This tutorial takes about 40 min and explains one of the most important concepts in STRAP: WIKI:Drag_and_drop. Objects like proteins, ligands and residue selections can be moved around with the mouse and attached to other objects.

Dragging proteins from the Web browser

The Web pages MolEvolFormats* and EBI_Formats* contain examples of different file formats. For each example you can try to drag the "download" link into STRAP. The common file formats are supported by STRAP, but some exotic formats are not supported. With the "view" link the protein file text is displayed in a Web page. Please select the protein or alignment text (and only this text without the comments around) with the mouse. Then drag the text selection into STRAP.

Dragging proteins

Please load a protein like UNIPROT:hslv_ecoli. The protein label in the row header can be dragged to different targets. The row header must be dragged first to the left or to the right. This is because dragging up and down just changes the order of proteins. Please try the following drag targets: For proteins that are part of a multiple sequence file two options are available: The protein is exported as a WIKI:Fasta formated file or the entire entire multiple sequence file is dragged. This can be specified in the Drag-and-Drop option panel which can be opened with a tool-button BUTTON:StrapAlign#drag_buttonOptions()!. This button is visible for a few seconds when the drag is started and vanishes after a few sec. Please load PFAM:PF00207 or PRODOM:PD000267. Then drag one single protein to the Desktop. Open the exported file in a text program and check the Fasta format. Then change the Drag-and-Drop option and drag the entire multiple sequence file to the Desktop. Again, open the file with a text program to check the format.

Vice versa, all protein files can be dragged from the Desktop back to STRAP. To test this, remove all proteins in STRAP (Context menu of proteins>Select>BUTTON:ProteinPopup#ACTION_select_all_p and Context-menu>BUTTON:"Close protein" ). Then, drag them all back. Also try dragging proteins from Web-services such as a Blast result into STRAP. This works for many important services. If the protein entries in a Web service are not working please send a report and also contact the maintainer of that Web-site.

Dragging entire alignments

Entire alignments including gaps and residue annotations, can be exchanged between two STRAP Windows. For testing use the example files BUTTON:Tutorials#bExampleFiles("13")!. Align all proteins with the tool-button BUTTON:StrapView#button(BUT_ALIGN)!. Open another STRAP session with a different project directory. Select some of the proteins and drag the selected proteins into the other view. The alignment of these proteins should appear.

Dragging a single residue selection

Residue selections are highlightings of certain residues. They indicate important sequence positions and may contain additional information. For the next exercise you need at least two different proteins. By dragging the mouse from right to left you can create a residue selection which is indicated by a different background. Now try to drag this selection up or down to the other protein. It is not that easy and requires exercise. It is important to drag up or down and not sidewards.

This works with all kinds of residue selections such as BioDAS*-sequence features. Now repeat it at another position.

Residue selections can be selected by CTRL-left-Click. Selected residue selections are highlighted by WIKI:Marching_ants. Select the residue-selections by CTRL-left-Click. If you drag a residue-selection to another protein, that is selected (i.e. has marching-ants) then all selected residue-selections are transfered.

Now load a protein file with 3D-coordinates and open a 3D-view. Drag the residue-selection into the 3D-view.

Rectangular region (rubber band)

As said above, CTRL-left-Click can be used to select several selections. This might become tedious for many selections. Similar to the computer desktop, several selections can be selected by opening a rectangle with the mouse. This rectangle is indicated as red-white marching-ants. Advanced users: Shift and Ctrl work the same as in Photoshop or Gimp: Union-set and cut-set.

Dragging Images

Image files can be dragged onto proteins. Please open a page with images like http://images.google.com/images?imgsz=icon&q=rabbit. Now drag an image file to a protein label to change the icon for the protein. If, however, the icon is dragged onto a residue annotation, the image will become the background image.

Dragging 3D Ligands, Hetero compounds and RNA/DNA structures

Please load PDB:1l4p. This protein consists of peptide chains G to R which are shown in individual alignment rows. Open the 3D-structure (Tool-button BUTTON:StrapView#button(BUT_WIRE)! or Context-menu>BUTTON:ProteinPopup#ACTION_backbone ) of chain G. Then drag all other peptide chains into the same 3D-view. This protein has RNA. The RNA structures are attached to peptide chains I, M, N, P and Q indicated by a vertical green bar left in the row header.

Please open another 3D -view for 1l4p_G.pdb. No RNA is shown because the chain 1l4p_G.pdb has no RNA attached. If the green bar of 1l4p_I.pdb is clicked, a list of hetero compounds can be opened. This contains two RNA molecules. When these RNA molecules are dragged to 1l4p_G.pdb, they appear in the 3D-view.

Using Drag-and-Drop, these RNA/DNA objects can be copied onto other proteins or to the Desktop. When they are copied to the Desktop, a PDB file is written using the current coordinate system.