink project and their free software offerings, but it will never meet the standards that we have set in this arena, which is mission-critical for GNU-Darwin. The Fink has nothing like this... http://gnu-darwin.sourceforge.net/gdc/mol.html or this, http://gnu-darwin.sourceforge.net/art.html or this, http://gnu-darwin.sourceforge.net/gdc/ccp4.html and it probably never will. (Heh, I bet there will be Fink PyMOL and Megawidgets right away now! ;-). > Finally, I installed povray with Fink, > if I give the command 'ray' in pymol it works. Here again is a problem. ray by itself invokes PyMOL's own internal rendering engine. You need to add an argument to ray to invoke POV-ray as an external rendering engine. PyMOL-0.7.3 is requred for this. Type "help ray". I believe that PyMOL looks for x-povray in the PATH variable, so that the Fink's non-standard installation directory should not matter in this case. Sorry, if this seems tedious. I really love the Fink as a fellow free software project, although I do not use it myself for anything. GNU-Darwin is sufficient without the Fink. TDC is sufficient. It gets tiresome answering questions about the Fink all the time, and I do not believe that the others on the GNU-Darwin list are interested. The GNU-Darwin infrastructure was built expressly for projects like PyMOL. If you want to use GNU-Darwin PyMOL, then I highly recommend using the GNU-Darwin packages that were built to support it (instead of the Fink). Be sure to consult the PyMOL documentation. Warren has done an excellent job with the PyMOL website. I printed out a color copy of the manual. It's so beautiful. http://pymol.sourceforge.net/ Regards, Michael L. Love MacCHESS Cornell University http://www.gnu-darwin.org/ -- Visit proclus realm! http://proclus.tripod.com/ -----BEGIN GEEK CODE BLOCK----- Version: 3.1 GMU/S d+@ s: a+ C++++ UBULI++++$ P+ L+++(++++) E--- W++ N- !o K- w--- !O M++@ V-- PS+++ PE Y+ PGP-- t+++(+) 5+++ X+ R tv-(--)@ b !DI D- G e++++ h--- r+++ y++++ ------END GEEK CODE BLOCK------ |
