Untitled Document

History and Motivation

I (Rob Scarrow) developed "Molecular Cruiser" with inspiration (and some javascript code) from Eric Martz's Protein Explorer web application. I have used RASMOL in my teaching for the past decade or more, and have also used web-pages which use the CHIME plug-in with RASMOL scripts. Martz's Protein Explorer is an impressive example of a web site exploiting the capabilities of CHIME, but despite the impressive array of menu options, the part I like the best is the RASMOL command line interface that is built in (i.e. one can run RASMOL from within the web page). So I borrowed that aspect in designing Molecular Cruiser, although I improved on it a bit by allowing the user to control what type of output shows up in the RASMOL output area (for instance, by showing just the RASMOL input commands, one can more easily cut and paste to make a script file).

Features

I also took the opportunity to add a few features that I've always wanted in RASMOL (or other macromolecular structure viewing programs).

"Cruising". Perhaps because of my chemical training, I've always wanted to look at protein structures a little bit at a time. The cruising features allow the user to just see the atoms and bonds that are within a specified distance (typically 5 - 10 Å) around a specified atom or atoms.
When the .pdb file is loaded, I use CHIME's "set connect save" mode. As a result, the CONECT records (usually present at the end of the PDB files, but ignored by RASMOL) are used to force bonds to be drawn between specified atoms. This can solve the problem that RASMOL doesn't find all the coordination bonds around metal ions.
- Unfortunately, not all PDB files specify all bonds, or they may miss a few bonds. It is a relatively easy task to add them. For instance, in the pdb file for the BTUF protein (1N4A.pdb) only 5 of the 6 bonds to cobalt are specified. To specify the sixth bond, I added the line 'CONECT 3900 3983' right before the END statement of the file (see 1N4A_conect.txt). The format for CONECT statements is CONECTxxxxxyyyyy, where xxxxx and yyyyy are the atomno's for the bonded atoms (xxxxx must be < yyyyy), and enough spaces are inserted to make a total of 5 character spaces for each number.
When the coordinates are loaded, I define atom sets called "metals", "nonmetals" and "semimetals" (I put only a few elements into the semimetals category - Si, Ge, Sb, Po and At; I consider B a non-metal). These are useful for RASMOL scripts later on (including the "Spacefill Metals" option that appears in the "Appearance..." menu).

System Requirements

The Molecular Cruiser has been tested on the following systems:

Windows XP, Internet Explorer 6, Chime 2.6 (SP5) and on
Macintosh System 9.2, Netscape 4.78, Chime 2.5.

Known Bugs

The pdb code entry for the Generic Cruiser (which generates a URL for fetching the coordinates from the RCSB site) works on Windows, but not Mac/Netscape (at least not on my computer)
In early testing, I encountered some memory problems on the Windows XP systems when the windowsize was too large or many Internet Explorer windows were open. I may have fixed this problem when I fixed some other JavaScript errors.

How to use

Here are some hints to get you started. If you haven't used RASMOL previously, you may want to start with a RASMOL tutorial (see next section). Here are some hints:

You may want to start with the pages that are designed for specific proteins. These pages load in a copy of the pdb file from the Haverford web site (in a few cases, the pdb file has been modified by addition of CONECT lines as noted above, but in that case the file name of the pdb file has been changed to make it clear that it has been modified).
Try typing in RASMOL commands followed by the "Enter" key (on the keyboard). To get you started if you haven't used RASMOL before, I've included a different RASMOL hint at the bottom of each page. Semi-colons are used to separate multiple RASMOL commands, but for beginners, type in one command at a time.
On the left side of the Molecular Cruiser control panel (which has a peach colored background) there are buttons to execute standard RASMOL commands for the picking action (what happens when you click on an atom in the CHIME graphics window). On the right side are cruiser buttons. When either "cruiser picking ident" or "cruiser picking monitors" are chosen, the RASMOL picking mode is set to ident, so that the atom will be identified when it is clicked upon. But when these cruiser modes are active, a special script is run after each atom is identified.
- In "cruiser picking ident" mode, all the atoms within the specified distance are displayed in ball and stick mode. I'll call this making a "cruise visit".
  - The bond thickness is given by the stick value xxx (this value is put into a "wireframe xxx" command)
  - The atom thickness is given by the ball value yyy (put into a spacefill yyy command; yyy can be "on" to give vdW radii, but this isn't very useful).
  - The "recenter" checkbox, if checked, causes the selected atom to be moved to the center of the picture. Regardless of whether this is checked, the selected atom becomes the center of rotation (but both RASMOL and CHIME have trouble with rotations if you zoom in too much).
  - If the "restrict" checkbox is checked, all bonds and atoms outside of this radius are disappeared.
  - If the color by CPK button is checked, this color will be applied to all atoms within the selected radius (however, the CPK coloring is not applied to the bonds that extend to atoms outside of the selected radius).
  - The selected atom can be given a bigger size, which is useful for being sure you know which atom was selected.
  - The "size by distance" gives intermediate sizes to atoms that are closest to the selected atoms. Assuming that the selected atom is given a size of 1.2 and the ball value is 0.2, then the following sizes will be used:
    - atoms > 4.0 Å will be 0.2 Å balls
      atoms 3.2 - 4.0 Å will be 0.3 Å balls
      atoms 2.4 - 3.2 Å (i.e. H bonding O-O, O-N or N-N distances) will be 0.5 Å balls
      atoms 1.6 - 2.4 Å (i.e. coordination bond range) will be 0.7 Å balls
      atoms 0.8 - 1.6 Å (i.e. normal bonds) will be 0.9 Å balls
      atoms 0 - 0.8 Å will be 1.1 Å (these are probably disordered alternate atom positions)
      the selected atom will be 1.2 Å
- In "cruiser picking montior" mode:
  - The first click works just the same way as in "cruiser picking ident" mode
  - The second click adds a monitor between the previously selected atom and the newly selected atoms. Monitors show the distance between two atoms, and add a dotted line.
  - The third click starts over - i.e. executes a new "cruise visit" and selects a first atom for a new monitor.
- The "cruise current selection" button executes a cruise visit to whatever is currently selected. You can use this to generate a view of the vicinity of a dinuclear metal site in a protein by first choosing "set picking selection", clicking on the two metal atoms to select them, and then "cruise current selection". Or if all atoms are selected ("select all") this will show all the atoms in ball and stick mode.
The CHIME window size is specified in the bottom frame (with a blue background) in pixels (W means width; H means height). Changing these values has no immediate effect, but the new values will be used if you "Reload" or go back to the Cruiser Index and load a different page.
I avoided putting fontsize specifiers in the HTML code so that font sizes can be changed using the menus of Internet Explorer or Netscape.

Learning more about RASMOL

Try these web sites:

Rasmol home page at U. of Massachusetts: http://www.umass.edu/microbio/rasmol/index2.htm

Rasmol and OpenRasMol home page: http://www.openrasmol.org/

Feedback

Please send comments and suggestions to me at rscarrow@haverford.edu

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