better test (SSS)

a new test of this green material. Less rendering time on a more powerfull computer...(25min)...
This can be for sure optimised...but I like the way the atom appear behind the surface...(clic to enlarge).

Docking contact pairs occurence

Docking or montecarlo procedure produce a huge number of conformation that have to be analysed. As bioinformatician we generally wrote some script to help in such task. In the present exemple, I explain how to calculate/analyse the amino acid occurence of presence at the interface, and furthermore, the occurence of particular pairs of residues in contact. All is done in the ICM package (http://www.molsoft.com/), and lead to produce 3D plot of matrice of pair contact.

The icm code (for example, not complete for clarity purpose):

#All this script is place in the loop exploring all the conformation (ie stack or trajectories) load conf i OR load frame i #method1 get the residues from each partnairs at the interface for a particular pose show surface area a_1.// a_1.// inter1=Res(Sphere(a_2.//* a_1.//* 4.) & Acc(a_1./*)) show surface area a_2.// a_2.// inter2=Res(Sphere(a_1.//* a_2.//* 4.) & Acc(a_2./*)) #method2 get the pairs residues at the interface for a particular pose t=Area(a_2./A, a_1./A) read column group name="aa" input=s_out #given the list of pair, creating the matrix of occurence RI12=Matrix(72,50,0) for j=1,Nof(aa) y=Integer(Name(aa.2[j])[3:Sz]) x=Integer(Name(aa.3[j])[3:Sz]) RI12[x,y]=RI12[x,y]+1 endfor #Zscore/normalisation of the matrix Ntot=Sum(Sum(RI12)) for i=1,Nof(RI12[1,?]) for j=2,Nof(RI12[?,1]) nobsi=Sum(RI12[?,i]) fj=Sum(RI12[j,?])/Ntot ntheoij=nobsi*fj nobsvij=RI12[j,i] zij=(nobsvij-ntheoij)/Sqrt(ntheoij) ZRI12[j,i]=zij endfor endfor #normal plot plot area RI12 grid link ds #3D plot x=Rarray(50,Min(ZRI12),Max(ZRI12)) y=Rarray(72,Min(ZRI12),Max(ZRI12)) make grob solid "3dp_plot_name" ZRI12 x y 0.5 # scales for x,y and z