MGLTools PMV - Gelato

I have recently discover the MGLTools-PMV software and its amazing number of possibility...(see http://mgltools.scripps.edu/ from http://mgl.scripps.edu/ ). Playing with, its seems really easy to add plug-in and new functionality. Like I did here to integrate the nvidia rendering engine gelato as a plug-in accessible for the file menu of pmv :



A simple capture from pmv (with antialiasing) look like this (and this is a realy simple one...):



Using gelato, I can select which object inside Pmv I want to render with gelato, and choose an apropriate shader. Currently, the plug-in only handle CPK and ball&stick style.
The ambiant occlusion is still a good choice to increase the quality of picture :

Then I just have to combine this two picture using imagemagic, gimp or either the vision software (part of the mgl tools... http://mgltools.scripps.edu/packages/vision ), i will try to show something later with this.

IBISC gift

From skecth to final crystal printing picture. The idea was to unfold the dna double strand around a gene netowrk ....

metaBALL blender

PDB -> metaball blender -> Kerkythea

home protein contemporary art

Same protein as previous, but this time put in a room with daylight (the scene comes from http://www.mrcad.com/?p=166)...I don't know if I would like such art in my appartment ...

protein breakfast & lunch

I dedicated this picture for all people who think, live, wakeup etc... with protein structure. The scene is come from http://www.3dm3.com/tutorials/mr/. The protein come from the PDB (http://www.rcsb.org/)...

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).

rendering test

Its just a test, but it took more than 4hours on my poor computer...(click to enlarge the picture)

small heat-shock protein

During my last post-doc i had work on small heat shock protien assembly using some nice tools for doing symmetrical restrained computational docking. Thus, as usual i try to produce some nice graphism, and here is a exemple of the HSP16.5 24mer respresented as cartoon ribbon fitted in the molecular shape computed in the molsoft icm package.

Pushing the Boundaries of Biomolecular Simulation

I am really happy to show the poster that I will present during the Pushing the Boundaries of Biomolecular Simulation meeting (http://web.mac.com/laveryr/ISQBP08/Welcome.html). Many important people from the molecular modeling fields will be present and I hope they will enjoy my litlle poster...

Proteins Blocks

A litle attempt to get nices pictures illustrating proteins blocks. You can find more details on the web site of Alexandre De Brevern.

hand shadow

For me, beautifull results happens accidently.Here is an exemple of hasard. Thats fun this face appearing in the background, like hand shadow coming from the "Nightmare Before christmas" movie.

Nice video that i have found on a friends web site (volta.fr):

"The video was created by me (Michael Wesch), working alone from my house in St. George, Kansas. I used CamStudio for the screen captures and Sony Vegas for the panning/cropping/zooming animations. Someday I might make a video tutorial for those who are interested."

Protein-Protein Interaction Website

The most relevant place to find information about protein-protein is the JBC Protein-Protein Interaction Website : http://www.imb-jena.de/jcb/ppi/

You should find all the litterature, software, database, company, meeting, course, tutorial etc...about protein-protein interaction. Put it on your favorites if it is not the case!

bezier curve for protein ruban

Thats dones! I am quite happy to finally get a nice protein worm representation directly in blender. But there is still the coloring method problem...I have to associate vertex with material according physical property...And try to display arrow and helix for secondary structure type...
(thanks to the blender tutorial here :http://jmsoler.free.fr/didacticiel/blender/tutor/cpl_celticknot.htm and the API help)

Can a Biologist Fix a Radio?

This is not news, and I am not the first to post this, but as much it is diffuse the better it is!
here it is the : Can a Biologist Fix a Radio? (PDF - 469 KB), by Yuri Lazebnik. It’s all about how experimental biologists would try to find out how a radio works. The article suggests that an engineering-like approach would lead to a deeper understanding of how cells work (last time i have saw it reasonable deviation, also on Freelancing Science and God Plays Dice).

blender protein ribbon

I continue to play around python and blender API. Thats not easy, but copy/past technics gives some result...Thus, i currently explore the curve system. Each point have the coordinate of an atom, and define a nurb curve. Thats not realistic, I had to improve it to use bezier curve (BezTriple class).



The result (simple, not sophiticated as it is just modeling test, and I have no idea of what color is good or not...dyschromatopsy!):

dsimb

DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques

My laboratory have his new web site on-line at this url : http://www.dsimb.inserm.fr/.
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!!.

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 http://www.malefico3d.org/blog-en/?p=13.

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

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