User Manual - Overview

User Manual - Overview - GUI

This document will introduce the main graphical user interface elements.

Main window

The Sculptor window is partitioned into two columns, with the left column showing the current list of loaded documents and their properties, whereas the right column is reserved for the 3D and text output. The columns are separated with thin dividers that can be moved to adjust the size of the different areas of the GUI. They can also be used to completely collapse subelements, which is useful to maximize the space for the 3D window. Of course the collapsed elements can be brought back by moving the divider again.

Document panel

The document window maintains a list of all loaded data sets. It is also the main GUI window, the place where one can adjust most of the global properties of the program, and also a number of settings relating to an individual document.

Here you will find only a basic description of the icons of the main document window - details about the usage of the features of the program are described in the other tutorials. The icons can also be found as functions in the menubar.

- enables or disables the rendering of this document (the menu item "data/view" can also be used to toggle the state).

- if this icon is displayed, the document will be the center of the transformation. If the document is rotated, for example by using the mouse, the rotation will be around the geometrical center as pivot point. Attention: The coordinates of the document will change if a rotation is applied. If the "Sculptor Scene" document is the center, a global rotation around the center of the 3D scene will get carried out. In that case, the actual coordinates of the documents will not change, only the viewpoint gets adjusted.

One can change the center of the transformation by selecting a document and by clicking on the menu item "data->move". Alternatively one can also directly click into the document list, into the area where the crosshair would be. The 'm' key on the keyboard also allows to toggle the status of the current document - if is already the center, the scene will be the new center. In a visual multi-scale docking process one very often wants to adjust the position of one or multiple probe molecules relative to a 3D volumetric map. To check the position and orientation of the molecule it is often beneficial to alternate between a local and global transformation. This can also be accomplished very efficiently by selecting the probe molecule in the document list and by toggeling the status via the key.

- deletes the selected document(s).

- opens a dialog box with which the visualization of the selected document can be adjusted. See other tutorials for details.

- moves the selected document up in the document list. The geometric center of the first item will at the same time also be the origin of the 3D scene. That way, the first document will always be clearly visible after being loaded. If more documents are loaded the origin can be changed by moving another file up and thereby the first in the list.

- moves the selected document down in the document list.

- makes the selected document the top in the document list.

Save and Restore States

Sculptor can store the current state of the program in an xml file with the extension '.scl'. This state file will keep all the information about the current documents and the visualization modes and settings. One can save and load a state file with the menu items 'File->Load State' and 'File->Save State'.

Attention: The state file will only store the location of the document files like '.pdb' or '.mrc' files. If the location of the files changes, the state cannot be restored properly. The state files are ascii xml files, so by editing in a text editor one might be able to restore the file.

Global rendering settings

In Sculptor you can find under the view submenu all the global settings and rendering functions. One can take screenshots of the renderings, change the background color, zoom in and out or change to orthographic mode. The settings should be self-explanatory.

Transformations

In multi-scale modeling applications a very precise control over the transformations applied to the probe molecule is necessary to ensure an accurate docking result. Therefore Sculptor provides two basic modes of interactions: With the mouse molecular structures can be moved on the X-Y plane (right mouse button), on the X-Z plane (middle mouse button) and rotate around the origin (left mouse button).

- if precise control is needed, a transformation dialog can be activated (menu: 'Docking->Transformation'). Six dials control the six degrees of freedom of a transformation in 3D space. The top dials determine the three translation components, a translation along the X, the Y, and the Z axis. Each step on one of the dials corresponds to 0.1 Angstroem.
The lower three dials determine the three components of the rotation, along the X, the Y, and the Z axis. Each step rotates the object by 1 degree.