[Chimera-users] Curiosity regarding amino acid category in UCSF chimera

[Elaine Meng]

Hi Prathvi,
Yes, these default classifications are all from a specific publication, as mentioned in the help, but you can change them using the ResProp tool (menu Tools... Structure Analysis... ResProp):

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html>

There are also other ways to select or specify the residues you think are hydrophobic:

(1) by residue name, e.g. command:

select :phe,tyr,trp,leu,ile

(2) by Kyte-Doolittle hydrophobicity value, e.g. command:

select :/kdHydrophobicity>0.5

Command-line specification:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 30, 2021, at 9:50 PM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> In UCSF chimera, when I go to Select > Residue > Amino Acid Category > Hydrophobic, the LYSINE residues also get selected. However, according to the Kyte-Dolittle scale, LYSINE is a fairly hydrophilic residue. Is there any specific reason why chimera lists them as hydrophobic residues?