<div dir="ltr">Yes it helped a ton. Thank you!</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Dec 1, 2021 at 10:26 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Prathvi,<br>
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):<br>
<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html</a>><br>
<br>
There are also other ways to select or specify the residues you think are hydrophobic:<br>
<br>
(1) by residue name, e.g. command:<br>
<br>
select :phe,tyr,trp,leu,ile<br>
<br>
(2) by Kyte-Doolittle hydrophobicity value, e.g. command:<br>
<br>
select :/kdHydrophobicity>0.5<br>
<br>
Command-line specification:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html</a>><br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy</a>><br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Nov 30, 2021, at 9:50 PM, Prathvi Singh via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi,<br>
> 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?<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Prathvi Singh,<div>Research Fellow,<br><div>Department of Biological Sciences & Bioengineering,</div><div>Indian Institute of Technology, Kanpur-208016</div></div></div></div></div></div>