PACKAGE:charite.christo.strap.
This tutorial takes about 40 min and explains the basics of STRAP.
The quality of the text can be improved by typing CTRL-* (asterisk) at the expense of speed.
The tutorial contains menu items that are located in menus of the menu-bar and in WIKI:Context_menus.
As you press these menu-items the containing menu is indicated.
Also consider to watch the Flash videos
http://www.bioinformatics.org/strap/#DOCUMENTATION.
Printing
As you press CTRL+P this text appears in the
Web-browser where it can be printed. Remember to give the text the key-board input focus by left-click. If not go the section
"trouble-shooting" at the end of this text where configuration of
the Web-browser is explained.
Computer-Basics
Before you continue with STRAP, it is recommended that you are
familiar with a few elementary concepts of graphical computer
systems. They are common to all Desktop systems like Windows,
Macintosh, KDE and Gnome. Macintosh differs slightly from other systems.
The best is you take your text processor and your file browser (On Windows this is the Explorer.) and check the following:
-
Important key strokes you should know by heart:
- CTRL-X Cut Text and add it to the Clipboard (German Zwischenablage see WIKI:Cut_paste)
- CTRL-C Copy text
- CTRL-V Paste text
- CTRL-F Find text pattern
- CTRL-+ Enlarge font
- CTRL-- Smaller font
- F1 Help
- SHIFT Arrow left SHIFT Arrow right: Select text at the text cursor
- Zoom in and zoom out: CTRL-+, CTRL-- and CTRL-mouse wheel
-
Selection of list elements. Considering a file directory which is viewed in the file browser. The files are listed:
- Left click: Selects only the file under the mouse.
- CTRL Left click: Toggls the selection of the file under the mouse.
- SHIFT Left click: Selects all files between the previous position to the current position.
- CTRL-A Select all.
- WIKI:Context_menus For example right click a file in your file browser.
- WIKI:Drag_and_drop
Obtaining example proteins for this tutorial
In this tutorial we compare three subunits of the core of the WIKI:Proteasome.
The protein files are downloaded into the project directory and appear in the Sequence alignment pane below.
BUTTON:Tutorials#bExampleFiles("INTRO")!
Aligning some sequences
The button BUTTON:DialogAlign! opens the WIKI:Sequence_alignment dialog.
First you need to select an alignment method and the proteins that
should be aligned.
Take COMBO:MultipleAlignerClustalW, which is the most popular sequence alignment program.
After starting computation by pressing the button LABEL:ChButton#BUTTON_GO
a result panel with the alignment preview appears.
Generally, dialogs in STRAP may have several result tabs.
Return to the main tab of the dialog.
Start the computation again with a different set of proteins or with different WIKI:Gap_penalty ( tool-button
ICON:IC_CONTROLPANEL).
Each computation brings a new result tab with an alignment preview.
Selecting more than one protein: CTRL+left-click toggles selection and SHIFT+left-click selects a range.
Evaluating the alignment
When the alignment process is finished a preview with the result appears.
You can inspect the result and accept it by pressing LABEL:DialogAlignResult#BUT_LAB_Apply.
By accepting the alignment the alignment gaps are conferred to the working alignment in the main alignment pane.
Would you consider the sequence alignment to be accurate?
Let's evaluate the alignment using additional information from WIKI:protein_structure.
In the tool-bar the shading style JCOMPONENT:StrapView#choiceShading()! should be set to "secondary structure".
Please drag the slider
JCOMPONENT:StrapView#sliderSimilarity()!
below the alignment panel
so that the scroll-bar is shaded according to the secondary structure (Helices red and sheets yellow).
Sequence insertions and deletions during evolution usually avoid the middle of helices and beta sheets.
Apparently, this is not the case her since gaps are found in the middle of helices.
The active site residues Gly 129
The β-subunits are catalytically active whereas the α-subunits are not.
Now we regard the active site residues of the sequences hs_... and b1_...
The active site has a Gly-Ser-Gly-motif.
