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

Part VII YASARA visualizer.

A sidetracking journey.

In a previous post I started a short journey through the valley of Energy Minimization. One of the forcefields I made use of is the YASARA forcefield available locally or via a web server. The server returns an interesting file format called sce. To open said file you need to get the YASARA view which is available for free. So to further our collective knowledge I’ll take the plunge and review YASARA View for you.

Although available for free YASARA requires you to register to obtain a serial number and the download. View binaries are available for Windows, Linux and MacOSX. 

Ok, let’s dive in. 

For starters, View allows you to load YASARA format object or scenes. It also lets you load local PDBs, PDBs from internet Protein Database or from a local database. As a final option, you have the “other format” which translates to import. View supports a plethora of file formats. I did try mol2 but not other formats. 

As for saving options, you can save your work as Yasara scenes, objects, PDB, FASTA files, normal screen shoots, ray traced images or any file format suppported by View. 

It is nice to see a proprietary visualizer to support import and export of such a variety of formats. 

If you open the Edit menu you’ll be greeted with a wide array of options such as add, delete, remove, center, transfer, transform, split, join, build, swap and more. While having these option is impressiveI would expect some to require energy minimization afterwards (such as adjust bond orders). 

As we move to the Analyze menu you can find the usual options, superpose, align, RMSD of, geometry, radius of ..., sequence, list, count, occupancy, B-factor, secondary structure, mass and check. 

Surprisingly, the align options has many many internal options. You can align pairwise using MUSTANG, Sheba, Multiprot, CE. Mustang can be used to align molecules or for  multiple structure alignment. PDB neighbors can be found with FatCat. Sequence based alignment can be done based on the Smith & Walterman or Needleman & Wunsch algorithms. 

Radius... calculates nuclear radius, Van der Waals radius or radius of gyration. 

Next, the view menu controls how things look on the screen. Among the most interesting options is the Color options that allows you to tap in to the Consurf server and get your protein colored by conservation. The rest of the options are very common. 

The effects menu controls things like the model quality, orientation, labels and the display quality. It also let’s you label elements in the scene as well as create some objects such as arrows. 

The options menus seems to be devoted to stuff like text output and macro running. It also shows details for the input devices. Sadly, in this version the 3D connexion controller is not enabled. 

Lastly, the window menu controls the appearance of the window like size, full screen or windowed. It also controls the appearance of the menu, the console and other messages. 

So far the YASARA view sounds good and useful. For me, that already use two or three other visualizers, the learning curve is too steep. Now, some of the most interesting options must certainly make sense for the Model or Dynamics versions in view they are just teasers. Still I can recommend it, you should try it.