Yes it helped a ton. Thank you! On Wed, Dec 1, 2021 at 10:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:

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.h...

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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

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< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hiera...

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< https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descr...

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

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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?

-- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016