Hi Ben,

Yes, my group was using this Restrainer module as you mentioned with a very early version of IMP. Thanks for the detailed info about the two IMP modules and how to use them.

Kind regards,

Altair

El vie., 17 abr. 2020 0:08, Ben Webb ben@salilab.org escribió:

> On 4/16/20 11:22 AM, Altair Hernández wrote: > > I used to work with a Diameter restraint in the past using IMP version > > 2.2 where I specified in a XML file the *max_diameter* and *std_dev* > > between pairs of particles. I would like to know how to use this > > function with the latest version of IMP (2.12). > > XML input implies you were using IMP.restrainer, which was removed from > the code a long long time ago. But IMP.core.DiameterRestraint is still > there: > > https://integrativemodeling.org/nightly/doc/ref/classIMP_1_1core_1_1Diameter... > > DiameterRestraint takes an input a UnaryFunction (usually we use > IMP.core.HarmonicUpperBound) and a SingletonContainer. If you just have > a simple list of particles you want to restrain, use > IMP.container.ListSingletonContainer. > > You can see how IMP.restrainer set up the restraint (in C++) at > > https://github.com/salilab/imp/blob/2.1.1/modules/restrainer/src/simplify_re... > > > Also I would be grateful to know which is the main difference between > > the DiameterRestraint and the Harmonic Upper Bound > > HarmonicUpperBound scores the distance between two particles, keeping > them from exceeding a certain distance. DiameterRestraint scores the > distance between each of a set of particles and the center of mass. > > > and how to justify a > > given k value when using the HarmonicUpperBound restraint. > > The larger the value of k the less likely particles are to exceed the > diameter. > > See also > > https://integrativemodeling.org/nightly/doc/ref/classIMP_1_1core_1_1Harmonic... > to convert std_dev to k. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >