Structure Tab
The JSmol JavaScript plugin is used to display antibody structures where these are available.
Basic Controls
The Region Definition dropdown (present if the chain has been numbered) allows the region boundaries to be defined according to the alternative definitions available in abYsis. See the About / Defintions page for information.
To rotate the structure, simply click on the structure with the left mouse button and move it around.
To rotate the structure in the z-axis (i.e. the axis coming out of the screen), press and hold the shift button, click the left mouse button and move the mouse left and right.
To zoom the structure either use the scroll on the mouse, or press and hold the shift button, click the left mouse button and move the mouse up and down.
Display controls
If the query chain is paired, both heavy and light chains are loaded into the viewer. Use the corresponding checkboxes to hide or display the chains.
For each chain, there is a table of display controls. The radio buttons allow individual loop or framework regions to be displayed in different ways, or hidden. Un-numbered (Other) parts of the PDB chain can also be selected.
The checkboxes in the bottom row of the table toggle the display of Chothia numbering for the corresponding region. For un-numbered residues, the three letter residue code rather than the Chothia number is shown.
Buttons
The button reset the orientation to the initial view.
The button resets the display styles and numbering to the initial default state.
The button resets the entire display to its initial state.
The button allows a PDB format coordinate file to be downloaded. This contains all the atom coordinates used for the display with numbering according to all three numbering schemes included in comment lines.
NOTE! The protein sequence held in abYsis is derived from both ATOM and SEQRES records in the original PDB file. There may be numbered residues in the sequence deriving from SEQRES data which do not appear in the structure viewer.
Advanced Controls
Finer control of the display can be achieved via the JSmol Console. To launch the JSmol Console, right-click in the viewer panel. A menu will appear. Select Console.
Predefined atom expressions have been set up to allow the user quickly to select regions and numbered positions. For example:
- To select the residue at Chothia position H3 and change its display to spacefill, enter the bottom panel of the console and enter select H3; spacefill;.
- To select the L1 loop and set its display to wireframe, enter select CDR_L1; wireframe; (Note: the underscore is important, JSmol will not understand 'CDR L1' or 'CDR-L1').
- To set the first heavy framework region to spacefill, enter select HFR1; spacefill.
To select a whole chain, use its abYsis accession preceded by all_, or to select residues that have not been numbered in a chain precede its abYsis accession with unnumbered_. For example:
- To select the whole light chain of PDB file 1FIG and spacefill it enter select all_1FIG_L; spacefill;
- To select just the unnumbered parts of the light chain of PDB file 1FIG and spacefill them, enter select unnumbered_1FIG_L; spacefill;
To close the console click the close text at the top left of the console.