The subject for this animation is an antigliadin human antibody (PDB: 5IK3), in complex with a gluten-derived peptide that acts as the epitope. The antibody is responsible for the triggering of the immune system in celiacs, and is a dimer (4 chains in total), with each unit able to interact with one peptide molecule.

This time I focused on showing the H bonds that are involved in the epitope recognition, while also playing around with movements and surfaces.

The scenes

I split the animation in four scenes, to work more easily with each effect.

Scene one:



wait 25;

zoom 2 180;

turn y 1 180;

wait 180;

Simple rotation and zoom of the model, at the end of the scene one of the peptide chains is at the center of the screen.

Scene two:



wait 20;

zoom 1.5 88;

wait 88;

crossfade;

hide /A,B,C,D;

crossfade;

surface /A,B,C,D transparency 60;

wait 40;

Atoms of the antibody’s chains are hidden, and the surface is shown with a 60% transparency

Scene three:



wait 20;

crossfade;

show /Y :< 4;

ribbon /Y :< 4;

hide /Y ribbon;

style stick;

wait 20;

crossfade;

hide surface;

hide /X

surface /Y :< 5;

hide #2.6;

wait 40;

Lines 3-6 show atoms and ribbons of the antibody next to the chain Y (gluten peptide); the first command change automatically also the style of the peptide, so I added 2 lines to bring it back to stick style.

In the other lines I hide the entire surface of the model as well as chain X, which is the second peptide present in the model, and show only the surface next to chain Y. Again here, the command shows also the surface of the peptide, so I added line 12 to hide it (#2.6).

 

Scene four:



turn -x 1 20;

turn -y 1 20;

wait 20;

crossfade;

show #2.7;

wait 25;

crossfade 20;

color #2.7 gold;

wait 30;

crossfade 20;

color #2.7 #66b8ff;

wait 20;

crossfade 20;

color #2.7 gold;

wait 30;

crossfade 20;

color #2.7 #66b8ff;

wait 45;

I added a little rotation to the model, and I showed the H bonds (#2.7) that I previously calculated using the Hbond menu. Lines 7-12 are repeated 2 times, to add a flickering effect on the Hbonds, which go from the standard light blue to gold.

 

Final render

 


 

Note: the final resolution of the video is 1800x1800, and this can be done by changing the window size using: windowsize 1800 1800.

Windows of this size make problems by hiding the command line, which I suggest undocking (right-click on the command line) and putting on the high-left of the model. Then changed the background color from the standard white and set the light to full.

 

The movement commands were put in between the two lines necessary to record the movie:

movie record;

…

movie encode ~/Desktop/HD.mp4

 

You can download the original cxs file from here, you can also visit my other posts on the section Gallery, for the explanation on commands that I didn’t focus on this time.