Go with the cursor to the pdb residue number 129: in hs_... and b1_... .
In the alignment header the residue index, and the residue PDB number,
and the alignment column is written.
PDB numbers are recorded in the PDB-file (see the PDB listing
below) whereas residue indices count from 1 to the total number of residues.
To distinguish residue indices and PDB numbers
the latter are followed by a colon and the WIKI:peptide chain letter.
Move the cursor to the PDB residue number 129:.
You may use the cursor keys but a convenient way is to type "129n".
You can also search for the text string "GSG" to quickly find the position BUTTON:DialogHighlightPattern!.
Comparing hs_... and b1_... you see that the active site sequence
motif Gly-Ser-Gly is not well aligned with sequence based
methods.
Conclusion: Computations based on amino acid sequence alone fail for remote homologs
Structural Alignment
Next we perform a WIKI:Structural_alignment using 3D-structure.
We compute the alignment with COMBO:ClustalW_3D which is a
combination of WIKI:ClustalW and a 3D superposition program. It can
perform alignments for structures and sequences.
Result: The active site residues are aligned well.
Editing the Alignment
Click in the alignment to get a text-cursor.
Cursor navigation and text editing works like in MS-Word
with the difference that only white space can be inserted or deleted, but
the amino acids cannot be changed.
The row headers with the protein names can be dragged up and down
to change the order of proteins.
Dragging them outside the application frame results in a copy of the protein file on the desktop (see WIKI:Drag_and_drop).
right-clicking a protein name brings up the context-menu.
Hovering with the mouse over the protein icon brings up a tool-tip.
For more info see DIALOG:StrapKeyStroke.
Exercise:
- Insert and delete gaps using the SPACE, DELETE and BACKSPACE keys.
- Change two proteins simultaneously by selecting the two proteins".
- Insert exactly 13 white spaces by typing "1" "3" "space-bar".
- Change the order of the proteins.
- Drag a protein to the desktop.
Cut-and-Paste and Drag-and-Drop (D&D)
As an example for a 3D-structure file create a WIKI:Plain_text file with the
following PDB-text (WIKI:Protein_Data_Bank) in a text editor like WIKI:Wordpad.
Use CTRL+C and CTRL+V
to copy the text into the text program (see WIKI:Cut_paste).
Drag-and-Drop text selection: This does not work in WIKI:Notepad but in WIKI:Wordpad.
Now select the entire text in the text editor.
The drag the selection with the mouse into the STRAP application.
Drag-and-Drop a file:
Next, D&D of files will be demonstrated:
Save the file as plain text and not as MS-Word- or HTML- or RTF-document and avoid white space in the file name.
Then drag the file with the mouse to the STRAP application (see WIKI:Drag_and_drop).
ATOM 7121 N TYR E 8 -48.777 48.007 60.590 1.00 93.66
ATOM 7122 CA TYR E 8 -48.065 47.524 59.366 1.00 94.20
ATOM 7123 C TYR E 8 -46.621 48.045 59.286 1.00 93.97
ATOM 7124 O TYR E 8 -46.388 49.225 58.982 1.00 94.01
ATOM 7125 CB TYR E 8 -48.843 47.939 58.113 1.00 93.81
ATOM 7126 N ASP E 9 -45.660 47.159 59.562 1.00 93.07
ATOM 7127 CA ASP E 9 -44.236 47.509 59.520 1.00 91.34
ATOM 7128 C ASP E 9 -43.460 46.529 58.631 1.00 89.29
ATOM 7129 O ASP E 9 -43.402 45.326 58.893 1.00 88.80
ATOM 7130 CB ASP E 9 -43.636 47.510 60.929 1.00 92.28
ATOM 7131 CG ASP E 9 -42.367 48.335 61.017 1.00 93.09
ATOM 7132 OD1 ASP E 9 -42.464 49.577 60.879 1.00 94.24
ATOM 7133 OD2 ASP E 9 -41.280 47.746 61.214 1.00 91.48
ATOM 7134 N ARG E 10 -42.847 47.067 57.586 1.00 86.76
