March 2014 - IMP-dev - salilab.org

Harmonic restraint on rotation in IMP
by Barak Raveh 25 Mar '14

25 Mar '14

Does anybody know of an existing implementation of a harmonic restraint on rotational degrees of freedom? Namely, I have two reference frame of two particles p1 and p2. For simplicity, assume xyz(p1) = xyz(p2). I would like to add a harmonic restraint over the delta in their reference frame, for some definition of that delta. Thank you Barak

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Preparation for the 2.2 release
by Ben Webb 20 Mar '14

20 Mar '14

So, the next stable release of IMP is coming up soon. My release criteria are pretty simple (let me know if you disagree ;) 1. The nightly build should be close-to-clean: http://integrativemodeling.org/nightly/results/ i.e. a) it should build, b) the documentation shouldn't be full of broken links, and c) the tests and examples should work (as completely as we can manage). I've already taken care of a) and b) and am working on c). If you can take a moment to look at any modules/applications you work on and see if you can help out with any test failures, that would really help! 2. All the IMP issues attached to the "IMP 2.2 release" milestone should be addressed[*]. If you have a "favorite" IMP bug that isn't in the list at https://github.com/salilab/imp/issues?milestone=7&state=open, go add the 2.2 release milestone to your issue, otherwise it likely won't get fixed. (And if it doesn't have an open issue at all, open one...) Those currently in there shouldn't be too disruptive, although I will be removing the code we deprecated in 2.1, which will likely break a few things. 3. The biological systems at http://integrativemodeling.org/systems/ should all work with latest IMP. (I'll start a run of them once the deprecated code is gone - most likely some of them use at least one deprecated function.) [*] Not necessarily "fixed"... we may decide to push some issues back to the next release. Ben -- ben(a)salilab.org http://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Moving on
by Daniel Russel 04 Mar '14

04 Mar '14

As many of you know, I'm moving to a startup in the next couple of weeks. I've had lots of fun with IMP and will miss it a lot and hope it continues to thrive. If people have particular things that they would like me to do before I go (e.g. areas to add to https://github.com/salilab/imp/wiki/Internals) please let me know. Not that I won't have email later on too :-) --Daniel

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