Ok, transparent water can be activated by checking enviormental effects on the graphics settings, Mikhayl told me the reason the conning towers are invisible is because the SH3 conning tower .dat is set up wrong for SH4. Mikhayl fixed this problem with his IIB, if you compare his conning .dat with a stock SH3 .dat you will see the diffrence. You can see how the conning towers are invisible by enabling enviormental effects, submerging the sub, and looking at the conning from the surface. Hope that helps more than before
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