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

            One of the many products of a (successful) macromolecule crystallization experiment is the publication of a Cartesian coordinate file that represents a 3D structure (proteins, DNA, RNA, etc.). These files, faithfully deposited at the RCSB protein databank are usually referred as “3d structures”. Many tools for structure analysis have been produced but not all of them offer a GUI (graphical user interface). Although experience 3d structure users may scoff at the need of a GUI in my experience a GUI will lower the entry barrier for new minds (eyes and hands) to venture into the realm of structure analysis.

The purpose of this blog entry is to bring an update to the reviews for free visualization software available. I will cover three main topics: ease of use, available features and overall strengths and weaknesses.

First off, I’ll review Deep View (a.k.a. Swiss-PDB viewer).

N.B.  I am a Mac user (10.6) so most of the software reviewed will be running via Aqua or X11.

Deep View v4.0, ease of use:

I have been using Deep View since, well, since the Pentium era (I think). That will set time around 1995. It sounds about right. At first I used it in Windows but I experimented with the Linux version. Around 2003 I switch to Mac and have been using so since then. During this 15 year interval I think it has change little.

The overall experience seems derived from SGI guidelines namely five main and three optional ones.

The main windows are: Toolbar, Control Panel, Alignment, Layers info and the Graphic. The latter is not explicitly list on the Windows menu but it is treated as an independent window by the system.

The main Apple menu is available despite which window is selected. The Toolbar contains 16 tools not available elsewhere. Among them is the movement control. Translate, zoom and rotate must be clicked on order to effect such transformations with the mouse (left click). It seems that, regardless of this selection, left click will always translate the selection.

Control Panel and Alignment allow residue level selection both for single or multiple residues. Layers info allows for some of the functionality otherwise located on the Display menu and Control Panel window. However, when displaying multiple structures the windows allow an easier way to handle display properties than the menus.

The three optional menus light up upon loading the relevant files: Ramachadran Plot when you load a protein file, Electron Density and Potential Maps when either is loaded and Cavities and Surfaces when those are loaded. Now, Deep View can calculate Potential Maps as well as Cavities or Surface Maps. I’ll cover those on the Available features section.

Overall, most of the common functions are accessible through the Apple Menu or the Main and Optional windows.

Available features.

DeepView will read PDB files and MOL (SDF) structure files. It will read Surface files on MSMS, DeepView and Grasp format. For the electrostatic potentials it can read SPDBV or Grasp/Delphi. Electron Density files on DN6, CCP4 and XPLOR format.

By now it should be obvious that SPDBV refers to the surface and electrostatic potentials that DeepView can itself calculate.

The import menu allows for PDB loading straight from the Network.

This is also evident by the Save submenus full with options ranging from saving layers, surfaces, single sequences or sequence alignments, images and PovRay/MegaPOV scenes. In that regard, DeepView has very unique options.

At this point it might necessary to say that DeepView seems to be geared towards X-ray model refinement even if so at very basic level. Thus, it also offers options such as Blast searches against Uniprot. The Build menu contains options for loop building as well as addition/subtraction of atoms, bonds or even water molecules. Removing water molecules is useful when preparing PDBs for another program/process.

In the Tools menu is where Surface, Electrostatics, H-Bonds, as well as Energy Minimizations are available. Except for the Electrostatic Calculations all of these functions have their preferences hidden in another menu, which sometimes can a bit bothersome. Energy minimization also shows by residue results on another text window. Energy minimization will add H atoms to the structure.

The Fit menu is devoted to pairwise structure fitting allowing for a wide variation of parameters. The results for most of these calculations are usually displayed on the Toolbar (colored red).

Display, Colors and Prefs are, in a sense, all devoted to preferences. Personally, the Color menu for Protein problems is unique since it is very useful to pinpoint unusual residues even on a very large structure.

Swiss Model menu is another unique menu. This one links DeepView with the server for protein structure modeling, SwissModel. If you are taking your first steps into homology  modeling there are very few free interfaces with this much ease of use.

Overall strengths and weakness.

There is a very useful feature in DeepView, chain reconstruction upon protein loading. This one is very good. I haven’t find any other utility on par with the one on DeepView even UCSF Chimera (review coming soon). Another strength is the ease of use.
This ease is hampered by the interface design which makes it slow to use.  Another downside is that DeepView runs on less than millions of colors. So it will change you screen color display system wide. In terms of overall speed, I have found that only when displaying Surfaces (electrostatics or otherwise).

Another strength is the availability of plenty of tutorials on the DeepView website.

I haven’t used the script function but I have heard it is useful.

Conclusion.

DeepView is a very useful, easy to use GUI protein structure analysis tools. Most of the outputs are explicit (text windows or red text) and allows for many file format read and write functions which means it is very compatible with other tools. Have I mentioned it is free? Well, it is.

By the way, if you have any comments, suggestion or think I miss a key feature please chime in!