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
>>>
>>
>>
>>
>
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