Hi Edward: Actually as I mentioned in the original thread, I have 2 proteins, and wanted to randomly put the smaller one around the larger one, and quickly tell whether there is some steric clashes. The smaller protein has a radius about 20A, and therefore I plan to generate a mask around the larger protein with a probe radius of 20A, and if I random select a point falling inside this mask, I won't even give it a try for the smaller protein. (I need to generate huge amount of conformations and trying to save time for steric clash judgment).
Anyway, I will try MAMA as you suggested, and see how it work. Thanks again for your effort! Best Regards, Hailiang > Do you really want atomradius 20A? > Molecules separated by 40 A atomcenter to atomcenter will > be in contact, exclude solvent? Maybe you should tell us what you > are trying to do? > > Using fft mode atommap to make a protein mask you could use a > low threshold when converting map to mask, which would expand the > atoms somewhat, but not to 20A. > > The uppsala program mama lets you make a protein mask with > setting the atom radius. It has all kind of other neat tools > which may be useful for whatever you are trying to do. > > http://xray.bmc.uu.se/usf/mama_man.html > > ######################################## > #Make a mask in ref cell, grid, etc: > setenv MASKSIZE 4573536 > setenv MApSIZE 4573536 > mama -b <<eof > new Cell 170.900 181.400 240.200 90.000 90.000 90.000 > new Grid 168 168 240 > new radius 2.0 > new pdb m1 ref.pdb > smooth m1 10 > smooth m1 10 > smooth m1 10 > island m1 > fill m1 > write m1 ref.msk > eof > > I think the Uppsala mask format is different from the ccp4 one, but that > it is easy > to convert. > Hailiang Zhang wrote: >> 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 >>>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> >> > > >
