PDB FILES, ACCELYRS VIEWERPRO, and PyMol

PDB Files. Macromolecules for which 3-dimensional structures have been solved contain sets of "coordinates", or collections of numbers, that describe the structures of the molecules. Various computer programs can use these coordinates to generate 3-dimensional structure for visualization and manipulation. All proteins for which 3-dimensional structures have been determined have their coordinate data deposited in the Protein DataBank, in the form of PDB files. The accession of this data is free to everyone. The PDB database can be accessed here. Once you have selected a protein of interest, you may download the PDB file containing the protein coordinates to your own computer. You will then need to have a program that is able to read the coordinates and use them to render a structure that you can manipulate.

The coordinate data for a protein, obtained from the PDB, often contains additional details, such as water molecules, heavy atoms, salts, etc. that you are not interested in visualizing. In addition, the structures of many proteins contain multimers of the protein of interest (even multimers of the multimers of a multimeric protein). Thus, the structure you first access may appear busy and contain more information than you want/need. Therefore, your program must have means to "turn off" or delete portions of the structure that you are not interested in. I will briefly show you how to do this in class using the program "ViewerPro" (see below).

ACCELYRS VIEWERPRO and VIEWERLITE. There are a number of PC-based programs available to view PDB files. My favorite is WebLab ViewerPro from Accelyrs. ViewerPro is expensive to purchase, but the department owns licenses for several copies, loaded onthe computers in the student computer lab. In addition, a free version, ViewerLite, has most of the features of ViewerPro. Importantly, you can view, rotate, highlight, manipulate, and print PDB files freely using ViewerLite. Download ViewerLite by clicking on the link below. You may choose to run and install the program directly, or save it to your computer's hard disk for later installation. ViewerLite is not compatible with macintosh operating systems.

You can view any ".pdb" file with ViewerLite. Do this in one of three ways:

  • Open the pdb file from within the program itself.
  • Drag the icon for the ".pdb" file of interest onto the program icon (or a shortcut thereof) for ViewerLite
  • Right click on the ".pdb" file itself, and select "open with.." from the pop up menu. The ViewerLite program should appear as one of the options.

Once you have opened and modified a ".pdb" file, save it as a ViewerLite file with a new unique name if you wish.

A nice feature of ViewerPro is that you can copy and paste ChemDraw files into open pages (either a blank page or a page with other data). ViewerPro recognizes the ChemDraw structure and automatically adjusts the atom colors, bond angles, distances, etc to generate a properly rendered 3-dimensional structure.

Download WebLab ViewerLite here

SOME PDB FILES AND LINKS OF INTEREST:

  • A zipped file containing sample ViewerPro files (proteins, DNA, small molecules, etc) ready to visualize can be downloaded here
  • The Protein Database
  • Klotho: Biochemical Compounds Declarative Database: An excellent and extensive collection of PDB files for biomolecules (sugars, nucleotides, cofactors, drugs, etc) can be accessed and downloaded from this website. You can download individual PDBs, or a zipped file containing the PDBs for all 439 biomolecules on this site
  • Hetero-compound Information Centre (Hic-Up): a great resource, check it out. Use the search engine to find PDB files for a compound or macromolecule of interest

Using Kinemage software to visualize PDB files. The "kinemages" page contains the kinemage program and some kinemage files for visualization, arranged according to the lecture content of Chemistry 5700/6700 (syllabus for this course is here). The advantage of the kinemage software is that it is extremely easy to use. In addition, a number of "tutorial" files have been created by various people (for example, the Protein Society) that you can download and walk through. The disadvantage of the kinemage program is that it is not particularly powerful for manipulating or rendering high resolution, publication quality graphics. Still, I like it for its simplicity and the tutorial files available. Importantly, the Protein Society has created a program, "PreKin", that will convert PDB files into kinemages. Simply download a PDB file and drag the file icon onto the PreKin program icon. This tool is especially useful for small molecule files, and protein files that have already been cleaned up to remove waters, salts, and other extraneous information.

Download PreKin software here.

 

 
© 2007 Scott A. Ensign