[chimerax-users] Command "mlp"

[Elaine Meng]

Hi Cosmin,
Yes, but as I said, they are the min/max values found at the surface (as determined by interpolating values in the 3D MLP map to those spatial locations), but not necessarily the min/max of all of the grid points in the map.  I.e. there might be higher or lower values somewhere else in the map that is not next to the surface. These surface values are reported to help the user adjust the surface coloring range, if the user wants to do that. I hope this helps,
Elaine

> On Apr 6, 2020, at 12:50 AM, Cosmin Stefan Butnarasu <cosminstefan.butnarasu at unito.it> wrote:
> 
> Hi Elaine,
> 
> Thank you so much for the useful inputs!
> 
> So if I get it right, the min, max and mean values reported in the Log after computing the MLP command, are referred to MLP calculation itself. They are obtained from the 3D MLP map, right?
> 
> Thank you again Elaine.
> 
> Wish you a good week!
> 
> Cosmin
> 
> *********************************************************
> 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
> *********************************************************
> 
>> Il giorno 03 apr 2020, alle ore 18:21, Elaine Meng <meng at cgl.ucsf.edu> ha scritto:
>> 
>> Hi Cosmin,
>> Molecular lipophilicity potential (MLP) is not just a ChimeraX concept, it is general method that existed long before ChimeraX.  The idea is that different atoms have different hydrophobicity (lipophilicity) values and that a set of atoms in 3D generates a lipophilic potential.  So some parts of the protein surface will be more lipophilic than others, as shown by the coloring.  The whole purpose is to get some visualization of which parts of the protein might be more likely to bind hydrophobic membranes or hydrophobic parts of ligands.  It is analogous to coloring by electrostatic potential, except it is a (molecular) lipophilic potential, hence "MLP."
>> 
>> The "mlp" help page describes all of this and gives the literature references so you can read more about it.  It also explains "mlp" command options:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html>
>> 
>> Potential is not a single overall number but varies in space (which is actually the definition of "potential"), so it's really a map or 3D grid of many values.  There is a "map" option to the "mlp" command to open the map as a separate volume model which could then be saved to a file with the "save" command.
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map>
>> 
>> Solvent-excluded surface (SES) is just the molecular surface that ChimeraX displays, so that is what gets colored by the MLP values. First the values at the surface points are calculated from the 3D MLP map, and then the min, max, mean of the surface point values are reported and the surface is colored.  I'm not sure what you mean by "SES value" but maybe it was the surface areas reported in the Log.  That is a totally different thing and has nothing to do with the surface coloring.   There is an explanation and diagram of SES in the "surface" page:
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Apr 3, 2020, at 2:47 AM, Cosmin Stefan Butnarasu <cosminstefan.butnarasu at unito.it> wrote:
>>> 
>>> 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
>>> 
>> 
> 
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