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