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Hi

I would like to calculate the relative rotation of one helix relative to another in a dimer to see how the contact surface between the two changes,if at all. I am unsure how to set this up.

thanks,

Jeremy

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rmv Online Content
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COOR HELIX with a double atom selection will do that (corman.doc)

In principle obtaining two HELIX time series (correl.doc) and then computing the helical axes dot product should also work, but I had some trouble with the HELIX time series recently. Instead, I computed the dot product of vectors from CA of residue i to CA of residue i+14 (where i may be different for each helix).


Rick Venable
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Hi Dr. Venerable

wouldnt that calculate the angle between helix axes? I am interested in the rotation of one helix on its axis relative to the surface of the other helix- like if two rolling pins on top of one another roll on eachother and the contact surface changes

hope ive made my question clearer.

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The proper way to do this is to first discuss with your supervisor to find out what would be a reasonable physical quantity (equation!) to use for this purpose, then come back and ask how this can be implemented in CHARMM.


Lennart Nilsson
Karolinska Institutet
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I was thinking more of the helix crossing angle when I first read the question. I've used the CA-CB bond vector of selected side chains as a measure of rotation around the helical axis.


Rick Venable
computational chemist


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