[Chimera-users] hydrophopic interaction

Elaine Meng meng at cgl.ucsf.edu
Wed Oct 23 11:10:53 PDT 2013

Hi ZL,
The way that you would identify only the hydrophobic contacts is to only designate hydrophobic atoms for checking.  For example, if you consider the carbons to be the hydrophobic atoms, you would first select all the carbons in your protein, "designate" them for checking, choose the option to check against "second set of designated atoms," then select all the carbons in the membrane and designate them as the second set.

In the "Treatment" section, the "Draw pseudobonds" option means to draw the lines.  You can turn that off if you don't want to draw lines, and/or you can color the contacting atoms, and/or select them for subsequent actions such as residue label display.

There is no quantification of the possible energy contributions, sorry.  It is all based on distances between VDW surfaces of the atoms.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 23, 2013, at 10:54 AM, LU Zen wrote:

> Hi All,
> I have a amphipathic helix/membrane complex assembled with CHARMN-GUI and I'll like to show those residues that come into contact with the lipid bilayer. Using find clash/contact function, I can see many lines joining the atoms of both the residues and lipid bilayer. However,  I don't really know how to pick the true hydrophopic interaction from the rest of the clashes/contacts. In addition, is there a way to quatify which these interactions may be tighter than the other. 
> Any suggestion is appreciated.
> Thanks,
> ZL

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