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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 <[log in to unmask]> 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

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Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: [log in to unmask]
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