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

[Prathvi Singh]

Yes it helped a ton. Thank you!

On Wed, Dec 1, 2021 at 10:26 PM Elaine Meng <meng at 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.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?
>
>

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