[chimerax-users] Command "mlp"

[Cosmin Stefan Butnarasu]

Hello,

Hope to find you doing well. 
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.

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?

Thank you in advance!

Cosmin Stefan Butnarasu





*********************************************************
Cosmin Stefan Butnarasu, PhD Student
Department of Molecular Biotechnology and Health Sciences
University of Torino
Via Gioacchino Quarello 15, 10135
email:
cosminstefan.butnarasu at unito.it
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