Hello Jim,
I have downloaded the version (0.79.dmg.gz) of the PyMol package
suggested by Luca Jovine, but don't know how to get a working version of
Python installed. The only links I can find are to Python .exe files for
versions 2.1 and 1.5.2, and I have no idea which of the other downloads
(xx-contrib, ext) are needed. For that matter, is the v. 0.79 really the
latest for OS X, or is 0.82 or 0.83 options? Which Python will run in
the Mac Unix environment and how do I invoke it (presumably from the
terminal) if it will? You (W. Delano) make it clear that running PyMol
within Python is not the way to go, then in the Mac, what is? I also see
no links to documentation, nor do I find any obviously labeled
documentation files in the download.
At least in my opinion, the easiest way to get python and many other UNIX/
X11 packages on your machine is to first install Fink. This is a package
manager that will allow you to first install and then update (when
required) almost anything else you might ever want to use. To learn how to
do this, please have a look at: http://fink.sourceforge.net/index.php
After you installed Fink and then python through Fink, you can either
install and run the Xfree version of pymol, or run the native one, or have
both and run whichever you like to depending on your particular needs. The
speed of the native version certainly makes it much more usable than the
Xfree one, but, the latest version of the native program really is 0.79,
so (at least for now) you miss out on the latest features of 0.82. Also,
on my machine native pymol seems to freeze whenever I use the "show
surface" command, which works just fine on the slower Xfree version (is
this a problem of my particular setup, or did someone else also stumble
into this?)
In general, does anyone have any tips on finding needles of required
information in this massive haystack of a website? If you follow links
like "Mac OS X", you get dumped into a 10>n page listing of all
imaginable open source apps in reverse chronological order. Are there any
search tools or internal pages with links to documentation (maybe
something on the download page http://prdownloads.sourceforge.net/pymol
that I don't recognize as such?) Finally, there was a "somebody ought to
bell the cat"-type discussion about uploading "How TO?" files and
tutorials back in May - did anything come of that? A basic intro to
PyMOL is what I, a confirmed nonprogrammer (and damned proud of it) need,
no doubt like many others. Maybe some academics have already put
something like this together to prep strudents in their courses to use
PyMOL?
For pymol-specific info, have a look at Carly Huitema's tutorial at:
http://pymol.sourceforge.net/tutorial/index.html
which I found very useful as it nicely complements the manual:
http://pymol.sourceforge.net/html/toc.html
For more general information about installing crystallographic/structural
biology software on OSX, the best page I know is my friend's Bill Scott:
http://chemistry.ucsc.edu/~wgscott/crystallography_on_OS_X.html
his site has a lot of extremely useful information clearly arranged and
explained. Although it might not be directly related to what you want to
achieve at the very moment, it will certainly give you an idea of the
issues involved in installing and running this kind of software on OSX.
I'm sure things can only get better in the future, but in the meanwhile I
hope these pointers help a bit...
Luca
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Luca Jovine, Ph.D.
Department of Molecular, Cell & Developmental Biology
Mount Sinai School of Medicine
Annenberg Building, Room 25-18
One Gustave L. Levy Place, New York, NY 10029-6574, USA
Voice: +1.212.241-8620 FAX: +1.509.356-2832
E-Mail: lucajov...@mac.com
W3: http://www.mssm.edu/students/jovinl02
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