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salilab
The Integrative Modeling Platform
`IMP::cgal` makes use of CGAL functionality from `CGAL/Convex_hull_d.h` and `CGAL/Regular_complex_d.h`. This functionality is deprecated in newer versions of CGAL. Use the [Triangulation package](http://doc.cgal.org/latest/Triangulation) instead.
I ran into some strange behavior in CloseBipartitePairContainer when it includes pairs that are both contained in a single rigid body. When one tries to do this, the container only...
IMP currently takes as input files in a variety of formats, but doesn't care where those files originate. This becomes a problem when we come to publish a modeling study...
When creating high-resolution EM map with SampledDensityMaps, some of the density planes are empty (missing?), creating a stratified effect not present when comparing to maps created with other softwares. I...
I've been running my simulations using pmi, and the IMP.pmi.macros.BuildSystem class before adding restraints, and I've noticed that passing a hierarchy to the ExcludedVolumeSphere object will fail silently. model =...
`IMP.pmi` currently supports mmCIF output, but it is strongly tied to PMI1's representation. We would also like to be able to output files in mmCIF format using PMI2, or even...
RMF trajectories are slow to read in Chimera, and RMF support is unlikely to be added to ChimeraX unless we really really push for it. We can't reasonably use mmCIF...
`core::TransformationSymmetry` and `core::TransformationAndReflectionSymmetry` make sure that a particle P' is kept with its coordinates derived from a reference particle P (by transformation and optionally also reflection). However, any forces on...
Currently the only way to get ALL leaves of all representations is a bit clunky, you have to use selection: ``` python selB = IMP.atom.Selection(hsel,resolution=IMP.atom.ALL_RESOLUTIONS, representation_type=IMP.atom.BALLS) selD = IMP.atom.Selection(hsel,resolution=IMP.atom.ALL_RESOLUTIONS, representation_type=IMP.atom.DENSITIES)...
RotamerCalculator is very useful for generating ResidueRotamer objects for an actual Residue, but internally, ResidueRotamer doesn't seem to store any reference to the original Residue. It just gets some coordinate...
