In the Protein Preview tab you can see the Jmol Application, which is integrated in the membraneeditor in order to
allow the 3D display of molecules structure of a protein and to change the position of a protein in the lipid bilayer membrane.
About Jmol
Jmol is molecule viewer for use in chemistry and biochemistry. It is free and open source.
It can be used as a teaching tool or in research.
It is Java based and runs on Windows, Mac OS X, Linux and Unix systems.
There a is a standalone application and a development tool kit that can be integrated into other Java applications.
The most notable feature is an applet that can be integrated into web pages to display molecules in a variety of ways.
For example, molecules can be displayed as ball and stick models, space filling models, etc.
Capabilities of Jmol/ Protein Preview
By clicking the button Toggle Axes you can switch the visibility of the Axes. If you change the rotationmatrix, the axes may help you in getting a better impression of the actual changes.
If you want to have a look at the secondary structure, you may click on the button Toggle Secondary Structure.
The lipid bilayer can be activated or hidden by right-clicking Render->Lipidmembrane->On/Off or by clicking on the button Toggle Lipidmembrane at the bottom of the tab.
You can change the vertical position of the protein by Strg+Alt+drag. In this case you change the YTranslation of the protein.
Further you can rotate the protein around X,Z by draging it. Thereby you change the rotationmatrix. The YTranslation and
rotationmatrix are listed in the Properties tab.
You can control the atom size by right-clicking in the Jmol Viewer and selecting Render->Atoms. The different options
change the spacefill and CPK (for Corey, Pauling, and Koltun) value.
Jmol allows you to specify your size as a percentage of the van der Waals radius.
Besides you can change the bindsize (wireframe) by right-clicking Render->Bonds. The value is given by the bond radius in angstroms.
Additionally you can select Render->Scheme in order to choose some given models, which are specified by default atom size and bindsize values.
There are following schemes:
Spacefill and CPK (for Corey, Pauling, and Koltun): Spacefill and CPK are 100%, such that the atoms have maximum size
Ball and Sticks: Spacefill and CPK are on (20%) and the wireframe has the value 0.15.
Sticks: Spacefill and CPK are off, wireframe is 0.3
Wireframe: This is a command to control the bindsize. The value of this parameter is the bond radius in angstroms.
You can select after right-clicking Render->Structures for a better visualisation of some structures in the protein:
Backbone: This shows the backbone of a protein macromolecule by creating artificial
'backbone' bonds between alpha carbons.
Backbone radius can be specified in angstroms and the default value in Protein Preview is 0.3 A.
Trace:This shows a spline trace of a protein backbone. The hermite spline curve passes through the mid-points between alpha carbon atoms. Default value is 0.3 A.
Cartoon: Cartoon displays show sheet strands as arrows pointing toward the C-terminal end of the chain. A pair of chains with arrows at the same end are parallel. If arrows on neighboring strands are at opposite ends, the strands are antiparallel.
Ribbons: Ribbons offer a representation the protein backbone using a ribbons which smoothly traces the midpoints of adjacent alpha carbon atoms (or phosphorus atoms in nucleotide chains). The ribbon is perpendicular to the peptide plane.
For futher information about Jmol please visit the Jmol-website on http://jmol.sourceforge.net .