Structural Classification of Proteins

Help on Graphics interfaces to scop

Interfaces to Rasmol and Chime are provided in scop for the display of protein structure backbones coloured by region.

Rasmol links from scop

With the rasmolscript system correctly installed, clicking on a rasmol icon () in scop will cause a local copy of RasMol to be started, displaying the molecule selected.

Chime links from scop

With the chime plug-in correctly installed, clicking on a chime icon () in scop will cause a WWW page to be displayed, showing the molecule selected.

Colour scheme

With either interface, the backbone of the protein chain is displayed, coloured 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)

Comparison of the interfaces

RasMol

Pros:

Works with most unix platforms, Macintosh
Fast loading of structures where there is a local copy of PDB
Support for multiple RasMol Viewers
Benefit of all features of RasMol

Cons:

Installation requires some work
No interface for PC's provided, although should be possible to implement one.

Chime

Pros:

Relatively straightforward installation on PC's and Macintosh
Structures automatically cached by Netscape

Cons:

currently no support for unix, but plug-in for SGI soon
Coordinates must be sent over network, so downloading may be slow
Only mainchain coordinates are sent to reduce transfer times
Chime plug-in has currently has feature user accessible features than RasMol

December 1999