Accessible volume (AV) simulations

AV simulations are performed similarly as described in (Muschielok et al, 2008). Parameters are defined as shown in Fig. 4A in (Sindbert et al, 2011). In “Three radii AV” simulations, a superposition of AV clouds calculated using three dye radii is taken. Please note that the program is not aware of the linker chemistry. For instance, if the linker is attached to a C atom, the remaining side chain should be manually removed from the pdb file. Otherwise, it is very likely that empty AVs will be generated.