Chemistry Visualisation and Tools Meeting

marcus@cryos.net (Marcus D. Hanwell) — Thu, 20 Mar 2008 18:20:00 +0000

Last week I was privileged to be invited to speak at a meeting about molecular modelling with a focus on tools, GUIs and visualisation. The meeting was held at the Holiday Inn in Runcorn and the Daresbury Laboratory (England). I wasn't expecting to be back in England quite so soon, having only just returned to Pittsburgh at the end of January.

The meeting was a great opportunity to present some of the latest work I and others in the Avogadro and OpenBabel communities have been doing to create tools that enable the building of molecules and structures, as well as their visualisation. It was also a great chance to hear some very interesting talks by the developers of other building tools and some quantum codes. Donald and I were also invited to Daresbury Laboratory to work with some of the CCP1GUI developers.

I presented my talk on Avogadro on Wednesday morning and have made the slides available here. Donald gave an introduction to Avogadro, some of the history and the architecture before I gave my presentation. We finished by taking questions while I demonstrated the Avogadro application. I think it was extremely productive. We had many more conversations over dinner and drinks later as well as in a workshop setting on Thursday afternoon.

It was great to be able to put a face to a few of the names and discuss current issues more informally in the evening. The talks were all of a very high quality and from a varied list of speakers from other open source projects, some of the free quantum codes as well as commercial products. I have come away from the meeting with a much better appreciation of the needs in the community and I feel that Avogadro is in a great position to fill the apparent void.

I am glad that we were able to get surface and orbital support working in Avogadro before the meeting. Right now we only support Guassian cube files but the implementation is general enough that I will be able to add support for further formats. I really think that if we can get enough people collaborating on a common project everyone can get the tool they need to effectively do their research at a much lower investment than could be achieved by working on many separate projects.

I met Tristan Youngs, the developer of Aten, who had implemented some really nice features in his molecular builder that is much more focussed on molecular mechanics. It is well worth checking out. As is Zeobuilder which was developed by Toon Verstraelen. They both implement some great features and have strengths in different areas. Of course my dream is to integrate many of these features via Avogadro plugins and have one editor which is capable of being used in a diverse range of applications.

It was also great to speak to Mario Valle who is doing some very interesting work in the area of new visualisation methods and supports a large user base of computational chemistry users. There were of course so many other talks but you can look at the schedule yourself and I think the slides of all the talks should be available in the near future.

I feel sure that many good things will come out of this meeting and hope to be able to attend similar meetings in the future. I would like to thank Jens once again for hosting the meeting and taking care of everything. I hope to see some patches and/or commits from him in the near future

Postdoctoral Associate Position at University of Pittsburgh

marcus@cryos.net (Marcus D. Hanwell) — Fri, 07 Dec 2007 11:48:00 +0000

At the start of October I began my first postdoctoral position, at the University of Pittsburgh in the Chemistry Department working in the newly formed Hutchison Group for Geoffrey Hutchison. Life has been so hectic these last few months finishing my doctorate and preparing for my biggest move ever.

Louise and I arrived on the 27th of September and had less than a week to find a suitable apartment out here ready for me to start work. I am now a legal non-resident alien (I think - someone correct me if I got it wrong). I am very excited to be starting this new job, the move has been really tough but the research looks very interesting and I am sure that my time here will be very productive.

I have already been to quite a few interesting talks in the department and am making the transition from physics to chemistry. It is OK though as I get to do lots of physics and programming along with some more chemistry. Exciting times and I am sure I will talk more about my work in future. I have already posted a tutorial article on installing Sun Grid Engine on a Mac OS X cluster.

Dax made it out here and we are both enjoying the recent snow. This entry sat in drafts for about a month or so as I have been so busy sorting things out, coding, reading and going to physio for my high ankle sprain which I am told is both unusual and the worst kind of sprain...

Marcus D. Hanwell's Blog - Academia

Chemistry Visualisation and Tools Meeting

Postdoctoral Associate Position at University of Pittsburgh