BLOGGER TEMPLATES AND TWITTER BACKGROUNDS

vendredi 15 février 2008

DARC-Docking

I have made a litle script in the ICM (molsoft) package. It permit me to observe the position of the docking search by sphere (one sphere one ligand position), color by the number of visit. The representation is load in VMD and render to Gelato. The different pass were merged in gimp using the "value" mode.
For interested people, here is the litle icm script:

#generate a polyA sequence string
s1=""
for i=1,Nof(conf)
s1=s1+"A"
endfor

#build the polyA peptide and make only the Ca
build string IcmSequence( s1 "nter" "cooh" ) name= Name( Name( "dot" simple ), object )
makeCaTrace a_dot.
delete a_dot.

#for every conformation generatd during the docking, assign to the Ca atom the position of the Center of Mas of the ligand, and assign the number of visit to the atom's Bfactor

for i=1,Nof(conf)
load conf i
t=i+1
set a_dot_ca.m/t/ca Mean(Xyz(a_2.a))
set bfactor a_dot_ca.m/t/ca Real(tm.nvis [i] )
endfor

#then color by bfactor
color a_dot_ca.//* Bfactor(a_dot_ca.//*)


and the resulting figure :



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