BNFO 491 
Molecular Biology Through Discovery
Protein Explorer - Help
Fall 2012 

Protein Explorer is a resource that enables you to visualize proteins in three-dimensions and provides tools that help you focus on different features within the protein. It has great capabilities, but most of them require you to interact with it through a specialized language. The language is simple, but even so, if you want a menu-driven interface, you might prefer FirstGlance, at the expense of some capabilities.

There is a lot of online help available through Protein Explorer. The purpose of this web page is to help you find that help and figure out which brand is what you need.

Getting Started
Going to Protein Explorer gets you to the following page:
Your ticket inside is a four-character PDB (Protein DataBase) code. If you know the protein you want but don't know its PDB code, you might be able to find it by searching the Protein Data Base.

After you enter the PDB code, you'll be brought to the First View screen. There's little you can do here that you can't do on the more powerful Quick View screen. Go there by clicking 'Quick'.

The Quick View screen allows you to do some things easily, using the preset interface at the top of the page. If you play with it, you'll be amazed at its abilities. Some things, however, require the flexibility offered by the command box at the bottom of the page. But what commands to use? The help pages described in the next section may be of some help.

Summary of Help Resources

  • RasMol Manual
    RasMol is one of the two languages that drive Protein Explorer. Its manual is gigantic. There's a reasonable chance that what you're looking for is there, somewhere.
     
  • Select Commands in Jmol and Rasmol
    Jmol is the other language that drives Protein Explorer. The most common commands you'll use are those that select certain parts of the structure (e.g. specific chains or certain amino acids). This help page focuses on those commands.
     
  • Jmol Command Summary
    List of available commands and links to full descriptions
     
  • Index/Glossary (alphabetical)
    Once you scroll past the first page, an alphabetical list of concepts
     
  • Some suggested commands
    Command Meaning
    select glu
    select glu:A
    select 24
    select 24:A
    select glu24
    select glu24:A
    select all     		Selects all glutamates
    Selects all glutamates only in chain A
    Selects residue #24 in all chains
    Selects residue #24 only in chain A
    Selects residue #24 only if it is a glutamate
    Selects residue #24 in chain A only if it is a glutamate
    Selects all atoms
    color red Changes color of selected atoms to red
    cartoon only
    wireframe only
    spacefill only
    spacefill 1.0 only     		Represents selected atoms as secondary structure
    Represents selected atoms as atoms and bonds
    Represents selected atoms as spheres using Van der Waals radius
    Represents selected atoms as spheres using given radius (in Angstroms)
    zoom 200 Zooms image to 200% of original
    hide :a
    display :a
    hide glu     		Make chain A disappear
    Make chain A reappear
    Make all glutamates disappear
    write c:\temp\filename.gif Writes currently displayed image to given file