samedi 29 mars 2008

DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques

My laboratory have his new web site on-line at this url :
Currently under construction, this web site gives some information on the different research thematics handle by the lab. Except mine as i already didn't send my contribution to the webmaster!!.

mercredi 26 mars 2008

blender armatures and protein's cube

As I work around molecular graphism, i am trying all methods that can be available. This time it is the powerfull blender and his python API. Generally, I first generated the protein object using an ancilliary software like VMD or ICM, but i was thinking about a direct way to use PDB files in 3d modeling package. There is some plug-in for blender, 3DSmax or maya, but they just get atom as sphere. In the other hand you can easily find on the web some python API dedicated for molecular modeling. Thus, i am currently trying this path. And here are my first result. All sphere or cube are group in amino acid. And you can select any subselection available for protein (amino acid, atom, secondary structure, etc..).
The script is at his begining so i cannot put it here, but when or if I have a clean version i will post it for sure. Because, for instance i need to add material for each type of atom or amino acid.
The first one is just an idea i have with a friend (richard eudes), about why always visualize protein as sphere and not CUBE...

This second exemple illustrate the carbon alpha (Cube) connected using blender armature's bones. The bones are rendering using the script from

I think about trying metaball of type Cube, and also some collision in blender.....

mardi 25 mars 2008

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 (, 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
for j=1,Nof(aa)

#Zscore/normalisation of the matrix
for i=1,Nof(RI12[1,?])
for j=2,Nof(RI12[?,1])
#normal plot
plot area RI12 grid link ds

#3D plot
make grob solid "3dp_plot_name" ZRI12 x y 0.5 # scales for x,y and z

jeudi 20 mars 2008

logo DSIMB

Continuation of the logo's work. This time i have tried the svg import option of blender. Namely, you can export spline made in inkscape or gimp to blender in order to extrude them.
Here is an exemple, the text comes from Aurelie Bornot and are then convert to path in inkscape and save as svg file. Loaded in blender to extrude and modify (blend) to follow the sphere shape.
There is still work to do, get plain text, modify the D color, modify the M form, and change the background to transparent...

mercredi 12 mars 2008

structural alphabet soupe

I like this animation. For the details it is a molecular dynamic (gromacs) play in reverse mode. I have produce the letter using ... that I have made for some reason..
The rendering was done using VMD and gelato

molecular gift

I have found this web site, I think they propose origninal gift for you entourage!

(i found the link on the Inkling Magazine - On the hunch that science rocks web blog: