<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hello,<div class=""><br class=""></div><div class="">Hope to find you doing well. </div><div class="">I am a PhD student in Pharmaceutical and Biomolecular Sciences and I am writing this email because I would like to better understand the mlp command. First of all, I have to say that I am a very novice on ChimeraX, I discovered this software basically few days ago, so I will write concepts that maybe are not properly correct.</div><div class=""><br class=""></div><div class="">I would like to calculate the surface hydrophobicity of a protein. I saw that the mlp command graphically displays the molecular lipophilicity potential, which I suppose is somehow close to the surface hydrophobicity. However, when mlp command is compute, in the Log panel are shown three values, a minimum, a mean and a maximum, which I have not completely understood what they are for (see the picture attached). I searched on ChimeraX manual and I found that the SES surface could stand for “solvent-excluded surface” but I’am not sure about this. If so, could the mean SES value be a measure of the surface hydrophobicity of the protein? If not, can you suggest me a method to obtain not only a graphical display but also a value of the overall molecular lipophilicity potential?</div><div class=""><br class=""></div><div class="">Thank you in advance!</div><div class=""><br class=""></div><div class="">Cosmin Stefan Butnarasu</div><div class=""><br class=""></div><br class=""><img apple-inline="yes" id="200F0598-5B58-4128-A9CA-F3EBAD79AD4A" src="cid:90EAD43E-BE64-4DDE-B1AD-F428478D9121@station" class=""><br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-size: 11px;" class=""><font color="#515151" class=""><font face="Courier" class=""><br class="Apple-interchange-newline"><br class=""></font></font></span></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;"><span style="font-size: 11px;" class=""><font color="#515151" class=""><font face="Courier" class="">*********************************************************<br class="">Cosmin Stefan Butnarasu, PhD Student<br class="">Department of Molecular Biotechnology and Health Sciences<br class="">University of Torino<br class="">Via Gioacchino Quarello 15, 10135<br class="">email:</font></font></span></div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;"><font face="Courier" style="color: rgb(81, 81, 81); font-size: 11px;" class="">c</font><font face="Courier" style="color: rgb(81, 81, 81); font-size: 11px;" class=""><a href="mailto:osminstefan.butnarasu@unito.it" class="">osminstefan.butnarasu@unito.it</a></font><span style="font-size: 11px;" class=""><font color="#515151" class=""><font face="Courier" class=""><br class="">*********************************************************</font></font></span></div>
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