Molecular Graphics Display on OS X

Hardware:

David Gohara has figured out how to use SGI dialboxes with Apple computers.

Powermate dials (see below) can also be used for dials.

Stereo is still the biggest single shortcoming of the Apple platform for crystallography. Someday we would like to have LCD stereo on OS X.

Well, that day is apparently today! Stereo in a window (requiring a CRT) has arrived.

Software:

a. If you need rasmol , issue the command % fink install rasmol

b. A nice OS X native alternative is iMol. More info here .

c . O : Alwyn Jones's full-featured molecular display, building and editing program I think was the first piece of crystallographic software to run as a native OS X application. He updates this regularly. . Here are my directions and suggestions for installing on OS X. I installed into /usr/local. Gamepads and dials can be used as input devices. I bought (on his suggestion) a PowerMate dial and configured it as described here.

d. Molmol : You can download an X-windows based binary file from here or install and compile it with fink.

e. PyMol : Two versions are available, OS X native and X-windows based. The x-windows based version is available just by typing % fink install pymol . You need Apple's X11.app to use the x-windows based version; otherwise the display is too sluggish to be usable. More details here. I now use it with a PowerMate dial and configured it as described here for x, y, and z rotations and translations. This forced me to do a little bit of python scripting.

f. You may also wish to install povray, which you can also do with % fink install povray .

g. Ribbons : An OS X port is available for download and installation here . You need to register first, as described on this page.

h. Chimera is a highly extensible, interactive X-windows-based molecular graphics program. An OS-X native version is promised for the future. Chimera is the successor to UCSF Midas and MidasPlus; however, it has been completely redesigned to maximize extensibility and leverage advances in hardware. It is also python-based.

i. OpenDX extension modules (xtm) for crystallography. You can use fink to install this following my directions here.

j. Deep-view Swiss PDB viewer is now available as an alpha-release.

k. Raster3d can be installed with fink via the unstable branch of the distribution.

l. VMD (Visual Molecular Dynamics). VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

m. The popular crystallographic molecular display program Xtalview is now available for OS X.

n. Bobscript, Robert Esnouf's extensions to Molscript, version 2.6b was kindly compiled for OS X by Evan Kantrowitz.

o. A new graphics display and crystallographic object-oriented toolkit (Coot) is now available via fink.This is in fink unstable, along with a bunch of dependencies (clipper), mccp4, etc, and you will go nuts unless you temporarily activate the unstable branch of fink to install this. I've made a COOT installation page that describes how to do this. In addition, you can get a version of coot compiled for OS X that works with SGI dials from David Gohara's website.

p. CCP4mg (the CCP4 molecular-graphics project) is a self-contained OS X application installation available as a download from the York website.