Hi Edward: Yes, this is really a good way to do it. Now I am trying to generate a solvent map using CCP4 sfall (MODE ATMMAP). The thing is I want to specify a large probe radius (~20A), but it seems that sfall can't change the probe radius at all. Do you know any other tools to do that?
Thanks again for your time! Best Regards, Hailiang > 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 >>>> >>> >>> >>> >> > > >
