Dave.Buss at studorg.uio.no
Thu Mar 10 10:30:31 EST 1994
In article <2lne9v$otq at hermod.uio.no>, rushing at titan.ksc.nasa.gov (Sam Rushing) says:
>In article <Pine.3.85.9403081855.A15756-0100000 at fox.cce.usp.br>, szeinfel at FOX.CCE.USP.BR (Rafael N Szeinfeld) says:
>> Hi Netter's
>> I would like to know if there is any program that takes as input
>>a pdb file with atomic coordinates of a protein (let's say from Brokheaven
>>protein databank) and inserts it in a cubic lattice (you define the
>>dimensions of the unit cell) so that as output you have a matrix M(AxBxC)
>>where each element of the matrix M(i,j,k)=1 if the this unit cell is
>>ocuppied by one or more atoms or M(i,j,k)=0 if this unit cell is empty.
>>By adjusting the dimension(l, where V(volume)=l^3) you can select how
>>accurate is your lattice model if your unit cell have the dimensions of
>>an atom, your lattice model will be equal to the atomic coordinates file.
>>I'm not sure if I expressed well my idea but I'll appreciate any comment.
>> Rafael Najmanovich
>very good idea and it's new, so I think you won't have chance to find out an
>however since you've got such a clear idea, it wouldn't take long for people who
>has experience to build such a one from sratch.
>ps. I'm not sure what you are going to do with this arigorithm. but would you
>agree that, since a protein is almost as compact as any crystalls, there won't be
>so many zeros in the matrix? regardless what kind of cordinates you are going
>to make use of.
More information about the Proteins