tips and tricks

Continuing from yesterday, thanks to Dave Gohara my USB-to-serial adapter is now working. All it took was the driver downloadable from his web site. In the package is a little script that lets you verify that the dials are recognized and in working order. That worked for me, but I haven't had the opportunity to try them with real software yet. PyMOL apparently does not support dials, coot might require some tweaking, and O I haven't even installed. Fine, off to further issues.

Trying to compile blt (a requirement for ccp4), I kept running into a host system not recognized error. In one of the configure scripts, there was indeed a host variable that was left blank. How do I know which system name to use? Well,
/usr/share/libtool/config.guess
told me. It's i686-apple-darwin9.2.0. Good to know.

Another thing that annoyed me for a while is that Time Machine only shows visible folders. For reasons unknown to me, UNIX-related system file, i.e. things normally residing in /usr/, are hidden. How do I restore them? I can get to them in a shell, but not in the Finder window Time Machine proudly presents. Typing
defaults write com.apple.finder AppleShowAllFiles TRUE
and restarting the Finder (Option right click - Relaunch) remedies that. It would be nice if this could be set as default whenever Time Machine is launched in restore mode. But that would be a little bit too much customization for a Mac.

projects

The MacBook is running smoothly. Being the restless person that I am, smooth operation has never given me reason to lean back and enjoy but rather to tinker and play. After connecting the external hard drive for backups and the 24-inch screen for wowing visitors, SGI dials are next.

This peripheral was originally manufactured for Silicon Graphics workstations and allowed a user to rotate and translate objects on the screen around and along precisely defined axes, normally x, y, and z. We use it a lot for molecular graphics. Rotations and translations can of course be accomplished with the mouse, but the molecule will sooner or later tumble from its original orientation. Moving back is never the exact inverse of going forward with a mouse. With dials, no problem.

Since they date back to the stone ages of computing, older even than O2s, connecting them to modern computers is tricky. They come with a serial cable. The MacBook doesn't have a serial port. David Gohara describes how to get it all to work in theory. I decided to follow his instructions, downloading USB-to-serial adapter and dials drivers.

I got the adapter from digitus. The driver supplied with it does not work on Intel Macs. For some reason, David Gohara's generic Prolific (maker of the chip in the digitus adapter) driver (v. 1.0.9b1) doesn't work either, though I'm not sure why. I managed to get rid of the drivers by deleting them from /System/Library/Extensions. Apparently, that's all it takes. Installation, by the way, is a bit more involved and requires rebooting. With kextload' and 'kextunload' one can load and unload extensions, except I cannot load the extension because it 'does not contain code for this architecture' and unloading simply fails, presumably because nothing is loaded in the first place.

I hope I can continue this post with a successful continuation at some point. Until then, this is work in progress.