Hi IMP users,
I want to create pairwise distance restraints between IMP particles (spheres XYZR of a given radius) with a maximum distance condition.So I want a given sphere to be in a range between 0 and max distance of 17 Aº. How can I do it in IMP? Given a set of sphere pairs, and a distance between them, how can I apply a IMP function to force a maximum distance restraint in a similar way then a Harmonic function?
f = IMP.core.Harmonic(float(tag_list[1]), float(tag_list[2])) s = IMP.core.DistancePairScore(f) r = IMP.core.PairRestraint(model, s, (bait_p, tag_p))
How can I substiute the IMP.core.Harmonic with a maximum distance function?
Thanks in advance! Altair
On 10/28/19 4:33 AM, Altair Hernández Chinchilla wrote: > How can I substiute the IMP.core.Harmonic with a maximum distance function?
Use HarmonicUpperBound instead: https://integrativemodeling.org/2.11.1/doc/ref/classIMP_1_1core_1_1HarmonicU...
Note also that individual IMP restraints are expensive. If you have a number of such restraints with the same distance, better to create a PairsRestraint: https://integrativemodeling.org/2.11.1/doc/ref/classIMP_1_1container_1_1Pair... and put all the pairs of spheres you want to restrain in a ListPairContainer: https://integrativemodeling.org/2.11.1/doc/ref/classIMP_1_1container_1_1List...
Ben
Hi!
Thank you very much, it works! In my case I am working with different pairwise restrains, so I cannot apply the ListPairContainer in this case. However, I applied it when ExcludedVolumen is used with all the spheres I create!
Kind regards,
Altair
On Mon, 28 Oct 2019 at 15:50, Ben Webb ben@salilab.org wrote:
> On 10/28/19 4:33 AM, Altair Hernández Chinchilla wrote: > > How can I substiute the IMP.core.Harmonic with a maximum distance > function? > > Use HarmonicUpperBound instead: > > https://integrativemodeling.org/2.11.1/doc/ref/classIMP_1_1core_1_1HarmonicU... > > Note also that individual IMP restraints are expensive. If you have a > number of such restraints with the same distance, better to create a > PairsRestraint: > > https://integrativemodeling.org/2.11.1/doc/ref/classIMP_1_1container_1_1Pair... > and put all the pairs of spheres you want to restrain in a > ListPairContainer: > > https://integrativemodeling.org/2.11.1/doc/ref/classIMP_1_1container_1_1List... > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >
-
Altair Hernández Chinchilla -
Ben Webb