Structural Classification of Proteins
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Using RasMol to look at scop structures

SCOP provides interfaces to RasMol for displaying protein structures colored according to domain definition and secondary structure content. The release that is currently used at MRC, and for which we can provide support for unix/linux users, is RasMol 2.6b2. Click here to download the debian package.

Responsible for the RasMol interface for Windows and Macintosh platforms is Raphaël Leplae (

RasMol interfaces

Once RasMol has been installed on your system, there are two kinds of interfaces that can be used to view structures classified in SCOP by clicking on the rasmol icon (): a simple shell script (rasmolscript) and a more laborious tcl/tk script (rmscop).

Both rasmolscript and rmscop will display the selected molecule, colored as follows:

alpha helix (magenta)
beta strand (yellow)
turn residues (blue)
remaining residues, i.e. random coil (white)
parts of this PDB chain not in this domain (red-orange)
other chains in this PDB file (violet)

RasMol will then allow to rotate and manipulate the molecule and select among plenty of useful display options.

The main difference bewteen rasmolscript and rmscop is the ability of the latter of talking to an existing RasMol window (instead of opening a new window at every invocation) and selecting the window to which the image should be sent. This permits to see two or more structures at the same time. To use rmscop you will need to install tcl/tk.

rmscop comes in two flavors. The original version, implemented by Tim Hubbard, has been made easily configurable and tested both on old and new tcl/tk releases for compatibility. It will be supported at MRC, and is primarily intended for unix/linux users. Instructions for installing rmscop.

The new version, RmscopII, is an improved version of the original rmscop program, providing some extra functionalities and a more advanced graphical user interface. The program is available for UNIX/Linux. MAC, and MS Windows platforms and maintained by its author, Raphaël Leplae ( RmscopII requires Tcl/Tk version 8.3 or higher which may cause compatibility problems with software based on previous tcl/tk releases installed on your system.

Both rmscop and RmscopII are locally configurable, allow to specify an ftp site for downloading pdb files in case these are not locally available, and are optimized to download a pdb file only once (from then on, it will be found at a location of your choice on your machine).

If you don't have tcl/tk already installed on your system and you don't want to install it, you can still view structures in SCOP using rasmolscript.

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June 2009