rushing at titan.ksc.nasa.gov
Thu Mar 10 10:27:59 EST 1994
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