I am an undergraduate student and recently trying to use UCSF Chimera to learn about amino acid tertiary structure, but I am confused about the explanation on the calculation of relative exposure of an amino acid. There is a link on the internet explaining exactly that, but I still don't really understand because I don't have any basics on UCSF Chimera and the computer programming itself. Can anyone please help me to understand how to know if an amino acid is buried or exposed by using UCSF Chimera? Thank you.
The relative exposure of an amino acid indicates its degree of burial in a structure. Relative exposure can be calculated by normalizing the surface area of the residue in the structure by the surface area of the same type of residue in some reference state. Although raw (non-normalized) surface areas could be used to classify residues as buried or exposed, normalization reduces the bias toward classifying smaller residues as more buried and larger as more exposed.
Hi Abdullah,
Could you attach the chimera result to support you? Most of the programs that determine SASA (solvent accessible surface area) values, which indicates the degree of solvent exposition for an atom or grup of atoms (residue or ligand). The lower the SASA values for a residue the lesser the solvent exposition and viceversa. At the same time this SASA value is divided in polar and non-polar contributions.
Hi, Martiniano Bello
I followed the steps explained in the link below:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html
After doing just that, the Chimera program I used gave me the result like this. I don't understand about the interpretation of the protein after it being rendered by attribute relSESA, which I got after doing the "Define Attribute" part and the "Attribute Calculator" part. I attached the picture of the "Render by Attribute" dialog window, I thought the interpretation might came from that dialog window, either quantitatively or qualitatively.
I hope you understand. I am sorry for the bad English.
Thank you.
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