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<p class="MsoNormal">Hi Elaine,</p>
<p class="MsoNormal">Thank you so much for your help. I managed to change it.</p>
<p class="MsoNormal">Have a nice day!</p>
<p class="MsoNormal">Han</p>
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<p class="MsoNormal" style="border:none;padding:0cm"><b>From: </b><a href="mailto:meng@cgl.ucsf.edu">Elaine Meng</a><br>
<b>Sent: </b>Tuesday, 18 May 2021 18.12<br>
<b>To: </b><a href="mailto:han.le@aalto.fi">Le Han</a><br>
<b>Cc: </b><a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><br>
<b>Subject: </b>Re: [chimerax-users] How to change the palette of hydrophobicity in ChimeraX</p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Han,</p>
<p class="MsoNormal">Although the icon just uses the "mlp" command with the default palette, you can use the "mlp" command with any palette that you want. The "palette" option specifies palette and "range" specifies value range.
</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Instructions on "mlp" command and how to specify palettes:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html></p>
<p class="MsoNormal"><https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The hydrophobic coloring icon in the Toolbar "Molecule Display" tab uses command:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">mlp</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">...which is same as:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">mlp palette lipophilicity range -20,20</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">To use the same value range but get blue for hydrophilic and red for hydrophobic, you could use, for example, command:</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">mlp palette blue-white-red range -20,20</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Since red-white-blue is traditionally used for electrostatic coloring, however, you will have to be sure to explain the image so that people understand it is showing hydrophobicity instead.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In the "mlp" instructions linked above, you can see there are several other options of the command that may interest you.</p>
<p class="MsoNormal">I hope this helps,</p>
<p class="MsoNormal">Elaine</p>
<p class="MsoNormal">-----</p>
<p class="MsoNormal">Elaine C. Meng, Ph.D. </p>
<p class="MsoNormal">UCSF Chimera(X) team</p>
<p class="MsoNormal">Department of Pharmaceutical Chemistry</p>
<p class="MsoNormal">University of California, San Francisco</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">> On May 18, 2021, at 6:55 AM, Le Han <han.le@aalto.fi> wrote:</p>
<p class="MsoNormal">> </p>
<p class="MsoNormal">> Hi, </p>
<p class="MsoNormal">> I’d like to change the colour palette of hydrophobicity to red (most hydrophobic) – white – blue (most hydrophilic). Is it possible to do so in ChimeraX and how can I change?</p>
<p class="MsoNormal">> Thank you in advance,</p>
<p class="MsoNormal">> Han</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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