jeudi 28 février 2008

Chemical sunflow

A new test of the sunflow rendering engine. Just to see how render the metal material in a simple scene...

DARC docking

I am actually working on some report on my research. And for that purpose I have this several images representing my preliminar results which comes from rigid-body and flexible docking.

mardi 26 février 2008

DSIMB logo

I have play around the DSIMB motif, which is the new name for my actual laboratory (EBGM).
DSIMB is for "Dynamique et Structure des interactions des macromolécules biologiques".
The first one were using my ABCgen web server, which have produce the pdb file for the text "DSIMB", and then using VMD exported to gelato. Layer were add in the gimp.
The second serie comes from Blender.
The last one correspond to an idea from Aurélie Bornot which is a phd in the lab.

vendredi 15 février 2008


In my search for nice molecular graphism, i am trying a lot of 3d render engine. I would like to put here some picture done with the last I have found on the web : Sunflow ( It is a java based rendering engine, and he works really fine. It is really easy to use, and the API seems well documented.
The following image was done from their aliens_shiny exemple merge with the cornell_box exemple.
I have to tried the ambiant occlusion shader, and see if it simple to automatize sunflow in a pipeline.

My first test:


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
for i=1,Nof(conf)

#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
set a_dot_ca.m/t/ca Mean(Xyz(a_2.a))
set bfactor a_dot_ca.m/t/ca Real(tm.nvis [i] )

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

and the resulting figure :