hate the mac

I'm working with my MacBook many hours each day. I love certain aspects of it, and overall, I think it's a solid machine and the most useful tool available for my job. But there are things about it that I just hate. And they drive me nuts because they'd be mostly easy to fix.

• The touchpad – This is so pathetic. Try using Illustrator with one mouse button, or PyMOL, or coot. I'm inclined to think it's possible, but I'm dead certain that you wouldn't want to because it's as productive as banging your head against a stone wall.
• The display – Now, I like the screen for its size and brightness, but I hate it for the fact that I can't open it as I like. Try working with the MacBook on your lap. In order to look directly at the screen and to get full brightness, you'd have to push the cover back farther than is possible. So you end up looking at the screen from a suboptimal angle, and the top half of the screen appears brighter than the bottom half, or the other way around, depend on your viewing angle. This might be because of the LED backlight.
• General sluggishness – Despite being three years older, my ThinkPad is much more responsive to clicks, there's no spinning ball of death, and I can flatten layers in Photoshop with Alt-L + F.
• X11 – What makes OSX so powerful is not the OS, but the X. You can relatively easily modify most of the serious software running under Unix and Linux to run under OSX. But why is X11 shipping with OSX not nearly as user-friendly as the one that came with RedHat 5.2, which I installed on my little Sony nine years ago? What happened to middle-click to paste? I why is it so poorly customizable? I would like the focus to follow the mouse. I would also like to see the individual X11 programs in the dock. Here, a lot of development work remains to be done, but I don't think Apple takes this seriously. X11 has been crashing left and right since OSX was upgraded to version 5.
• Transparency – Some people go off about how beautiful OSX is. I want my computer to be fast. For beauty I turn to women. So just give me the option to turn all this eye candy off.
• The keyboard – Whose idea was it to put the return key out of reach of my pinkie, and why is it almost the smallest key around? Apparently, this flaw has been addressed in the latest incarnation of the MacBook Pro, but there is still no forward delete key. Does anyone who designs this stuff actually use it?
• Preview Icons – What good does it really do me if the contents of a text file are previewed in its icon in illegible 0.25pt font? What's the point of icons if I have to look at the file name's extension to see what kind it is? I love clear and unambiguous Windows icons. Sometimes I get these with OSX as well, for pdf files, for example. But why do Illustrator files (*.ai) sometimes get a pdf icon?
• Microsoft Office – MacOffice on a blazing MacBook Pro is about ten times slower than Office XP on my old PC. MacOffice 2008 is supposed to fix things but is highly unstable. The blame lies squarely with Microsoft, and yet I hate the Mac for it because it's supposed to work splendidly.

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.

time machine

When I first saw the official video promoting OSX v.5 (take the tour), one of the things I was most impressed with was Time Machine, a backup solution that allows to you fly back through time and recover data in a very slick way. Now that my external hard drive has finally arrived, I can give this a try – and finally back up my main disk.

The first snafu was that the external disk came formatted in NTFS, which OSX doesn't like. It's mounted as read-only, and Time Machine refuses it as a backup device but offers to format it (ever the helpful assistant). I went with that, but only after burning the data on the drive, Maxtor's own backup software + manuals, to CD – just in case. Now the icon on the desktop doesn't show a USB drive anymore but a Time Machine Backup. I configured Time Machine for the initial full backup, but five hours later, when I was ready to call it a day, the job wasn't even close to done. I turned the computer off, to be continued the next day.

This day is today. I started my system and learned from the Time Machine entry in System Preferences that the next backup was scheduled to start an hour from now. Hallo Mac! There is no obvious way of starting things now. The obscure way is to put the Time Machine icon into the sidebar and right-click it. Backup now is one option, but returned an error, caused most probably by yesterday's unfinished job. Once all files were removed from the external drive, things started to move.

Unfortunately, they still moved only glacially. After two hours, not more than 4GB had been written to the disk. At this pace, my weekend would not start before Sunday morning. The solution I finally found in a macrumors forum involves excluding the backup drive from Spotlight and disabling the virus scanner's Safe Zones (both in System Preferences).

An hour or two from now, the initial backup should be finished and hourly incrementals will be created as long as I keep the backup drive connected. I hope this works smoothly even when file scanning is reactivated.

good and going

This is probably the last post in a while. I'm getting used to the MacBook. I took it home over Christmas just by sliding it into my backpack between t-shirts, chocolates and books. It's very slim indeed.

