[Chimera-users] depict hydrophobicity surface in super large molecules in chimera

Marta Perez Illana marta.perez at cnb.csic.es
Sun Oct 13 07:09:01 PDT 2019

Hi all

I was trying to analyze the hydrophobic surface of two very large 
structures ( 3 chainsx 900 aa each so 2.700aa). As expected the default 
surface calculation has failed. Normally for electrostatic potential 
what works for me is making a mol map (molmap  #3  4 gridSpacing  0.5) 
and then calling the pdb2pqr and apbs servers directly from chimera, 
which is very convenient.

However I cannot find an analogous way to make it with hydrophobicity... 
Since the surface fails for such big molecules, the straight forward way 
(present-3interactive surface hydrophobicity) does fail as well...

Then... is there any server than can be called from chimera, to get 
hydrophobicity as an attribute to be depicted? Or alternatively could 
you suggest any server that gives output hydrophobic column, compatible  
to get it after to chimera attributes? Reading a bit I found that, not 
as electric fields, that can be computed for structures, hydrophobicity 
comes just for the sequence, without taking into account the neighbours 
and context...

P.D: I have managed to represent in other programs the hydrophobic 
surface, but I really want to make it in chimera, to make it more 
consistent and easy to organize myself...

Thanks a lot! and sorry if the question goes beyond Chimera...


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