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
Hi Jacob,
Principal component analysis (pca) might work but it will modify the
original dimensions as a linear combination, which might make it difficult
to derive physical meaning out of it. May be, you could use decision trees
which give results that are easier to interpret. Looking at decision
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Dear Jacob,
information about Thomas Schneider's program 'escet' that you remember
can be found at
http://www.embl-hamburg.de/~tschneider/escet/index.html
Best,
Tim
On 07/08/2015 03:03 AM, Keller, Jacob wrote:
> Is anyone aware of a way to classify
Sounds like a perfect application for principal components analysis. Check out
Bio3D: http://thegrantlab.org/bio3d/index.php.
Cheers,
Tristan
Tristan Croll
Lecturer
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Techno
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 a
