PACKAGE:charite.christo.
PACKAGE:charite.christo.strap.
To print this text, click into the text and type CTRL+P (German keyboard Strg-P).
To improve quality of text at the expense of perfromance type CTRL-* (asterisk).
The text will appear in the Web-browser and can be printed.
Introduction
With this viewer you can
- View and align amino acid sequences,
- Display, superimpose and align 3D-structures of proteins from the PDB-database,
- Export sequence alignments to the text-processor or to Jalview (Michele Clamp: PUBMED:14960472)
- Identify remote homologs
You might want to watch the Shockwave Flash demo animations at http://www.bioinformatics.org/strap/swf/.
For convenience it is recommended to print this help text as explained at the top.
Further help is provided by WIKI:Tooltips.
Information messages which are occasionally shown can be reviewed by typing CTRL+I.
The user interface follows the paradigms of office applications to make the
usage as intuitive as possible. It implements
- WIKI:Drag_and_drop in and out with the mouse
- Copy-and-Paste: CTRL+C and CTRL+V
- Zooming: CTRL++ or CTRL+WHEEL
- Marking sequence text regions: SHIFT+CURSOR-LEFT or SHIFT+CURSOR-RIGHT
- Context menus: right-click
- Multiple selection of proteins and list elements: CTRL+left-click
toggles the selection of a single element and SHIFT+left-click selects all elements between the current and the previous position.
For Macintosh mice that have only one button context menus are opened with CTRL+ALT+left-click.
Loading proteins
STRAP supports WIKI:Drag_and_drop: Drag a file with the mouse from a
file browser or from the desktop to the STRAP application frame. Release
the mouse over the alignment panel.
The dropped protein will be loaded and the amino acid
sequence appears in the alignment-panel.
A unique feature is that protein links from Bioinformatics resources can be dragged directly into STRAP.
Visit http://www.bioinformatics.org/strap/dragProteinLink.html for details.
To close a protein use the context menu (right-click).
Copying protein files
To copy the loaded protein file to the desktop or any other location you can
drag the protein label sidewards to the desktop.
It is important to drag it first to the left or right since dragging up and down only changes the order of alignment-rows.
Also see the downloaded protein files in the working directory of the current STRAP session: STRING:ChUtils#dirWeb()
Aligning sequences
On pressing the tool-button BUTTON:StrapView#button(BUT_ALIGN)!
the protein sequences will be aligned.
If a few proteins are selected in STRAP, only the selected proteins are aligned.
If there are at least two protein files with 3D-coordinates
the alignment is performed by superimposing the 3D-structures upon
each other using the program TM-align (Y Zhang, J Skolnick: PUBMED:15849316).
If there is at least one protein file without 3D-information ClustalW
(PUBMED:17576686) is used next respecting the results from TM-align.
The resulting alignment can be exported to the web-browser, text-processor or to Jalview (PUBMED:14960472) using
the tool-button
BUTTON:"<i><b><font color=0000FF>W</font></b></i>".
Protein names and icons
Open dialog "file => Rename" in the context menu of protein labels (right-click).
The rename dialog provides several additional rename options like displaying the organism name in the protein name.
INCLUDE_DOC:ChIcon
Copying amino acid sequence
To get the entire sequence in WIKI:Fasta-format the alignment cursor must
be on the respective sequence and CTRL+C (C for "copy") need to be typed
typed.
To copy a sequence segment to the WIKI:Clipboard_(software) (Zwischenablage) select the amino acids with the mouse.
From the clipboard it can be pasted into other applications with
CTRL+V.
Displaying 3D-structures
For protein files with 3D-coordinates (PDB-format) 3D-views
can be opened by pressing BUTTON:StrapView#button(BUT_WIRE)!.
To get a further protein into the same 3D view
drag the protein file or the protein label into the 3D-view.
To compare the proteins three-dimensionally press the button "superimpose".
For proteins given by a sequence file without 3D coordinates
3D-structure cannot be viewed. For some sequence files appropriate 3D-structures may be found by WIKI:BLAST against the WIKI:Protein_Data_Bank
BUTTON:DialogBlast!.
Identifying catalytic site residues in 3D structures
The catalytic site residues are highlighted red.
The balloon text and double click show detailed information.
The positions are obtained from the catalytic site atlas (C.T. Porter,
G.J. Bartlett and J.M. Thornton, PUBMED:14681376).
Those with evidences in the literature are marked bright red.
Database links
A few database links are generated from the PDB-ID and the
EC-number and appear by click on the left edge of the protein name.
Hetero compounds and DNA/RNA
Many PDB entries contain ligands like FMN, FAD and Metal ions or
DNA/RNA. These proteins are marked by a green (for DNA/RNA) or red
mark at the left.
Saving the alignment project:
In Web mode the alignment data is lost after the STRAP session.
However, you can run a full STRAP-session by
clicking the Web-start link in: http://3d-alignment.eu/.
You will be asked for a project directory where the data is stored.
The complete alignment can be transfered by WIKI:Drag_and_drop.
For this purpose select all proteins. This is done by clicking the first one with left click and the last protein with shift-key left click.
Then drag the selected proteins.
Full functionality
Users can enable full STRAP functionality using the "Options" tool-button.
In full STRAP mode the menu-bar and additional control elements become
visible.
Bugs/Problems
Report any problems and suggestions to christoph.gille@charite.de
INCLUDE_DOC:charite.christo.Web
Author: Christoph.Gille@charite.de
Group for Computational Biochemistry