Hello PyMol and APBS communities,
I am here to report the successful compilation and installation of APBS
on a Macintosh (Powerbook G4, OS X 10.3.5, XCode1.5, gcc 3.3 20030304
(Apple Computer, Inc. build 1666),g77 3.4.1, and Python 2.3.3), and
integration with PyMol via Michael Lerner's APBS plugin for PyMol. I
thought I would just tell people of my experience and spread the good
word that electrostatics are possible on a Mac.
I first installed the 0.97 version of PyMol via fink as per Bill
Scott's instructions:
Hi Folks:
Thanks to the efforts of Jack Howarth, who has volunteered to maintain
the pymol package in fink, we now have an up-to-date version 0.97 of
the x-windows pymol in the 10.3 unstable branch of fink (or will as
soon as cvs updates it -- usually within 24 hours or fewer).
If you don't have the unstable branch activated, the easiest way to
install this is to do the following:
sudo mkdir -p /sw/fink/dists/local/main/finkinfo
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol.info
/sw/fink/dists/local/main/finkinfo/pymol.info
sudo ln -s /sw/fink/dists/unstable/main/finkinfo/sci/pymol.patch
/sw/fink/dists/local/main/finkinfo/pymol.patch
fink install pymol
I had some problems with this step because I had several versions of
Python installed via fink. Although the actual version in my path was
2.3.3 there must have been several librarys, etc that were lying around
my /sw/ folder and these were being referenced during the pymol compile
resulting in an unusable pymol binary. The solution was to completely
uninstall all fink versions of Python and reinstall only python23.
I also had a previous version of pymol.info and pymol.patch (0.86 I
think ) already in the unstable branch of /sw and when I did a
selfupdate-cvs I don't think the newer 0.97 version of pymol.info and
pymol.patch were being downloaded. I eventually had to delete the 0.86
version of pymol.info and .patch and ran selfupdate-cvs again. Then I
followed Bill Scott's directions above, and everything worked fine.
Thanks again to Bill Scott for the fink install scripts for maloc and
APBS. I have been playing around with this on and off for a few months
and although I have been able to compile and install maloc I was having
problems with APBS.
Hi folks:
I was alerted to the fact that I made a mistake in my original fink
install scripts for apbs and its dependency called maloc. The
corrected ones are here:
http://chemistry.ucsc.edu/%7Ewgscott/fink/info/apbs.info
http://chemistry.ucsc.edu/%7Ewgscott/fink/info/maloc.info
I can't put these into fink because apbs requires a password download
(sorry) so you have to download these scripts manually and put them in
/sw/fink/dists/local/main/finkinfo and download the source code for
apbs and put it into /sw/src .
The only problem I had was that the name of the source file in Bill
Scott's apbs.info file was apbs-0.3.1.tar.bz2 and the source file that
I downloaded from the APBS site was apbs-0.3.1.tar.gz. So I changed the
name in the apbs.info file and although fink complained about the
checksum size I just told it to go ahead and compile anyways.
Everything went smoothly.
Here's another Thank You to Bill Scott, Michael Lerner, Jack Howrath,
and Warren Delano.
Scott
Scott Classen, Ph.D.
ACS Postdoctoral Fellow
Department of Molecular Cell Biology
University of California, Berkeley
237 Hildebrand Hall #3206
Berkeley, CA 94720-3206
LAB 510.643.9491
FAX 510.643.9290
