The Vagabond GUI is dominated by the "molecule window" where the current state of the model is displayed. The log file view can be toggled with L (see keyboard shortcuts) as well. Common functions can be obtained from the menu actions.
The start screen is launched on execution of vagabond-gui on the command line.
Navigating in the molecule window is achieved through rotation (click with left mouse button and drag), panning (hold the Alt key, click with left mouse button and drag) and zooming (click with right mouse button and drag).
Keyboard shortcuts (which actually have no longcut at the moment) can be supplied to the GUI when the molecule window is selected (click in molecule window if not selected).
| Key | Action |
| L | Hide or show log file alongside molecule window |
| B | Cycle through representations of bonds (full ensemble; average position) |
| D | Cycle through representations of electron density (none; weighted map, additional difference map) |
| G | Choose which residue (chain ID, residue number or both) to go to |
| + | Increase the threshold for drawing the contour map for the last toggled electron density. |
| - | Decrease the threshold for drawing the contour map for the last toggled electron density. |
| [ ] | Centre on current selected atom or group of atoms, if any [space bar] |
| , | Move selection one residue towards N terminus |
| . | Move selection one residue towards C terminus |
Menu actions
Most functions in the menu are disabled while Vagabond is performing an action (such as initial refinement protocol selected in the start screen). You will need to wait until an action has finished before using the menu items and/or cancel further refinement first.
| Menu: Scaling | |
| Shell-by-shell scaling | When scaling the model structure factors to those of the data, the full resolution range is divided into 20 bins, and the model structure factors are multiplied by a constant value to match the average amplitudes of the data and model within each bin. |
| Absolute scale only | The entire resolution range is scaled by a single multiplier to match the average amplitudes of the data and model structure factors. |
| Change real-space B factor | During calculation of model electron density, a B factor is applied in real space (default: 20 Å2) during the placement of every single atom. This value can be changed - sometimes the model may agree better with a smaller or larger value. Decreasing this global B factor means more needs to be corrected for by flexibility parameters of the model. |
| Menu: Model | |
| Change model sampling... | Change the number of times the model is sampled. This will increase or decrease the number of strands calculated and displayed in the ensemble. Note that low numbers of samples (less than 60) can become very unstable and may not scale to larger numbers if refinement is carried out with so few strands. Vagabond will re-refine positions to keep them stable after changing model sampling. Default number of samples in Vagabond is 120. |
| B factor HETATM multiplier... | Heteroatoms (water, ligands, etc., < 10%) are currently inherited directly from the PDB file and are governed by a position and B factor distribution. However, occasionally the overall B factor does not match that of the rest of the structure. Multiplying the B factors is one way of adjusting this - it has the disadvantage of perturbing the constant relationship between HETATM B factors, but the advantage that B factors cannot go negative. |
| B factor HETATM subtract... | To correct the pathology mentioned above, but using a constant subtraction (usually B factor subtraction of approx. 5 Å2 is a good starting point). Preserves differences of B factors between HETATMs, but has a risk of making some B factors negative. |
| Solvent probe radius... | Choose solvent probe radius in Ångströms for calculation of solvent mask. The default value is 0.2 Å. |
| Explore crystal... | Opens a new window listing all the chains in the PDB with additional options. Many strange features have been buried here. |
| Open in Coot | Opens Coot externally and loads the current electron density map, average PDB position and ensemble PDB. |
| Menu: Refine | |
| Positions to PDB | Refines torsion angles (and permitted bond angles, if any) to match the original coordinates of the atoms in the PDB file. Equivalent to a single cycle of the first step of the default automated refinement. |
| Positions to density | Refines torsion angles (and permitted bond angles, if any) to the electron density directly. At the moment this doesn't necessarily converge to the true minimum but can be capable of dragging a far solution to a near one. |
| Intermolecular movements | Refines 12 parameters per polypeptide chain to modify displacements of individual strands of the ensemble in order to improve the correlation coefficient with the weighted electron density. |
| Intramolecular movements | Modifies the backbone flexibility parameters to introduce a range of torsion angles at each C-alpha atom. These are refined to reflect the expected range of motions of each atom, as measured from the weighted electron density. |
| Intramolecular magic angles | Not recommended. |
| Sidechain positions to density | Refines torsion angles of side chains only, with large step sizes in order to drag a far solution to a closer one. This does not necessarily converge to the true minimum. |
| Sidechains to density | Refines torsion angles and flexibility parameters simultaneously to match the correlation coefficient with the weighted electron density, capable of introducing larger spreads of sidechain atoms. |
| Recalculate FFT | This manually performs recalculation of the weighted electron density, new R factors, maps and other output files. |
| Cancel further refinement. | Sets a flag to stop executing the refinement protocol after the next recalculation of the FFT. This then allows for manual intervention. |