OS X Crystallography Applets
Download a disk image (about 1 Mbyte) with them and put the
Xtal folder in /Applications or other appropriate
directory.
NEW: Make your crystallography applications
clickable!
If
you have ever wanted to click on your data files to see them
displayed, start CCP4i without a terminal, or drag and drop a CNS
input file to edit or execute it, here's what you need to do.
The
following description assumes:
(1)
You have X11.app installed and
running
(2)
You have the relevant software installed via fink (unless noted
otherwise)
If
you have installed into a different location than
/sw, you will need to edit a script inside the application
to make
changes.
These
are very basic OS X applications that you might find useful to run
some unix crystallography programs. I made them using a
freeware utility called Platypus, available from
here.
You
can put them anywhere that suits you. I recommend something
like /Applications/Xtal, and the descriptions below assume that
location, but there is nothing special about it.
These
are essentially wrappers to shell scripts that open and run
programs when you double-click them. However, they have two
other
advantages:
1.
You can drag and drop files onto them that you want to open with
the program. (Specific examples are described
below).
2.
You can use the Finder File> Get Info (or command-I) on a
selected file to set the program to open
it.
Examples:
ipdisp
allows you to either drag an image file onto it to open it up, or
else, in combination with the Get Info open-with option set to this
program, allows you to double-click on an image file and open
it.
(I
have made this particular version specific for ALS-type CCD images,
but by editing the file
/Applications/Xtal/ipdisp.app/Contents/Resources/script
you can set this with whatever flags you need. This is also
an easy way to make your own -- just copy the application, rename
it, and edit
/Applications/Xtal/yourname.app/Contents/Resources/script
to suit your
needs).
Here
is what I have made so far:
Please
feel free to suggest others or make your own and send them to me
for distribution to
others.
ccp4
--
ccp4i -- double-click this and it starts
ccp4i
(assumes ccp4 installed via
fink)
ipdisp -- drag and drop a CCD image (see above for other
options) to open it, or set it to open all your CCD images.
(assumes ccp4 installed via
fink)
molecular
viewers --
molmol -- double-click it to open, drag and drop a pdb file
to load that structure when opening, or set it to open specific pdb
files.
(assumes
molmol installed via
fink)
rasmol -- double-click it to open, drag and drop a pdb
file to load that structure when opening, or set it to open
specific pdb files.
(assumes
rasmol
installed via fink)
launch_o -- this
one isn't mine, and it is more versatile and programmable in that
it lets you set the path to where O is installed. It launches O,
and can also be enabled to do drag-and-drop, and supports
double-clicking a binary.o database file if you first set that file
type to open with this application. (The author is James Stroud.)
Download launch_o
from here.
cns
--
These
two are designed to work with the
Logan Donaldson distributed CNS
version that installs in /usr/local as well as the extra
hacks I put in. See
this
page for more
details.
cns_edit -- drag and drop an input file, foo.inp, and it
will open that file in the CNS web editor. You must
install one of my cns_edit OS X
hacks in order for this to
work,
available
here.
cns_solve -- drag and drop a foo.inp file to have
cns_solve execute it. This will first cd into the directory
in which you have foo.inp, and it will then execute cns. It
will produce a log file called foo.log in the same directory.
It requires CNS to be installed according to the instructions given
here.
Specifically, it refers to the cns executable in
/usr/local/cns_solve_1.1/bin/cns so you must either have a
copy there or a symbolic link to it with this name.
Alternatively you can edit the script file contained within.
Download a disk image (about 1 Mbyte) with them and put the
Xtal folder in /Applications or other appropriate
directory.
Back to
Crystallography on
OS X
