Re: [ccp4bb] Used AREIMOL to judge the steric clashes
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
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
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
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
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 170.900 181.400 240.20090.00090.00090.000 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
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
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 170.900 181.400 240.20090.00090.00090.000 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
[ccp4bb] Used AREIMOL to judge the steric clashes
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
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
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
Re: [ccp4bb] Used AREIMOL to judge the steric clashes
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