ATOM 7135 CA ARG E 10 -42.106 46.269 56.623 1.00 83.63
ATOM 7136 C ARG E 10 -40.747 46.902 56.347 1.00 81.14
ATOM 7137 O ARG E 10 -40.468 48.005 56.816 1.00 81.28
ATOM 7138 CB ARG E 10 -42.914 46.218 55.333 1.00 84.67
ATOM 7139 CG ARG E 10 -43.446 47.597 54.948 1.00 86.88
ATOM 7140 CD ARG E 10 -44.011 47.619 53.547 1.00 90.08
ATOM 7141 NE ARG E 10 -45.381 47.120 53.465 1.00 92.28
ATOM 7142 CZ ARG E 10 -46.457 47.899 53.403 1.00 93.17
ATOM 7143 NH1 ARG E 10 -46.327 49.224 53.414 1.00 92.66
ATOM 7144 NH2 ARG E 10 -47.664 47.352 53.311 1.00 93.60
ATOM 7145 N GLY E 11 -39.911 46.213 55.573 1.00 77.52
ATOM 7146 CA GLY E 11 -38.601 46.755 55.240 1.00 72.46
ATOM 7147 C GLY E 11 -38.700 47.944 54.298 1.00 69.15
ATOM 7148 O GLY E 11 -39.699 48.105 53.591 1.00 67.56
D&D makes loading of proteins much easier. Without the convenience of D&D the user would need the dialogs ITEM:DialogNewProtein! or ITEM:MainDialogProjectFiles!.
D&D is a very important concept in STRAP. Please see the D&D-Tutorial and http://3d-alignment.eu/dragProteinLink.html.
Several alignments simultaneously
Sometimes it is necessary, to probe a different alignment strategy or to
compare the loaded proteins with other protein files without
affecting the working alignment.
In this situation it is necessary, to open another independent
STRAP-Window with the same or a different project directory.
Data exchange between the two alignment panels works simply by WIKI:Drag_and_drop.
Select all proteins in one STRAP Window. Use SHIFT for selecting a range of proteins.
Start a second STRAP session.
Then drag the proteins to the other STRAP Window.
Altering the amino acid sequence
Protein files can be changed with a text editor such as WIKI:Microsoft_Word, WIKI:Wordpad, WIKI:VI or WIKI:Emacs.
As soon as the changes to the protein file are saved STRAP will reload the
protein.
The menu item
BUTTON:ProteinPopup#docuSelectedEditProtein()! is found in
the WIKI:Context_menu (right-click a protein label).
Go to section "Trouble-shooting" if no suitable text-editor is opened.
Text searching
CTRL+F opens the text search dialog.
For example to search for a menu item open BUTTON:StrapAlign#CMD_ALL_MENUS!
or BUTTON:StrapAlign#button(CMD_ALL_POPUP)!.
Click into the text to set the input focus.
Enter a query into one of the text search fields.
Trouble-shooting
Plain text format: Some text-editors like the default
editor on Macintosh create a document in WIKI:Rich_Text_Format
(RTF). Also office programs usually save text in special formats
but can be directed to produce plain text.
These special WIKI:Document_file_formats are not suitable for
STRAP and only WIKI:Plain_text is supported.
Starting programs like Web-browser from STRAP:
Starting an external program from STRAP such as a Web browser may not work properly.
To identify problems the log-panel of this process can be opened: Hold CTRL i while the mouse click is performed.
For example click the Google URL GOOGLE{strap proteins} holding the CTRL key.
With the control-panel you can watch and alter the shell command and read the standard output of the programs.
The standard programs like text editor and Web-browser can be specied in the Options-menu: BUTTON:Customize#newButtonAll("A")!.
Embedded Bioinformatics programs:
ClustalW and TM-Align are ready to use because pre-compiled WIKI:Executables are provided for
ClustalW and TM-Align for Windows, Mac and Linux386.
Other programs are installed from source code to ensure that the
programs are working on any operation system and are optimized for
the particular processor type.