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:white_check_mark::x:Evolutionary protein-protein interface classifier
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Improve the molecular potato #12

Closed josemduarte closed 8 years ago

josemduarte commented 10 years ago

Issue by josemduarte Wednesday Apr 09, 2014 at 16:58 GMT Originally opened as https://github.com/eppic-team/eppic-wui/issues/6

The pymol color-by-entropy surface PSE files (a.k.a. molecular potatoes) are great for looking at things visually, but still not good enough. One possibility for improvement would be to display the interface PSEs as "cartopotatoes" i.e. one side potato and one side cartoon (perhaps still with core residues as sticks). From that one can get a good idea of the interface and the conservation around it. One thing still to think about is what to do about heterologous interfaces. For isologous it's clear that showing the potato on one side is all one needs, but for heterologous one would want to see the potato on either side.

Any ideas? The code to produce them is pretty easy to hack, it's all in the PymolRunner class in the eppic project.

josemduarte commented 10 years ago

Comment by kumar-physics Thursday Apr 10, 2014 at 10:33 GMT

For heterologous interfaces, we may show two potatoes , with one potato as transparent/semi-transparent . One problem here is the actual colors may be affected.

josemduarte commented 10 years ago

Comment by gcapitani Thursday Apr 10, 2014 at 10:56 GMT

Another solution (a bit "heavy") would be to create two "complementary" cartopotatoes for each heterologous interface (for a complex AB, cartopotato1 would display A as potato and B as cartoon, cartopotato2 would display A as cartoon and B as potato).

josemduarte commented 10 years ago

Comment by kumar-physics Friday Apr 11, 2014 at 07:56 GMT

Pymol plugin is now ready for testing. Its is available in eppic-precal/pymolplugin . Now you can have both GUI and command line tool to load eppic interfaces. Once you install the plugin you can use load_eppic command to load eppic interface files. If only pdbid is given , then it will load all interfaces and if pdbid-interfaceid is given then it will load only that interface. Example:

load_eppic 2gs2 or load_eppic 2gs2-3

sbliven commented 8 years ago

Solved by the pymol plugin

josemduarte commented 8 years ago

And by surface rendering in NGL