Hi Fahimeh, what has happened here is that the interface area in the new file is very small, particularly after the periphery is "trimmed" (see the original paper for how this is defined). For the old file, the area is about 1100 Angs**2, for the new it is about 110 Angs**2. As the log file states, Sc is then not a very good measure of complementarity.
sincerely Mike Lawrence > Hello :) > > I am trying to find the shape complementarity of two structures. both of > them are two layer of betasheet, that I have excluded hydrogens. in one of > them (old.pdb, attached to the email) I have two complete layer in which > chain A are all the strands in one layer and chain B are all the strands > in > the other layer. and in the other structure (new.pdb) I removed two > strands > from the middle of betasheet. > I run Sc and the results are attached in sc_old.log and sc_new.log > > As you can see, sc factor is higher in the second structure , which is > missing two strands in the middle?! > How it is possible? I am confused ;) > Am I missing something? > > Thank you in advance > Fahimeh > ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________
