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PostPosted: Thu Sep 26, 2013 8:43 am 
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I am trying to create a realistic membrane, so it would be very useful to have a color scheme which shows the hydrophilic/hydrophobic sides of a molecule. Is that technically somehow possible?

Thanks for the excellent work so far,

Adrian


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PostPosted: Sun Oct 06, 2013 3:11 am 
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Hi Adrian,
There is no color scheme that will separate the heads and tales for you directly. Depending on the names of the atom types in your PDB file, you may be able to make a selection set that can isolate the tales and heads to color separately with ePMV. If you just want to see the polarized heads, in any color, then you can use the ColorBy Polarity (DavidGoodsell color scheme) which will make the tails white and the headgroups pink/light blue.
Selections are tricky, so you should do the tutorial in the advanced tutorials first, but if all of your lipids have the same atoms as most files do, you can, for example, select all of the tail carbons and color them or their surface mesh some color... here I made them bright yellow and left the head atoms the same. Here is the selection set I used to isolate those carbons in my example PDB file called topgl.pdb:
topgl:::C1,C2,C3,C4,C5,C6,C7,C8,C9,C10,C11,C12,C13,C14,C15,C16,C17,C18,C19,C20,C21,C22,C23,C24,C25,C26,C27,C28,C29,C30,C31,C32,C33,C34,C35,C36,C37,C38,C39,C40,C41,C42,C43,C44

Image

If you're using autoPACK to generate the molecules, or if the lipids are in a perpendicular plane, then you can use a gradient color material from the host software to colorize them... I often do this, as demonstrated subtly in this video (dark tails, light grey heads)
http://www.autopack.org/documentation/t ... rs-for-hiv


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