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@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?