Dear All,

I remember a post in the last couple months but cant find it.  In any case, by 
searching through van der groot et alls. papers, the -xmin, -xmax, -dim and 
-ngrid options third point, example: -xmin 3 3 3 -xmax 3 3 3 is for reading in 
the output 3d (projections on V1, V2, V3 or first three vectors, and is output 
as xyz points in a pdb file.  This can be read into various ploting or even 
pymol/vmd to illustrate the projection on a PCA of 3 dimensions.  From the lit 
it is supposed to show 2 or more conformational states, and a number of 
intermediary states in between (overall just a 3d PCA graph).  If I am wrong 
please correct me, but this is what the output for me was doing, and I 
personally prefer the 2D, as its easier to illustrait (as images in 3d lack the 
necessary rotation to show everything in a static image).

Sincerely,

Stephan Watkins
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