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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. 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 >> > > >