<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div><blockquote type="cite" class=""><br class="Apple-interchange-newline"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Kenji MATSUI <<a href="mailto:s214903z@st.go.tuat.ac.jp" class="">s214903z@st.go.tuat.ac.jp</a>><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">How to display hydrohobic area</b><br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">August 22, 2022 at 9:17:37 PM PDT<br class=""></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class=""><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">To: </b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class=""></span></div><br class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">Dear <span class="gmail-il">Chimera</span></div><div class="">Thank you for taking the time to answer my question the other day.<div class=""><div class="">I'm Kenji Matsui, a second-year master's student at a national university in Japan.</div></div><div class=""><br class=""></div><div class="">I would like to display the hydrophobicity of the protein around the ligand like the first picture, but I couldn't do it.</div><div class="">How can I do this?</div><div class="">When I actually did it, it turned out to be the second picture.<br class=""></div><div class=""><br class=""></div><div class="">I apologize for asking this question so often in your busy schedule, but I would appreciate it if you could confirm it for me.</div></div></div><div class=""><br class=""></div><div class="">First photo</div><div class=""><img alt="image.png" class="" apple-inline="yes" id="7F8D1661-328E-41F7-813D-B72FA980943A" src="cid:ii_l75o6e6d1"><br class=""></div><div class=""><br class=""></div><div class=""></div><div class="">Second photo</div><div class=""><img alt="image.png" class="" apple-inline="yes" id="ACF5C321-722C-4519-9BA4-B6FB0F5CDC63" src="cid:ii_l75llwv90"><br class=""></div><div class=""><br clear="all" class=""></div></div></div></blockquote></div>Hi Kenji,<div class="">If I understand correctly, you want to show the amino acid hydrophobicity coloring on the ribbon and sticks, not the molecular surface.</div><div class=""><br class=""></div><div class="">When you open the structure, it may already be displayed as ribbon and sticks. Do not show the surface. (Or, if you already are showing the surface, you can hide it with menu: Select... Clear Selection, menu: Actions... Surface... hide) Then you can use the "rangecolor" command to color protein ribbons/sticks by hydrophobicity:</div><div class=""><br class=""></div><div class="">rangecolor kdHydrophobicity min dodger blue 0 white max orange red</div><div class=""><br class=""></div><div class="">See rangecolor help</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html</a>></div><div class=""><br class=""></div><div class="">That command is part of the tutorial for surface coloring:</div><div class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#hydrophobicity" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#hydrophobicity</a>></div><div class=""><br class=""></div><div class="">However, when the surface is not shown, you can see that this comand also colors the other representations (ribbons and sticks).</div><div class=""><br class=""></div><div class="">I hope this helps,</div><div class="">Elaine<br class=""><div class=""><span class="Apple-style-span" style="border-collapse: separate; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; line-height: normal; border-spacing: 0px; -webkit-text-decorations-in-effect: none;"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">-----</div><div class="">Elaine C. Meng, Ph.D. </div><div class="">UCSF Chimera(X) team</div><div class="">Department of Pharmaceutical Chemistry</div><div class="">University of California, San Francisco</div><div class=""><br class=""></div></div></span><br class="Apple-interchange-newline"><br class="Apple-interchange-newline"></div></div><div></div></body></html>