Areaimol is good for determining the contact area from the difference you
mentioned. If you want to distinguish real clashes from comfortable
van-der-Waals
contacts, you can use pdbdist3:
http://sb20.lbl.gov/berry/for/pdbdist3.for
The two molecules have to be in separate pdb files. You give a
threshold distance. For every atom in the first structure, every
atom in the second structure that is closer than the threshold distance
results in printing out the pair of atoms and the distance separating them.
this gives a list of all contacts within the threshold distance.
For v-d-w contacts are around 3.4 A, H-bonds 2.7, and anything
closer than 2.0 could be considered a serious clash.
Hailiang Zhang wrote:
Hi,
I have 2 rigid and fixed proteins and want to quickly judge whether there
are some steric clashes. One quick way I am thinking is using CCP4
AREAIMOL to calculate the surfaces of each individual protein as well as
the heterodimer, and check whether the sum of the two individual surfaces
is larger then the dimer. I am wondering whether I can get some advices
about this method.
I also know there must be some other tools to quickly do it since this is
kinda a simple docking problem, and I appreciate if suggested some more
direct methods.
Finally, I am also wondering whether AREAIMOL considers the assymetric
unit during calculation.
Thanks!
Hailiang
