[Chimera-users] Hydrophoic and Hydrophilic solvent accessible surface area
meng at cgl.ucsf.edu
Sat Apr 9 09:34:13 PDT 2011
When you show a molecular surface in Chimera, it automatically calculates surface area per atom and per residue. You can sum the values for any sets of atoms or residues. However, you would have to decide yourself which atoms (or which residues) to call "hydrophobic" and "hydrophilic."
The surface area values are shown in a histogram in Render by Attribute and can be summed for any set of atoms or residues using the Attribute Calculator (both of those tools are in the menu under Tools... Structure Analysis). areaSES is area of solvent-excluded surface, where the surface probe touches, displayed by Chimera; areaSAS is area of solvent-accessible surface, where the surface probe's center goes, not displayed by Chimera, even though the values are calculated.
You would select the atoms of interest, then in Attribute Calculator:
Calculate attribute [some name, doesn't matter] for [models]
with just these two options checked on:
"Restrict formula domain to current selection, if any" (only sum over the selected atoms, not all)
"Show calculation results in Reply Log"
You want a "models" attribute because you want only one number per model, the sum over the selected residues. You could use areaSES instead of areaSAS, whichever you want. After clicking Apply or OK you can see the value in the Reply Log (under Favorites in the menu).
The part that requires thought is which atoms you wish to consider hydrophobic and hydrophilic. For example, hydrophobic could be all carbon atoms, or all aliphatic and aromatic residues, or just their side chains, or all amino acids with kdHydrophobicity (Kyte-Doolittle hydrophobicity, see <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>) greater than some value, which could be selected using Select by Attribute (the Select tab in the same dialog as Render by Attribute).
Other related possibilities...
(A) An nice visualization in Chimera is to color the surface by amino acid hydrophobicity - simply choosing "Presets... interactive 3 (hydrophobicity surface)" from the menu will apply a built-in scheme going from dodger blue (hydrophilic) to white to orange red (hydrophobic) based on kdHydrophobicity value. Example image here:
(B) Perhaps the GetArea server would give what you want more directly:
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 Apr 8, 2011, at 8:01 PM, Monisha Hajra wrote:
> Hi Team,
> Can I calculate Hydrophoic and Hydrophilic solvent accessible surface area in Chimera? If so, let me know how?
> Really appreciate help.
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