Author Archive

Canon Pixma ip4200

13 March, 2006

I finally bit the bullett and bought myself a new printer. The last new one I’d bought was a HP Deskjet 815C, sometime around 1999 so I was really impressed with how far the technology had come. I was used to inkjets skewing the paper with a dodgy feed and then leaving large lines through any section of colour.

This new (and cheap) Canon is nothing like that. It has a cartridge feed underneath in addition to the “normal” feed on top and all of the various places where dust can potentially get in fold up. The photo printing is also excellent. Using Canon’s expensive Photo Paper Pro produces results far in excess of most places you’ll find in town. I also like the 5 different colour tanks – should be much cheaper when I run out of ink.

Now for the bad points, the photo paper is really really expensive. It’s much cheaper to order prints online and wait a few days. Secondly the software for the Mac is terrible. I can’t seem to make the proper adjustment to get iPhoto to print at the correct size so I have to use Canon’s own software. This software is very different to the usual Mac UI and it’s quite painful to use, plus you can’t drag and drop images into it. I need to export my photo from iPhoto to the desktop, then load it into Canon’s print software and go through a nasty Windows-like process before finally getting the document to print. The provided help files (no printed manual BTW) are specially prepared for the Mac, pity they just don’t load into the help viewer. I found that if you use finder to view the conents of the bundle you can eventually find some html and view that – ugh!! The installer also dumps an icon for the help on my desktop – double ugh!!

So, short summary. Very nice hardware, very poor software.


Google Mars

13 March, 2006

My good friend tyme pointed out the new google map of the surface of mars to me via IRC. It’s colour-coded by altitude in a way that reminds me of a fractal. I think it’s pretty cool, although there’s not really a lot to see if you’re not into astronomy.

Cleaning out the cobwebs

13 March, 2006

Geez, I’ve left this place unattended for a while – I guess I should post something of an update.

My viva has been and gone and I now hold a PhD, I sometimes wondered if it was worth all that time and effort when I could have been out in the real world making some money but now I have the degree and a nice postdoc position I’m very happy about it all. I guess that I’ll be much happier in this line of work than if I was working in a bank or as a code-monkey somewhere.

My postdoctoral work is investigating how anti-cancer pharmaceuticals interact with DNA, which obviously involves much larger systems than my PhD work. The ideas that we have also mean that I’ll be doing some coding, it’s ages since I’ve written anything so I’m looking forward to it.

I’ll try and post more regularly, but no promises!

ACS now offering RSS feeds for journals

11 January, 2006

RSS has really changed the way I use the Internet, updates of my favourite sites are delivered at customisable intervals and it makes catching up with all the news (most decent forums offer RSS feeds now too) easy.

The good news is that the ACS are now offering RSS feeds of articles ASAP and the TOC alerts for all their journals.

If you’ve never used RSS before, there are some basic capabilites built into some browsers such as Firefox, but I personally find it much easier to use a dedicated aggregator (more like an email client than a web browser) – the following free (as in no money-cost) aggregators seem good to me:

Update: The ACS just don’t seem to get RSS. The feeds tend to get a couple of hundred entries per day, many of which are simple refreshes from the days previous – that’s very likely to cause me to hit the “mark” all as read button!

Webmo as a teaching tool

20 December, 2005

A new version of webmo has been recently released. For those of you unfamiliar with this piece of software it is a web-based front-end for several QC codes such as Gaussian and Molpro.

As part of the my teaching responsibilities in my new post I’ve had to “demonstrate” in the BSc and MChem practical sessions for molecular modelling where webmo is used. I must say that I was very impressed with it, as it is accessed with a web browser it’s OS agnostic and allows students to start running some calculations quickly. Whilst a student undertaking a final year project may benefit more from learning some UNIX and actually looking at the input and output files from QC codes, webmo seems ideal for one-off practical sessions or as part of a short course in QC – the graphical output allows for an easy intrepretation of results, and there’s no need to explain z-matrices as the GUI does a reasonably good job of allowing you to draw structures.

There’s a demo version (free to use) on the webmo website, and the software itself is available in both free (reduced features) and paid for (as Webmo-Pro) versions. I’d recommend anyone undertaking any QC work to check it out.

Schrödinger Maestro free for academic use

13 December, 2005

Schrödinger Inc are offering their molecular mechanics program maestro free for academic use. Although I personally don’t carry out any molecular mechanics calculcations as part of my research (yet), I thought it was probably worth grabbing a copy and giving it a go – it may be handy for producing starting geometries for QC calculations.

First impressions are that it’s quite difficult to use and the demo from the help menu is almost pointless, I was expecting some kind of tutorial to show me how to run calculations and instead I got the program doing various things on it’s own that you couldn’t interact with. Still, it seems capable of producing some really nice images so it may be worth a longer trial.

Density functional repository

29 November, 2005

I stumbled across this site today that acts as a repository for Fortran 77 subroutines that describe density functionals for use in electronic structure programs. The site is associated with the CCLRC so I assume these are the subroutines (or very close to them) that are used in GAMESS-UK.

Looking at the source code it seems that the subroutines have been generated automatically with Maple and the dfauto script that has been described in Comp. Phys. Comm. It may just be the computer/maths geek in me, but something about that seems very cool.

GOTO BLAS libraries make slashdot

28 November, 2005

The GOTO BLAS libraries have been mentioned on slashdot (and on the new york time website). I’ve been using this library for quite a while now and I’ve seen massive improvements in the speed of several codes (including the venerable Gaussian). I can really recommend them to anyone trying to save a little time with code that relies on BLAS or ATLAS.

Glad to see the author is getting some much deserved credit for his good work.

What is an orbital?

22 November, 2005

I thought of this interesting question today – “what is an orbital?”

I asked it to the various PhD students that I share an office with and it made some of them squirm, the answers ranged from the (hopefully) humorous – “they’re a bit like a donut”, to the not bad – “area of space within which there is a certain probability that an electron can be found”. I should probably state that none of these match what my answer would be.

The responses made me wonder if some of the frankly bizarre posts on CCL about how nothing meaningful can be obtained from orbitals (a purely mathematical construct) and only the electron density should be used stem from not properly grasping what an orbital (in ab initio theories) is?? Is this a deficiency in how QC is taught / what’s written in texts?

It would be interesting to get a few comments about how readers would answer “what is an orbital?”


16 November, 2005

I’ve found this great food blog called delicious.days. I know the links between chemistry and cooking aren’t all that great (sorry Heston Blumenthal), but hopefully some people out there will enjoy it! If you don’t like the food articles at least you should be able to admire the brilliant design of the site.

I particually liked the entry on the silver spoon, an Italian cookbook – check it out!!