@*~RSC_HELP_TUTORIAL_DND
This tutorial takes about 40 min and explains one of the most
important concepts in Strap: WIKI:Drag_and_drop.
Objects like sequences, ligands and residue annotations can be moved
with the mouse and attached to other objects.
Dragging sequences from the Web into Strap
For each example you can drag the "DOWNLOAD" link into Strap.
This is explained in the video
HTMLDOC_BUTTON:BUTS_MOVIE_Load_Proteins_web_uniprot!.
HTMLDOC_OS_WIN{Do not use MS-Internet Explorer. Use MS-Edge, Opera, Firefox, Chrome, Safari etc. instead.}HTMLDOC_OS_WIN
Also try dragging sequences from Web-services such as Uniprot or Ncbi into Strap.
This works for many important bioinformatics services such as Uniprot and NCBI.
You may request support of services which are currently not yet
working. Alternatively, you may ask the maintainer of that service to
directly include Strap Web start buttons.
Clicking the links for each file format opens an example text in the
browser. Please select the sequence or alignment text (and only this
text without the comments around) with the mouse. Then drag the text
selection into Strap.
Dragging sequences from the local file system into Strap
Type a text consisting of letters with a text editor and save it as plain text.
Drag this text file into Strap.
This text is interpreted as an amino acid sequence.
A common error is to save the file in a proprietary word processor format such as .doc or .docx.
Dragging sequences from Strap to other targets
Drag a sequence name at the left of an alignment row to the desktop.
It must be dragged first to the left or to the right. This is because dragging up and down is used to change the order of sequences.
Try different targets:
- The Desktop
- Directories in the HTMLDOC_OS_MAC{Finder}HTMLDOC_OS_MAC HTMLDOC_OS_WIN{File Explorer}HTMLDOC_OS_WIN HTMLDOC_OS_mac_win{file browser}HTMLDOC_OS_mac_win
- Other applications for example Jalview http://www.jalview.org
- Text editors such as MS-Wordpad
- A second Strap sessions
For sequences that are part of a multiple sequence file a WIKI:Fasta formated file is dragged.
This behavior can be altered in the Drag-and-Drop options from the Preferences menu
HTMLDOC_BUTTON:SBUT_DRAG_OPTS!.
Please load either PFAM:PF00207 or PRODOM:PD000267 (The IDs can be directly clicked).
Vice versa, all sequence files can be dragged from the desktop back to Strap.
To test this, remove all proteins in Strap (Click into row header and type Ctrl+A. Then hit the Delete-key).
Then, drag them all back.
Dragging entire alignments
Entire alignments including gaps and residue annotations, can be exchanged between two Strap Windows.
For testing use the example files HTMLDOC_BUTTON:SBUT_TUTORIAL_LOAD_EXAMPLE_1D3D!.
Align all sequences with the tool-button HTMLDOC_BUTTON:SBUT_ALIGN!.
Open another Strap session with a different project directory.
Select some sequences and drag the selected sequences into the other view.
The alignment of these proteins should appear.
Dragging residue selections
Create a residue selection by dragging the mouse over some residues.
Now try to drag this selection up or down to another other sequence. It is important to
initially drag vertically.
Copying more than one residue underlining:
Use Ctrl+click to select two different residue selection.
Selected residue selections are highlighted by WIKI:Marching_ants.
Now drag one of them two another sequence.
If the dragged residue selection is selected (i. e. has marching ants), all selected residue selections are transferred.
3D-view:Now load a protein file with 3D-coordinates and open a 3D-view.
Drag the residue-selection into the 3D-view.
Two alignment windows:Open a 2nd Strap session with a different project directory.
Load the same sequences. Now underline some residues and drag the underlining upwards and then drop in in the other Strap session.
Rectangular region (rubber band)
As explained above, Ctrl+click can be used to select several
residue 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: Shift and Ctrl work the same as in Photoshop or Gimp: Union-set and cut-set.
Dragging Images
Image files can be dragged onto sequences.
Please open a page with images like
http://images.google.com/images?imgsz=icon&q=rabbit.
Now drag an image to a sequence label to change its icon.
This works also for persistent residue annotation where the image will form the background for the residue selection.
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-view for chain G (Tool-button HTMLDOC_BUTTON:SBUT_3D! or item HTMLDOC_BUTTON:M_P_VIEW_BACKBONE in the context-menu).
If two monitors are attached to the computer, it might be convenient to detach the 3D-view and put it on the other screen.
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 which shows two RNA molecules.
Drag the RNA molecules to 1l4p_G.pdb. They will appear in the 3D-view.
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