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.

function follows form

Contrary to what they teach you in school, there are aspects of the Mac that suck. It might not be as bad as it was just a few years ago – and it's certainly much better than in the dark ages before X and Intel – but deep flaws and botches remain. The supremacy of design over engineering is the most notable.

Apple professes to live by the philosophy that simpler is better, or at least simple is good. Well, try changing the hard drive in the MacBook Pro and see if you agree with Apple's definition of simple. The drive sits in the corner of the machine. A little sliding door of the kind that any other laptop has would have allowed users to swap it easily. But there is no opening. The aluminum case wraps tightly around the innards of the computer. Thus, removing the hard disk requires loosening about three dozen screws in a process not unlike complete disassembly.

A second problem is also related to the slick edgeless case. One can only open the display screen to about 100 degrees. If the computer is placed on a low support such as a coffee table it's impossible to get a good viewing angle short of bending down like the Hunchback of Notre Dame or boldly placing an triple chocolate chip cookie or two underneath the front of the computer. Given how hot the laptop gets underneath the second rigging would quickly melt to gooey black disaster.

Function follows form even in peripherals. Take a look at the Mighty Mouse. (Read this review first – no, seriously.) Pretty, ey? Anyway, the mouse is indeed pretty sweet. Bluetooth connects it with any computer (so equipped, eg. my ThinkPad), the laser makes for accurate tracking, and the three buttons and the scroll wheel are all there. However and in contrast to my hands, the mouse is perfectly mirror symmetric. And while there are quite a few mice out there that aren't either, they don't have a double squeeze button to the left and right sides of the mouse's body and claim that's a functional addition. I have only one thumb on my hand and lack the dexterity to squeeze and click in the same position.

simple things

A friend told me yesterday that the root account in OSX is disabled by default. As I'm used to Linux, this seems very bizarre to me. Apparently, it's designed that way so as to not confuse the millions of Apple lemmings for whom a root is only something that might trip them on the race to the cliff where the next gadget is waiting. Anyway, this account can be activated. I don't know how yet, but I'll find out.

The same friend gave me company last night. We had what might not unreasonably be called a geek date, setting up and testing Bluetooth and Bonjour file sharing, hostile desktop take-over, video chat with iChat with our google accounts, and more. All worked flawlessly, once we had deconvoluted the half dozen networks flowing through the air simultaneously.

I was impressed with iChat, which was simple to use and very capable with the camera built into the frame of the screen, though screen sharing was furiously confusing and theater mode suffered from poor image quality. If you use certain distortive effects, you will inevitably make your counterpart burst out laughing. Great for making up after a fight.

Other things are, despite Apple's unrelenting marketing and the lemmings' fervent belief to the contrary, very far from simple. Try resizing windows. Assume your window is in the lower right corner of the screen and you want to extend it to the top left. What's the simplest way of doing this? Apple thinks moving the mouse to the title bar, clicking and moving the window to where you want its top left corner to be, releasing and moving the mouse to the bottom right corner, clicking again and resizing the window to where the bottom right corner was when the whole operation started. Fair enough?

Keyboard shortcuts are an ambiguous matter. They are designed to make you work more efficiently. I love Option-U to get umlauts. Then there are old standards like Apple-S to save, Apple-P to print, stuff like that. Works as long as things don't get too complicated. Under Windows, the only three-key combination in my repertoire is Alt-Ctrl-Delete to bring up the task manager. There are others like Context-W-F, which creates a new folder, something I would love to be able to do quickly but could never be bothered to remember. Apple takes it one step further. There are several four-key combinations like Shift-Command-Option-Esc to force quit the current application or Control-Option-Command-Eject to shut the system down promptly. I might even try to remember these two, but I'd argue all the while that their complexity is a bit excessive.

Lastly, and I present this as a good thing, I've found the combination that emulates the delete key. Press function and backspace simultaneously to get the desired result. Wouldn't having a dedicated key make this a bit simpler? I'm just glad they didn't emulate A by pressing fn B.

X's not Linux

After more than eight years with Linux, making sense of OSX is difficult. The system seems obscure. Many things are implemented differently, presumably to make things simpler. That's Apple's company policy, anyway.

In the Unix world, every system has a superuser called root. OSX has one also. So it says in /etc/passwd. However, the user is never prompted to give a root password. Is there not one? How do I log on as root?

I tried su - but couldn't get in. Then I created a superuser account called 'super'. I can now log on with su super but don't get very far. shell-init: error retrieving current directory: getcwd: cannot access parent directories: Permission denied is what is echoed upon logon. Who's denying the superuser permission? I try to change directories but nothing happens. Instead, another error message: chdir: error retrieving current directory: getcwd: cannot access parent directories: Permission denied.

Are things just not working, or has Apple reinvented the wheel? And why does the screen go dark after thirty seconds of inactivity? Try reading an article. It's unbelievable annoying, but I have no idea how to change that.

tap and scroll

To install Leopard, I have to click through a few screens answering questions such as "Which of your one hard drive do you want to install Leopard on?" I can then select the components I want to upgrade. Anyway, that's what another screen promises. I choose 'customize install' and am rewarded with ample selections, almost all of which are greyed out. Among them X11. It is selected by default and cannot be removed, and I am forced to upgrade to a buggy version of program which is running just fine at present. In the knowledge that I'm using a superior operating system, not only the best in this world but also in any other imaginable world, past present or future, I suffer silently and somewhat proudly.