Before I fall silent, I can't help but ask what's up with the laptop's drives. I've mentioned the idiocy of a hard disk that's unchangeable by the average user's grandmother. The DVD drive presents another example. It doesn't have a tray that slides out. Instead, you slide the disk into a thin slit. All fine normally. However, when things don't go normally, e.g. when a disk is not recognized after being inserted, you have a problem. The disk that doesn't show up on the Desktop cannot be ejected, on my computer anyway. A friend told me that the button in the top right corner always activates the ejection mechanism, but that's not the case for me. There is no button on the drive, and there is no pinhole to force-open the drive. On two occasions (trying to watch pirated DVDs, admittedly), a had to shut down the computer to get things working again.

This is not something I do regularly and not something that will drive me up the wall. So, for the record, I go so far as to say that I'd love the Mac if I could pick my own hardware. If there were only one hundredth the number of OSX-compatible laptops as there are Windows-compatible machines, I'd surely find something right. With the operating system itself, I don't have major issues (short of a real Alt key that gets me into an application's menu bar quickly and easily).

And that's it, folks.

more lame things

I don't feel in a particularly grumpy mood today, but I still have the urge to empty loads of criticism and complaints over my unsuspecting Mac, on which I type this post, on top of all. I have been mostly happy with it, but there are aspects that drive me nuts.

Take the mouse. As mighty as it is, it is already ill-conceived and further proof that at Apple, design brutally dominates over function. When I work on my computer, the screen is much larger than the space for the mouse to roam available on my desk. It happens frequently that the mouse bangs into the computer or assorted stuff scattered randomly on the desk before the pointer reaches its target. If one lets go of the mouse button, the pointer releases and the entire action will have to be repeated. Any other mouse I would just lift by its sides while keeping the button depressed. The mighty mouse doesn't have sides. It's one big button. There is nothing to hold on to. Well, almost nothing. I deactivated the fourth and fifth mouse keys, situated laterally on the body of the mouse. They now give my fingers traction and let me cover larger distances in limited space. That's not what Apple had in mind.

Another thing is the remote control. Nice to have a thought, really cool for presentations. However, Apple, having recently rebranded itself into a life-style company, supports only music, videos and photo slide shows, but not presentations. For that, one has to buy a third-party giffy. I might do that because presentations are a big part of my job, but I resent Apple for not offering the feature in its operating system.

That the laptop gets hotter than my Passat's engine used to when its head gaskets were blown doesn't bug me so much. After riding my bike to work through the London rain, at least I can dry my pants by putting the MacBook on my lap. It's not hot enough to burn through denim.

the big picture

Three weeks into its existence, this blog is clinically dead already. I'm not a fanatic in any way. A computer is a computer, and I can get along with anything that thinks in numbers. The Mac is a different kind of machine in many respects, but at its hearts, it's all zeros and ones.

I installed some crystallography software without much trouble but also without much passion. I'm not doing crystallography yet and haven't encountered the true challenges, either in the lab or on my desk. I can say that PyMOL is faster than ever. Making figures will be a snap.

What is going to keep me busy, on the other hand, is a humongous squat grey box with two silver buttons that's been occupying the better half of my desk for two days now. It's a Nikon Coolscan 9000 ED, the best film scanner there is. I used to shoot slides when I still owned my faithful 8008 SLR and loved the simplicity of the normal lens, the brightness of the viewfinder, and the air of superiority slides gave my photography. No more holiday snaps on negative film. Then came digital, and everyone started sharing memories. Mine were safely stored in three cardboard boxes.

This morning, some came out for the first time in four years. I slipped five slides onto the scanner's black tongue and stuck it into the opening at the front. After two-and-a-half hours, the scan was done, and I had five files on my hard drive. The images are brilliant, colorful, and extraordinarily clean, but the quality comes at a price. I'm not just talking about the scanner worth twice the MacBook Pro. No, each file weighs in at 24 megapixels and 136MB. More than one film won't fit on one DVD.

If I get the settings right, I should be able to dramatically cut down on the scanning times. Sixteen-fold sampling might just not be necessary. I had started out with only one slide, playing with the options, activating this and that and comparing the results. In the end, I decided for the all-out assault, to get the maximum I could because telling which scan was best was impossible on the PowerBook's LCD screen. Not only are LCDs notorious for their poor color reproduction, my screen is also LED backlit. While this technology is easy on the battery, it's much harder on the eyes. Lightness is far from uniform and colors seem to come and go. I couldn't even tell which black was the deepest.

Good thing there is no danger of the scanner moving anywhere in the near future. I have all the time in the world to feed it one handful of slides after another until all memories are ready to be shared. Maybe I'll even have a scientific break-through to report by the time all is done.