The Lure of the Sandbox
How a holiday lark became structural biology's Coot
A little over a decade ago, Paul Emsley, biochemistry professor at the University of Oxford, was looking to ditch his white coat. What he really wanted was to spend more time programming in the computer lab. “I was happy using existing software tools,” said Emsley, who had used O and other tools in his research. “But you go down the pub and think, if only the tool did this, and if only it did that. That festered for years.”
In the late 1990s, Emsley had the opportunity to join the lab of Kevin Cowtan at University of York with the task of implementing software to perform crystallographic “ridge line tracing” in three dimensions, a concept first imagined in the 1970s by Johnathan Greer, now Director of Structural Biology with Abbott Global Pharmaceuticals.
Early on in this work, and at the beginning of a Christmas holiday, Emsley realized that he wanted his program to be visual, to show the molecules, electron density maps and noncrystallographic symmetry. “There was no easy way of showing these with other people's tools,” says Emsley. “I spent that holiday playing with this idea, and I have just not stopped playing.”
That holiday's work eventually produced Coot.
Since then, Emsley, along with other contributors including Cowtan, have continued to expand Coot. It includes a feature similar to the Lego-like fragment selection tools in O. Coot also includes a novel way of representing electron densities in 3D using a technique called “marching cubes” rather than using contour algorithms. In addition, Coot provides very convenient ways to transform data and view from one representation to another.
That convenience comes from Coot's graphical interface. “Click-click on the data, and up pops a map,” says Emsley. The easy to navigate menu systems allow users to “discover” the program's features rather than memorizing commands. Also, the program “is forgiving,” he says. “You can drag things around in the model and then undo them. Coot doesn't punish you for exploring or experimenting.”
COOT is also an open source program with a GPLv3 license. Anyone can view the source code and submit suggested changes. Emsley recently updated Coot to include changes supplied by a researcher who models RNA. In addition, Phenix integrates with Coot through its Python interface.
In an upcoming release, Coot will include a novel model representation that is more familiar to chemists. “When you try to get medicinal chemists to look at Coot, it just doesn't work,” says Emsley. “They want to see a standard chemical structure diagram, so that's what we're working on.”
While it has become a bit of a standing joke, Emsley believes that version 1.0 will be released within the 18 months promised on Coot's website (http://www.biop.ox.ac.uk/coot/). Regardless, nightly builds provide fully tested releases daily, so users awaiting new features can begin using them as soon as they are complete. – Elizabeth Dougherty
Published October 15, 2011
Springsteen, Tolkein, Protein
A Welshman's journey into computer graphics
An unexpected side-effect of Alywn Jones' decision to write Frodo, one of the first computer graphics programs written for Xray crystallography, was learning to swear in German. His teacher? Johann Deisenhoffer, the 1988 winner of the Nobel Prize in Chemistry.
“He was always using my experimental versions,” said Jones, then at the Max Planck Institute for Biochemistry, now professor of structural biology at Uppsala University in Sweden. “He used to swear at me when my program exploded, which it often did.” Back then, in 1976, Jones had happened into computer graphics. “I took a wrong turn and I just kept going,” he says, his voice just slightly less gritty than that of The Boss.
Jones programmed on what at the time was a sophisticated computer. “I could have bought three Ferraris for what we paid for that system,” says Jones. But with only 32000 words of memory and just a megabyte of disk storage, writing modeling software was a challenge. To do anything, he had to link his computer to a larger system, creating a flow of data he thought of as a ring. That ring inspired him to name his program Frodo.
In 1979, Jones took Frodo to Uppsala. There he implemented Frodo's original Lego-like model building tool. He built the tool because he had noticed over the years that the same structure fragments kept reappearing in solved structures. He wondered if he could use these fragments to jump-start solving new structures. Pursuing this idea, Jones found many well-refined fragments. “I was surprised to see that I could use these fragments to build a whole protein,” says Jones.
Without such a tool, he says, “someone could end up sitting in front of one of these computer systems and fitting to noise rather than fitting to a realistic expectation. They might end up with models that have incorrect stereochemistry, or parts of the main chain pointing in the wrong direction.”
By the mid-eighties, Frodo's mini-computer hardware platform had become obsolete, replaced by Digital's VAX. “The VAX was the first computer where crystallographers could actually control their computing destiny,” says Jones. “You could do all of the computing on it and not have to use a computer center.”
Jones decided to write Frodo again from scratch for the new hardware, creating “O.” Jones closely guards the meaning of the name. Even collaborator Morton Kjeldgaard of Denmark, who contributed the cartoon representations of proteins in O, does not know. “O is the end of Frodo,” he guessed. Not so. Perhaps O is The One Ring? Jones will not tell.
Regardless, O includes a newer, more elegant implementation of Frodo's Lego-like graphics tool. In O, Jones used a database to store the fragments and other data the program needs, making it easy to support new features as he conceives them. In addition to updating O, Jones also still relies on O to take electron density maps and turn them into models of proteins. For more information about O, please see Essential O, available online.
– Elizabeth Dougherty
Published June 17, 2011
Escape from the Darkroom
Wolfgang Kabsch and the making of XDS
As Wolfgang Kabsch headed for the darkroom, facing another day of developing films of Xray diffraction patterns, he passed by a new machine sitting on a bench, unused. It was the mid-1980s and the machine was an early electronic Xray detector, full of new technology but lacking the software to make it usable.
