3D-lattice protein

Sam Rushing 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
existing program.

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.

best wishes!

Chuck An

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.



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