Hailiang Zhang wrote:
Thanks Edward! Actually Areaimol works well for my problem.
But now I have a new issue looking for some advice. I want to randomly
generate some points in the unit cell and make a quick judgment whether it
is outside of the solvent mask or not. It seems that Areaimol doesn't help
at this point, and wonder whether some others tools in CCP4 can help to
make it.
Convert solvent mask to a map, exress the random points as dummy atoms in a
pdb file, and see reent thread on "program to calculate electron density at
x,y,z"
for methods to print out density at arbitrary points in a map.
Thanks again for your help!
Best Regards, Hailiang
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