“It was just sitting there, looking at me,” says Kabsch, staff scientist emeritus in biophysics at the Max Planck Institute for Medical Research. “I decided rather than wasting my time in the darkroom, I could program the detector to do something useful.”
Kabsch's efforts led to the development of XDS, Xray Detector Software. First released in 1986, the tool is still widely used today to translate raw Xray data from a variety of detectors into standardized data that includes the H, K and L indices of reflection, the intensity of the reflection, and the standard deviation of the intensity.
At the time, Kabsch was working on his main project, solving the structure of the muscle protein actin. After 14 months of exploring the detector and coding all of its features into a Fortran-based software tool, he was able to solve the actin structure with the excellent data from the new detector, rendering the film-based approach obsolete. “It was a lot of work,” says Kabsch, “but when it was done, the structures just came out like nothing.”
Kabsch released XDS in 1986 and published the actin structure in Nature in 1990. He continued to use the detector for other projects, such as solving (in collaboration with SBGrid member Emil Pai, biochemistry professor at the University of Toronto) the RAS p21 protein, an oncoprotein in human cancer.
Since that first software release, Kabsch has run XDS as a one-man shop. As new detectors come on the market, he extends the software to support them. In all, the software supports over 22 different detectors.
Recently, Kabsch added support for a novel pixel detector called PILATUS from the Paul Scherrer Institut in Switzerland. This data-intensive detector delivers ten images per second, each 6 megapixels in size. On the docket is support for a new types of detectors assembled from may separate, planar segments for recording FEL (free electron laser) data at the Linac Coherent Light Source at Stanford.
Kabsch, now retired, is always looking out for ways to keep XDS up to date. “When I see a better algorithm or a better way of computing, I put it in,” he says. He announces improvements on the XDS web page. Kabsch has also contributed to other applications, including the development of a dictionary of protein secondary structure, used in applications such as Procheck.
While Kabsch remains the primary coder of XDS, he has tapped a successor. Kay Diederichs, professor of protein crystallography and molecular bioinformatics at the University of Konstanz, has worked with Kabsch and XDS for over two decades and will continue to evolve XDS when Kabsch starts taking his retirement more seriously.
– Elizabeth Dougherty
Published May 19, 2011
Better, Faster, Stronger, More
Advancing structural biology discoveries, methods, and tools
It took Victor Lamzin nearly a year to solve his first structure, an 800-residue enzyme formate dehydrogenase. Later, as a post-doc, he asked his supervisor to let him re-solve it, but this time in just 2 months.
Lamzin, now a group leader and the Deputy Head of the Hamburg Unit of the European Molecular Biology Laboratory, did it. “That's when I realized things could be done even quicker than that. I realized that much of the experience I had garnered and what I'd deciphered from reading the literature and talking to colleagues could be put into software,” says Lamzin. “Especially the boring, repetitive things.”
While Lamzin had scant knowledge of computer programming—in fact, he says, scant knowledge of crystallography—he dove in anyway. After all, as a scientist, learning is his job.
Lamzin's challenge led to the development of ARP/wARP. Pronounced “Arp-Warp,” the software transforms electron density maps of Xray diffraction patterns into 3-dimensional models. When ARP/wARP debuted in 1998, it was the only software of its kind. The program, written mostly in Fortran with scripting languages to support the user interface, was a collaborative effort between Lamzin's lab and that of Anastassis Perrakis of the Netherlands Cancer Institute.
“ARP/wARP, like human crystallographers, links model building and refinement together into a unified process that iteratively proceeds towards the final macromolecular model,” wrote Lamzin and Perrakis in a 2008 Nature Protocols paper describing a new release of the program. The software includes multiple, unified approaches to model building as well as ligand and solvent building components.
More recently, ARP/wARP's resolution range has expanded to allow the solution of larger structures and complexes, which have lower resolution diffraction patterns. “These structures don't always produce the Xray diffraction patterns that work best with ARP/wARP,” Lamzin says. “That means we need to develop novel methods if we want to get biologically relevant information from those structures.”
While the software still performs best at resolutions better than 2 angstroms, it can automatically solve 65% of structures at resolutions approaching 3.5 angstroms. Ultimately, Lamzin would like to solve much, much larger structures—his dream being the structure of a cell—so the software is continually under improvement.
The latest release, version 7.2, which will be available late spring 2011, contains an advanced molecular graphics front-end and an RNA/DNA builder. It integrates with CCP4 and also uses REFMAC for model refinement. For more details, visit the ARP/wARP website.
While ARP/wARP is a significant project in Lamzin's lab, his own structural biology work employs atomic resolution Xray crystallography to study the enzymatic action of proteins such as those using Nicotinamide adenine dinucleotide (NAD/NADH), the most abundant electron carrier in cell metabolism. Lamzin's work typically leads not only to publications about structural discoveries, but also to the development of technology to share. “We like to contribute with structural biology interpretations,” says Lamzin, “and at the same time with methodological advances.”
– Elizabeth Dougherty
Published May 17, 2011