When all is said, I send the install off by clicking OK. Oops, didn't work. I tap again. Still nothing. One of the first things I did when I started working with the Mac yesterday was activated tapping, clicking the touchpad with your fingers. I was excited when I found this feature available. The Mac doesn't like it and has already swallowed it. It might come back when all is done, but at the end of the day, the Mac's touchpad will remain brutally crippled, a faint shadow of what could be possible.

There is the issue with the lacking buttons, middle and right. Many lemmings devoutly belief that one mouse button is not only enough but simply more ergonomic and infinitely less confusing. Apple thinks so too. Curiously, when they invented the scroll mouse, they hid extra buttons underneath its smooth white skin. In my opinion, what resulted was the first usable mouse Apple had ever produced.

I need mouse buttons for fast work. Why cannot someone slip this extra functionality underneath the smooth silver skin of the elongated button of the MacBook's touchpad? I'm not asking for it to be marketed as the next revolution in personal computing. It doesn't have to be active by default. It shouldn't even be easily activatable lest the orthodox get confused. But if there could just be an unadvertised, well-camouflaged customization, a command-line jiffy allowing those who think different to degag their touchpad, I'd be eternally grateful.

The lemmings are happy with it as it is, even exuberant and happy to share their excitement. I was asked yesterday if I had already discovered two-finger scrolling. Two-finger scrolling, I was wondering? Why do I need to fingers to scroll? The Sony Vaio I bought almost nine years ago had one-finger scrolling, and so does the Thinkpad. Those who can't handle two mouse buttons readily use two fingers to scroll? I just don't get it.

As the install takes longer than even Fedora 7 the other day (Why exactly is verifying the integrity of the DVD mandatory?), I'm writing this post on my Thinkpad, immensely enjoying the luxury of a delete key and a right button on the touchpad. I scroll down and hit 'Publish Post'.

works out of the box

Fifteen minutes after the first power-up, the computer is humming away, and pleasantly quietly at that. Just like the Thinkpad, if I remember correctly. And just as XP needed to be upgraded to Service Pack 1 shortly after I received the IBM, the Mac comes with an upgrade-ready operating system. However, the upgrade is not a few days in the future, it has already happened, and the Leopard DVD is part of the package.

May I ask what kept Apple's army of cheap Chinese labor from installing the latest version of the operating system? The computer was ordered after the revision came out. Is this an indirect admission of the bugginess of the latest and greatest? Caveat emptor? Only upgrade if you really know what you're doing?

At this point, I restrict myself to a system update. Almost twenty packages are found whose installation proceeds speedily. In the end I have to reboot the computer. Apple tries very hard to make the transition from Windows to Mac as smooth as possible, it seems.

I have heard that, to ensure a satisfying user experience, one should not upgrade X11. I decide to play it safe and go with Tiger's X. Finding the optional packages on the installer CD takes me a while. I hope I'll eventually get used to Finder. I make sure to back up /etc/X11 and /usr/X11R6 to override Leopards files later.

Following at the heels of X (and the instructions on Bill Scott's website) come the Xcode developer tools, apparently a set of libraries, weighing in at a portly two and a half gig, without which X isn't even remotely useful, at least if you plan to do crystallography. What an ugly monster of a sentence that was. Sorry.

Gary Kerbaugh's pkgdiff script verifies that the installation of X11 is complete. No problem here. No problems at all? Well, I still haven't found the delete key.

Speaking about deleting, how do I uninstall applications? I don't need an Aperture demo version, and I don't want to test drive Microsoft Office. There is no reason for these programs to clutter up my hard drive. Do I just pull the icons into the trash? I have to ask someone more experienced.

Now, I'm off to see the Leopard, the wonderful Leopard of OS (X). Keep your fingers crossed.

first steps

I did this yesterday, but hadn't decided on the blog yet.

I unpack the computer and turn it on. The very same moment, all color seems to fade from my Thinkpad running next to it on the desk. The Mac's screen is a beauty, caressing my feeble eyes with brightness and intense colors. The IBM looks very pale indeed. In contrast, the Mac's keyboard doesn't feel right. It's metallicky in a weird way, and not all keys are where they're supposed to be. The enter key is small and far away. I kid you not when I say that my pinky is wider than the key. I don't have fat fingers, either. The tilde migrated three rows down, presumably to be less overlooked. There seems to be no delete key, or am I just overlooking it?

Before I can use the computer, I have to go through a few screenfuls of configuration with lovingly animated transitions. Welcome to Macworld. "In order to gain access, please give us your name, address, telephone number, date of birth, bank information, credit card numbers and your favorite color." Does Steve Jobs really need to know all this? Apparently, because if I refuse intimate details, the whole process stalls permanently. Wireless configuration is just like under Windows. The same goes for the Mighty Mouse.

Finally, the system is up and running. I install Firefox and a few essential extensions, namely Greasemonkey, Adblock Plus and Chipmark. Why can't I seem to get rid of the Chipmark toolbar folder? I remember having had prolonged difficulties with this on my Thinkpad, but I eventually overcame them. Don't remember how, though.

how it began

Yesterday, I received a MacBook Pro. Today, I'm sitting on my sofa trying to make it work as I see fit. Upgrading to Leopard, installing crystallography software, recreating the most of what I got used and warmly attached to in three and a half years of XP and eight years of Redhat/Fedora. From what it looks like so far, progress is steady.

I haven't don't anything outrageous or stupid yet, and before, inevitably, doing so, I want to document my steps so I can later retrace them. Maybe the blog will also serve as a guiding light for other Mac neophytes

As the title indicates, I'm doubtful about the Mac experience. While the operating system might provide the best basis for doing serious science, the abundance of smug lemmings and their wisdom stuck up in holy traditions and their pathetic follow-the-leader attitude won't ever win my heart over.