[Chimera-users] Morphing

James Naismith naismith at st-andrews.ac.uk
Mon Jan 20 05:17:32 PST 2014

I am experimenting with the morphing feature. I know I am being very stupid but I cannot get the analysis to work.

I am using a MAC OSX latest version.

I have created my morph which is running nicely.

What I would like to do is analyse the morph for VDW clashes.
(That is in going from structure 1 to structure 2, what residues would have to move).

First problem is when I run cluster (under analysis in MD movie) then generate residue interaction for cluster, up pop a new dialogue with warnings but seems to ask about calculations

When I click OK or apply I get a new box residue interaction contact parameters

This always generates an error “No atoms designated for clash detection’
I seem only to have four options 
all others atoms (default)
other atoms in same model 
second set of designated atoms

Any help gratefully received

(Ps I have installed the latest cytoscope but it does not have the structure.viz plugin; I keep getting errors trying to install older version)


Jim Naismith

The University of St Andrews is a charity registered in Scotland : No SC013532

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