Extracting 3D coordinates from PDB files with Groovy CDK

BioStar featured a question today about how to extract 3D coordinates from PDB files . Now, a simple script may actually do, and BioJava was mentioned too . Of course, it can also be done with the CDK . For example using this Groovy code:

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GitHub Tip: download commits as patches

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

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My professional network (according to LinkedIn)

LinkedIn has a nice new visualization app, InMaps. I quite like LinkedIn, though not all aspects, but most anyway. I particularly like it focuses on work-relationships. This new app visualizes my professional network, and colors it by network organization:

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"Atomic weights are not constant" !!!

In case you missed it, “standard atomic weights are not constants of nature” (doi:10.1351/PAC-REP-10-09-14)! Wow, chemistry upside down. This is bigger than the new arsenic life they found!

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GitToDo Install Guide #1: the command line utilities

Some years ago I was in need of a todo list tool. Of course, the requirements were simple: distributed, version controlled, command line support (I must be able to access it with minimal requirements). I also hooked it up with the Freemind mindmapping tool. I am in the process of installing it on my new laptop, so thought a walk-through might be useful.

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Is Nature really clueless about Blogs, Twitter, etc? WTF ?!

My apologies for this rant in the early morning, but WTF?? (what the fuzz??) I just got pointed to this Peer review: Trial by Twitter (doi:10.1038/469286a) by Mandavilli. Cool title, but before I even finished seventeen words of the intro… WTF?? Here it is:

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Re: How can cancer research be open-sourced?

Mark asked on Quora on how can cancer research be open-sourced. So, far I found Quora to be rather noisy, even after signing up only to science related groups, themes, whatever it is called. However, every now and then there is an interesting question like this one.

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