<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Yaikhomba,<br class=""><div class="">Depends what you mean by quick, but there are certainly better ways than choosing them one by one! </div><div class=""><br class=""></div><div class="">I would use "measure sasa" to define an "area" attribute of residues, then assign residue hydrophobicities from a file with the "defattr" command, and then use a single "select" command to intersect these two attributes. </div><div class=""><br class=""></div><div class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa</a>></div><div class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html</a>></div><div class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#attributes</a>></div><div class=""><br class=""></div><div class="">In the "defattr" example files I already happened to include a file kdHydrophobicity.txt to assign Kyte-Doolittle hydrophobity, as well as for several other hydrophobicity scales. Just download whichever one(s) you want to try from the links here:</div><div class=""><<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html#examples" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/defattr.html#examples</a>></div><div class=""><br class=""></div><div class="">The commands could be something like:</div><div class=""><br class=""></div><div class="">open 6g2j</div><div class="">measure sasa protein</div><div class="">defattr ~/Desktop/kdHydrophobicity.txt</div><div class="">select ::area>25 & ::kdHydrophobicity>0.0</div><div class="">surface protein enclose protein</div><div class="">color sel magenta</div><div class=""><br class=""></div><div class="">... which looks like this ... </div><div class=""><img apple-inline="yes" id="8EACEAD4-7890-4771-BBD4-6226C4994282" width="240" height="240" src="cid:EF0D38A6-51FF-4C5B-9123-A5D74D489271@gateway.sonic.net" class=""></div><div class=""><br class=""></div><div class="">... in pretty good agreement with MLP coloring, e.g.</div><div class=""><br class=""></div><div class="">mlp surfaces #1.3</div><div class=""><img apple-inline="yes" id="87E4E840-1466-47CB-AE39-80D85A96BB42" width="240" height="240" src="cid:E7EBD52A-093B-44A3-9412-2CE7E717D8B5@gateway.sonic.net" class=""></div><div class=""><br class=""></div><div class="">In the select command you may want to experiment with the surface-area and hydrophobicity cutoffs, as well as which hydrophobicity scale you use. I didn't try a lot of values for surface-area cutoff, but here is with all residues with values >25 colored red, reasonable at least as a first approximation:</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="85A13A6A-1797-4A19-A350-878541182654" width="240" height="240" src="cid:80EDEBD0-5829-44E2-B288-DB872A171D0D@gateway.sonic.net" class=""></div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine</div><div class=""><div class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""></div><blockquote type="cite" class="">On Sep 6, 2020, at 3:26 PM, Mutum Yaikhomba <<a href="mailto:mutum.yaikhomba@mrc-mbu.cam.ac.uk" class="">mutum.yaikhomba@mrc-mbu.cam.ac.uk</a>> wrote:<br class=""><br class="">Hi<br class="">I am working with a very big pdb model: pdb - 6g2j. I was wondering if there is a quick way to select all residues (surface residues) that are exposed to the solvent (including those facing the membrane)? This is instead of going over each residue one by one and selecting them.<br class=""><br class="">Additionally, say you have selected these solvent-exposed residues and now you want to filter them based on Hydrophobicity - is there a way to filter based on the standard Kyte-Doolittle Hydrophobicity index for these residues?<br class=""><br class="">If there is, it would be of great help and very much appreciated.<br class="">Thanks<br class="">Yaikhomba<br class=""></blockquote><br class=""></div></body></html>