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 rmscop script 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 all unix/linux platforms
Fast loading of structures where there is a local copy of PDB
Support for multiple RasMol Viewers at the same time
Benefit of all features of RasMol (rescaling, rotating, selecting atoms etc)

Cons:

Installation requires some work

Chime

Pros:

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

Cons:

Currently no support for unix/linux platforms
Coordinates must be sent over network, so downloading may be slow
Only mainchain coordinates are sent to reduce transfer times
More limited features for image manipulation (compared to RasMol)

June 2009