It's not ccp4, but I've successfully used MultiSeq in VMD to make a 1-dimensional tree from a large group of conformations. Though like you mention, the big conformational changes might not be handled well in the STAMP alignment of that package.
ProSMART might be more appropriate if you have rigid domains and a flexible connecting region, as it uses local structural alignments so keeps hinged movements from having a disproportionate impact on the alignment. Shane Caldwell McGill University On Tue, Jul 7, 2015 at 9:03 PM, Keller, Jacob <[email protected]> wrote: > Is anyone aware of a way to classify large numbers (100s) of > conformationally-diverse crystal structures of a single protein (here > calmodulin)? Pairwise RMSD matrixes seem possible, but may be complicated > since there are two somewhat stable lobes, and the flexible linker in the > middle. What I am imagining is a sort of multidimensional tree depicting > the relationships in conformation space of the various structures. > > I remember something for this called esct or similar, but can't seem to > google it. > > Any thoughts? > > Jacob > > ******************************************* > Jacob Pearson Keller, PhD > Looger Lab/HHMI Janelia Research Campus > 19700 Helix Dr, Ashburn, VA 20147 > email: [email protected] > ******************************************* >
