I'm currently studying at Imperial to complete my final year project for my MSci in Chemistry, but due to remote working I have to take on more of a computational project rather than something lab based and I'm not too experienced in the area and neither is my group. 

I have been told to use chimera to model the hydrophobic surface of proteins and determine a value for the surface hydrophobicity that can be later linked to data collected from HIC studies. I've been told to use chimera to model this but even basic visualisation of the hydrophobic surface does not work for proteins as large as rubisco. 

I know this is a big ask and an open ended question but are you aware of any extensions available to use to mitigate this issue? Or are you aware of any techniques I could use utilising the software to calculate an actual value for the surface hydrophobicity?

I hope you are all keeping safe and well, and thank you for any insight!

Best, 

Sam