CBSE Ribbons

Macromolecular structure visualization: a look at the applications that provide graphical interface to structure analysis. Part VI Ribbons.

It has been a while but I am back. You might notice the change in the name of the blog. It is there because I am getting old and so I must become a bit more serious. However, it is going to be the same blog.

Thus, I am back at the reviews. This time, I am taking notes for Ribbons. As with the software previously reviewed, Ribbons is free software. It is more difficult to install than the other and somewhat single-minded. Let me explain further: First, to install it you need to download between 3 to 5 tar.gz files. For Mac OS X, the famous Bill Scott from UCSC, there is a dmg file, which simplifies the installation. There is also a fink package to install Ribbons. Second, Ribbons is very focused on generating high quality 3D structure illustrations. It won’t give you access to electrostatic calculations or anything fancy. It is also a somewhat convoluted interface… but more about that in the body of the review.

Ease of use

Ribbons is different than most visualization in that it generates files to describe all its protein representations. So, to display any given structure you have two basic options: running the command ribbons –e your.pdb or run ribbons-data and go through the window system to generate your figure. Here is a screenshot of the windows you have to display in order to generate a surface representation:

Many, maybe several windows just to create a surface representation.

Doesn’t see very straightforward, right? It is difficult to master but IMHO it is very well worth the time. Why? Well, Ribbons is as unique in its interface as in the images you can generate with it. Here you have two images, one generated with the aforementioned ribbons –e your.pdb while the other was generated within ribbons-data generating the so-called Default Drawing.

ribbons -e your.pdb

Ribbons-data using Default Drawing.

The first one ignores the DNA molecule included in the PDB while the second does not.

However, further tweaking requires the navigation of the many menus. But you can get results such as this:

A more elaborate drawing.

A mock drawing.

 

Overall strengths and weaknesses

Strenghts: Beautiful drawings. It is also capable of simple animations such as rotations, translations as well as zooming in and out. With a bit of work, such animations can be assembled into a very complex movie.

Weaknesses: For most things you need to navigate several windows and modify settings until you get what you want.

Conclusion

Ribbons is program that might not be as accessible as others but it can be used to create very unique and beautiful drawings. Better try it before it fades away.