[Chimera-users] nonpolar and polar surface area

Bailey Onken onken031 at umn.edu
Tue Sep 17 08:31:28 PDT 2019

Thank you for the feedback.

Could you go into more description as to how to decide and choose which
residues are polar and nonpolar.

Thank you,

On Mon, Sep 16, 2019, 3:52 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Bailey,
> You will have to decide for yourself which residues you want to consider
> as polar and nonpolar.  Then after you show the surface of the protein, you
> can select any subset of the residues (or atoms) and then sum the surface
> area from that subset using the Attribute Calculator tool.
> This is described in more detail in this recent post.  Skip down to the
> fourth paragraph, starting "However, you can get the total surface area
> given some range of hydrophobicity values…”
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html
> >
> Alternatively, you could take a look at the GetArea web server mentioned
> in this follow-up:
> <
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html
> >
> (I changed the subject line of the message to something more descriptive
> to help others find it later.)
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Sep 16, 2019, at 12:23 PM, Bailey Onken <onken031 at umn.edu> wrote:
> >
> > Hello,
> > I am currently a student in Biochemistry. I have a protein and I am
> trying to separate polar and nonpolar residues located on the surface of
> these molecules and then finding the values for the surface area associated
> with polar and nonpolar areas. If you can help me get to this function I
> would be very grateful.
> > Thank you very much,
> > Bailey
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