Hi, I am modeling membrane proteins and I dont want a particular loop to enter in to the membrane. However as this loop is long (about 40 amino acids) and has nothing to model on (gap in template), it seems to form a sheet parallel to the transmembrane helices. This has to be avoided because the loop should not enter the membrane. My question is whether I can cause some restraints in Modeller by which any of the atoms in the loop donot have z-coordinate below a certain number.

Thanks in advance, Anurag Sethi