On Apr 3, 2009, at 3:05 AM, Simon Kolstoe wrote:
>
>
> 2) To point imosflm to this version of Tcl/Tk the line "export
> MOSFLM_WISH=/usr/local/X11/bin/wish8.4" needs to be in a file
> called .bash_profile NOT .profile for some reason (but not if you
> are using an X terminal in which case you need to use .bashrc)! Can
> any mac experts explain why there are so many options?

On normal X-windows-based unix systems (linux, the late irix, etc),
the root window sources .bash_profile and then subsequent windows
spawned from this are all created as sub-shells of the root window and
run .bashrc. Since they are subshells spawned from the root session of
bash, they inherit whatever was in .bash_profile. So in general, a
new bash shell will run one or the other of these files but not both.
(As far as I know, this is unique to bash; zsh and tcsh at least don't
appear to do this). X11 on OS X doesn't have a root window. xterm
doesn't know this, and only runs .bashrc. Other terminal programs
seem to run one or the other in a somewhat obscure (at least to me)
logic, but the main point is only one or the other file gets sourced.

On OS X, the safest thing to do is put everything into .bashrc, and
then in .bash_profile, put in the line

source ~/.bashrc

This confusing behavior alone makes me wonder why on earth Apple would
choose bash to be the default shell. I think it should have been zsh,
which combines the user-friendliness of tcsh (actually it is much more
so) and the functionality of bash/ksh. In zsh, anything in .zshrc
ALWAYS gets sourced unless you invoke it as /bin/zsh -f (as you would
in a shell script) , and anything in .zshenv ALWAYS gets sourced, even
if you invoke with /bin/zsh -f . Hence no unwelcome surprises.

Here's a bit more:
<http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Unix_and_OS_X:_The_Absolute_Essentials#Unix_Shells_on_OS_X
 >


>
>
> 3) Thanks to everyone who suggested I forget trying to install it
> myself and just use Bill Scott's fink installation, BUT what happens
> if someone like Apple offers Bill a large crate of beer and he
> decides to work for them instead of maintaining his crystallography
> software support? It has concerned me slightly how much mac users
> seem to rely on just one member of the community...

It would be a valid concern if the premise was correct, but there is
very very little that relies on me being alive tomorrow. Fink is one
of several options to install 3rd party unix software on OS X using
(in this case a Debian) package management system. (It isn't "mine.")
Although I maintain a few packages, I am not a "core" member of the
fink team, and people come and go all the time. There is no guarantee
OS X will much outlive Steve Jobs for that matter, or that the economy
won't collapse to such a degree that we will all be pushing around
shopping carts a year from now. Fink is simply a tool to assist those
of us who don't have infinite time to devote to sys admin tasks, but
it is by no means essential. It is simply a software management tool
that has benefitted greatly from the voluntary collaboration of many
in the community. The tcltk package in fink was originally ported to
os x by a guy at NOAA, for example. In the case of coot, I would find
it impossibly complex to install without the aid of fink, implicitly
incorporating the knowledge and help of many highly knowledgeable
individuals who maintain the packages for the hundreds of
dependencies. But you should feel free to install software in whatever
way you find to be the most convenient. CCP4 distributes their own
binaries, so if that is all you need, there is little reason to do
anything more than download and install their stuff.

Although I do occasionally have hallucinatory delusions about finding
a job that would pay enough to enable me to send my kids to college
someday, I think the chances of me getting hired away by apple are
about as great as me getting pregnant. I will confess however to
having now arrived at the point where, if I didn't have a family to
feed, I would be very tempted to sell the dog, flip the bird to the
funding agencies and back-stabbing "colleagues," and ride the mountain
bike off into the sunset. But, alas, no such luxury... Helping out
(real) colleagues and friends to the small extent that I have been
able gives me a great deal of satisfaction, so I wouldn't worry too
much. Besides, if an idiot like me can do this, anyone can.

Peace and joy,

Bill



>
>
> Simon