Re: [PyMOL] Coloring structure by hydrophobicity
Hi Andrew, regarding hydrophobicity coloring, we use the rTools from Kristian Rother. http://www.rubor.de/bioinf/pymol_extensions.html The coloring schemes are according to http://www.expasy.org/cgi-bin/protscale.pl It comes with a nice user interface, or on command prompt you would simply do something like color_protscale 10, selection where 10 is the coloring scheme (might differ in your installation): Normalized consensus hydrophobicity scale. Eisenberg D., Schwarz E., Komarony M., Wall R. J. Mol. Biol. 179:125-142(1984). (See also attached image) Cheers, Andreas Andrew D. Fant wrote: Afternoon all, I apologize if this has been hashed over on the list in the past. I haven't been keeping up like I used to. Is there a good way to calculate and color residues by hydrophobicity in pymol? A google search showed only a very simple script that was based entirely on a single-residue lookup table. I'm looking at a set of structure predictions, and it would be nice to easily see that a fold exposes a large patch of hydrophobic surface to solvent. Thanks, Andy -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de inline: hydrophobicity.jpg
Re: [PyMOL] Coloring structure by hydrophobicity
Is there a good way to calculate and color residues by hydrophobicity in pymol? A google search showed only a very simple script that was based entirely on a single-residue lookup table. I'm looking at a set of structure predictions, and it would be nice to easily see that a fold exposes a large patch of hydrophobic surface to solvent. Could you clarify what you're trying to do? I'd think that coloring residues by hydrophobicity, displaying the surface, and looking for whatever your favorite color for hydrophobic is would work fine. Why would a lookup table be inappropriate for what you're trying to do? Pete Pete Meyer Fu Lab BMCB grad student Cornell University
[PyMOL] Coloring structure by hydrophobicity
Afternoon all, I apologize if this has been hashed over on the list in the past. I haven't been keeping up like I used to. Is there a good way to calculate and color residues by hydrophobicity in pymol? A google search showed only a very simple script that was based entirely on a single-residue lookup table. I'm looking at a set of structure predictions, and it would be nice to easily see that a fold exposes a large patch of hydrophobic surface to solvent. Thanks, Andy -- Andrew Fant| And when the night is cloudy| This space to let Molecular Geek | There is still a light |-- f...@pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself
