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Introduction

[Menu-bar>Tutorials] Did you ever wish to compare protein sequences or to identify 3D structures of proteins that are similar to your protein? Are you interested in remote phylogenetic relationships to discuss the function of a protein? Do you want to take advantage of the experiences of the Bioinformatics community to explore your proteins?

Making sequence alignments of related protein sequences is a common task in biology. It reveals regions which are highly conserved and are functionally important. Automatic approaches alone are often not fully satisfactory and manual refinement is necessary in most cases particularly when the sequences are very dissimilar.

STRAP is a comfortable and comprehensive tool to edit multiple protein sequence alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface.
STRAP is tightly integrated into your desktop environment supporting Cut_paste and Word_completion and spell check. Drag_and_drop is available for proteins, nucleotide structures and hetero structures. Context_menu for proteins, annotations and files are triggered by right mouse click. The program appears to be complicated in the beginning. With the help of the integrated tutorials you will learn how to apply the currently available methods to compare proteins sequences and structures.

The key features are:

What it cannot do:
- Docking
- Gene structure, promotor analysis
- Structure modelling
- Molecular dynamics
- Gene expression
- RNA-3D-structure



Online documentation


Frequently occurring buttons


Report bugs to: christoph.gille(at)charite.de

Alignment Projects in STRAP

Each alignment project is stored in one folder. This file directory is specified by the user at the beginning of the session and cannot be changed during the session. The complete directory path appears in the title bar of the STRAP application frame.

Loading protein files: Protein files are loaded into STRAP by dragging one or more files from the desktop or any other location into the STRAP-application.

Web-pages may contain links to protein databases. These links can be dragged from the Web-browser into STRAP ( http://www.bioinformatics.org/strap/dragProteinLink.html for details).

Several STRAP-sessions can be opened at the same time and proteins can be dragged from one to the other.

Context menus

Context menus in STRAP: The term Context_menu is commonly used for menus which pop up when right clicking (right mouse button) an item in a graphical user interface, offering a list of options which vary depending on the item selected. On Macintosh computers there is sometimes only one mouse button and the right mouse button can be simulated by ALT+CTRL+left-click. Context menus are available for:
Selecting single items: List items are selected simply by left-click the respective node. Single residue selections in the alignment panel can be selected by clicking with the CTRL key.

Selecting more than one item: Selecting more than one list item requires the SHIFT and CTRL keys. The CTRL key is located at the lower left of the key board and is sometimes labeled STRG and the SHIFT key is sometimes termed "UMSCHALT". By dragging a rectangular region in the alignment, all contained residue selections are selected. With the SHIFT or CTRL key the union-set or cut-set is formed with the set of selections inside the rectangular region. The tool-button IC_SEARCH of the tree-panel allows to select items according to text matches.

Frequently used menu items can be dragged out the menu and placed on the desktop.

The tree view is located at the left of the application. It is usually hidden and can be opened by dragging the vertical divider bar. The tree contains all loaded proteins and their child objects.

Menu bar of STRAP

Note: The at-sign @ indicates that a menu item is only visible when certain check boxes in the User profile are activated.
File
Protein
View
Align
Predict
Residue-Selections
Analyze
Plugins
Options
Tutorials
Science
Help

Context menu of annotations

Context menu of selections

Context menu of files

User profile

To avoid that users are confused by the number of menu items and options only those GUI elements are shown that the user is interested in.

The sequence alignment panel

The central view of the STRAP application is the alignment panel. It shows the names and sequences of loaded proteins. The user can add and remove white space to align the sequences, so-called alignment gaps. Usually, only one sequence alignment panel is shown but additional alignment views can be opened New alignment panel[Menu-bar>View] . In any case only one alignment is present in one STRAP instance. Nevertheless, STRAP can be run several times in parallel and data exchange between STRAP sessions is conducted by Drag-n-Drop.

Shading: Three residue shadings are available: "charge", "hydropathy" and "chemical" (tool-bar below the alignment). Alternatively, secondary structure can be highlighted: Helices are painted red and sheets yellow. Further GUI controls are in the context-menu.

Editing: Manipulation of the multiple sequence alignment is performed with the keyboard. STRAP has many sophisticated keyboard commands. Please see Keyboard.

Cursor: The cursor position is highlighted in all views with the following symbol: IC_CURSOR16. Usually only the alignment row containing the cursor is changed when for example a gap is introduced by pressing the space bar. It is often necessary to add white space to a number of sequences and not only to one sequence. The number of adjacent rows edited simultaneously can be set by hitting "#" and subsequently typing a number.

Stacking proteins: Usually, each row contains exactly one protein. The proteins can be dragged up or down in the row header to change their order. A number of proteins can be stacked into one single row to be manipulated simultaneously while only the sequence of one protein is shown: Stacking proteins into a single line ....
Residue selections are highlighted in the multiple sequence alignment. When the mouse is over a highlighted residue a Tooltip with additional information appears. Right-click opens the context meny and CTRL+left-click selects the selection. It can also be selected by dragging a rectangular region.

Scrolling: The horizontal scroll-bar outlines the entire alignment and shows selections and plots. It can be enlarged with the mouse. If there are many proteins the vertical scroll-bar is visible. But also the horizontal scroll-bar can scroll vertically. Try mouse wheel turning with and without SHIFT and CTRL.

Keyboard

Alignment gaps are introduced and removed with the keyboard. Changes to the amino acid sequence, however, are conducted with an external editor. ([Menu-bar>Protein>File] ).
Cursor Movements
Arrow keys Cursor navigation
CTRL arrow keys move to beginning or end
ALT + arrow keysmove to next gap
HOME First row
END Last row
SHIFT HOME First column
SHIFT END Last column
Movement of the view-port
PAGE-UP / PAGE-DOWNScroll up and down
SHIFT PAGE-UP Scroll left
Deleting gaps
DELETE Delete gap right from or under cursor
BACKSPACE DELETE gap left from cursor
CTRL DELETE Delete next gap right from the cursor
CTRL BACKSPACE Delete next gap left from cursor
CTRL SHIFT DELETE Delete entire white space under cursor
CTRL SHIFT BACKSPACEDelete entire white space left from cursor
Inserting gaps
SPACE Insert gap under cursor
INSERT Insert gaps until next residue in above row is reached. Effectively it copies the gaps from the line above.
CTRL INSERT Remove gaps until previous residue in above row is reached
SHIFT INSERT Insert gaps until next residue in below row is reached
Perform an operation n times
4 2 SPACE Insert 42 gaps
4 2 DELETEDelete 42 gaps
Moving a sequence blocks: A group of consecutive residues that are not interrupted by gaps is moved left or right.
>Move continuous group of residues right
<Move continuous group of residues left
Window
CTRL N New alignment panel
CTRL WClose alignment panel
Miscellaneous
CTRL KClose protein
CTRL *Display letters in better quality
U Upper Case
L Lower Case
Font Size
CTRL "+"Zoom in
CTRL "-"Zoom out
Goto position
4 2 iMove cursor to residue index 42
4 r Move cursor to 4th row
42 c Move cursor to column 42
42 n Move cursor pdb-number 42

The mouse actions follow general conventions:
  1. Sequence alignment
    • left-click sets the cursor.
    • middle-click sets the focus without changing the cursor.
    • right-click opens a context menu either for the alignment pane or for a residue selection.
    • Dragging creates a mouse selection.
    • Dragging over more than one sequence creates a rectangular region. Residue selections and annotations within the rectangle are selected. SHIFT for union-set and CTRL for cut-set similar to the program gimp or the MS-Window desktop.
    • ALT + Dragging scrolls two-dimensionally. Under Unix/Linux also hold SHIFT
  2. Row-header
    • Dragging up/down changes the order of proteins.
    • CTRL left-click selects or un-selects the protein.
    • right-click opens a context menu for the protein.
  3. Scroll-bar or alignment pane
    • Wheel scrolls.
    • SHIFT + Wheel scrolls vertically
    • CTRL + Wheel zooms.
Sequence groups
G xDefine all currently selected proteins as group "x".
g xLoad proteins of sequence group "x" if not already loaded. Select these proteins.
h xUnselect and hide all proteins of sequence group "x".
Sequence Groups:
Sequences can be grouped. Groups are designated by a digit or letter. The names of all proteins of a group are listed in a file in ./annotations/sequenceGroups/.

Alignment gaps

When there are gaps occurring in all loaded sequences at the same position they are usually not displayed.
Consider the following case: 
ASGATA  YTG
ATGATG  YTA
ASGGTAG FSG
       ^
This is a common gap which is not displayed. The view shows: 
ASGATA YTG
ATGATG YTA
ASGGTAGFSG
When the sequence "ASGGTAGAFSG" was added to the multiple sequence alignment the gap would not be a common gap any more and would become visible. In the multiple sequence alignment panel is the following: 
ASGATA  YTG
ATGATG  YTA
ASGGTAG FSG
ASGGTAGAFSG
This is the reason for the following phenomenon: When gaps are added to one sequence it might seem that gaps are erased in all other sequences instead.

Open protein files

[Menu-bar>File] The file selector shows the protein files of the current project directory. They are ordered in different lists according the file endings. Protein files can be selected and loaded into STRAP by double clicking or with the button DialogProjectFiles#BUT_LAB_Load. Multiple selections are possible with the keys CTRL (same as STRG) and SHIFT.

Drag-And-Drop: The file selector is capable of Drag_and_drop: Files from the native file browser or desktop can be dragged into the file selector or into to the STRAP alignment panel (see See http://www.bioinformatics.org/strap/dragProteinLink.html).

Alternative directories: In the choice menu at the top a number of other folders can be chosen. For example a local mirror of the PDB-file collection may given.

Flags: The flags g,s,3 and n which precede the file names indicate the existence of gaps, residue-annotations, 3D coordinate transformations and nucleotide reading frames, respectively.

Multiple sequence files with the ending .msf or .clustalw contain the aligned sequences of several proteins: Clustalw: NexusFormat.

Customization: The list of file endings and the list of alternative directories can be altered.

File formats: Many * file formats are recognized: Swissprot, Protein_Data_Bank, Fasta, Genbank, EMBL. See http://www.molecularevolution.org/mbl/resources/fileformats/. The file text is analyzed and the file type identified without considered the name of the file. If no appropriate protein file type is detected then the sequences is formed from the letters in the file.

Drag-and-drop

Actions which are performed when objects are dropped on certain targets.
D r o p p e d   O b j e c t s
Drop target Proteins Residue selections Hetero groups Images
Proteins
 		 Copy selection to protein Add heteros to protein Set icon image
Residue selections
 		 Set background image
3D-backbone
 		 Show 3D-structure Show 3D-structure
Protein selection list
 		 Set selected proteins
Alignment panel
 		 Load or un-hide protein Copy selection to protein Add heteros to protein
Tree-node "Hidden"
 		 Hide proteins
Desktop or file browser
 		 Copy protein file Write PDB-file

Objects are dragged with the mouse and dropped on a target (see Drag_and_drop). The effect depends on the objects that are dragged and the destination where they are dragged onto. On Windows and Linux the presumed operation is written at the bottom of the Strap frame. The page Dragging Web-links contains examples of protein and alignment Web links that can be dragged.

Translate Genbank nucleotide files

[Menu-bar>Protein>Nucleotide sequence] 
   1    AAACATGGCG CTGGCTAGCG TGTTGCAGCG ...
   51   ACGGGTTTTT TGGGCTCGGA GGTGGTGCAG ...
   101  GGGAGTCCTG GTGATGGGCT GAGCCTAGCC ...
...
The Genbank file format and Embl file format are widely used file format for annotated nucleotide sequences (format specifications: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html and ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt and http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html). When a Genbank file is loaded into STRAP the entire nucleotide sequence will be extracted and appear in the multiple sequence alignment pane. These nucleotides can be translated into amino acids using the CDS-sequence-features within the protein file. The Genbank file contains fields with the keyword "CDS" (coding sequence). The text following "CDS" tells the translation direction and the translated nucleotides. The sequence may be continuous or interrupted by introns. The following example of a CDS field is from the file NCBI_NT:5757659. 
   CDS     5. .799
   /gene="Psmb5"
   /codon_start=1
   /product="proteasome subunit X"
   /protein_id="AAD50536.1"
   /db_xref="GI:5757659"
   /translation="MALA ...VSVP"
If the Genbank file contains several genes the user can chose one of them. Sometimes Genbank files already contain the translation in a field /translation. The sequence computed by STRAP should be identical to this sequence.
When the project is saved to disk an additional file will be created with the ending ".dna" coding the translation direction (forward/reverse complement) and the translated and un-translated positions.

3D-backbone view of proteins

The simple 3D-viewer visualizes the C-alpha trace of one or several proteins as a polygon. Helices may be drawn in red and sheets in yellow.
Mouse Actions: On clicking IC_ORIGINALCOORDINATES the model is viewed in the original coordinates as recorded in the protein file.
Residue Selections: Color-chooser: The color chooser is shown if tools is activated. Four color-schemes are available. Protein3d#docuColorChooser() With the CTRL key the color of all proteins can be changed at once.

Adding proteins to the 3D-view: Proteins are added by Drag_and_drop or with the context menu.

Context menu (right-click)
Advanced 3D-viewer Pymol
The Pymol-button at the top of the 3D-backbone view allows to load the proteins into the Protein viewer Pymol. Pymol is a widely applied 3D-viewer. It is stable, fast and has many functions which are accessible via a graphical user interface and a command line interface. If STRAP fails to start Pymol, the debug window might be helpful. To obtain this debug window the "Pymol" button is pressed with the CTRL key. To remove a protein from an external protein viewer press [Menu-bar>Protein>3D] .

Identifying similar proteins

The fold of a protein is much more conserved in evolution than the amino acid sequence. Therefore it is possible to identify remote homologs for a given protein by looking for structures with the same fold Similar structures regarding only the c-Alpha atom positions. For this purpose four Web-servers are contacted: For more details see Structural neighbors ...

Protein viewer Pymol

PyMOL http://pymol.sourceforge.net/ is an excellent and widely applied protein structure viewer. It has been developed by Warren Delano and many tools and scripts are added by the scientific community.

Residue selections: Dragging the mouse over a part of the amino acid sequence in the STRAP alignment creates a residue selection in Pymol. The STRAP cursor position refers to another Pymol selection. Users can refer to these selections to show [S] or hide [H] representations of residues like sphere, cartoon or stick. For example to show all atoms of the amino acid at the current cursor position as spheres open the corresponding [S] menu of the selection "cursor" and select "spheres".
Figure: Side pane of Pymol containing a list of loaded proteins and selections. [H]Hide style, [S]Show style, [L]Add Label, [C]Change Color
pymolSelections


Picking: Picking an atom in Pymol moves the alignment cursor to the respective residue in the alignment. This can be switched off: [Menu-bar>Options>Proteins]

Removing a protein from Pymol: If a protein would be removed in Pymol this would be unnoticed by STRAP. Therefore it is recommended to use the STRAP user interface and not the Pymol user interface to remove proteins. There are two possibilities:
  1. The STRAP menu item [Menu-bar>Protein>3D]
  2. The STRAP object tree which is visible at the left of the STRAP application frame in advanced user mode.
Figure: Automated installation on Windows, Linux and Mac
Pymol#canInstall()


Pymol commands: Pymol commands (see http://pymol.sourceforge.net/newman/ref/S1000comref.html) are typed directly into the Pymol-window. Most important commands:

Related links: http://www.rubor.de/bioinf/   http://www.rubor.de/anlagen/PyMOL_Tutorial.pdf

Residue Selections

Residue selections are objects attached to proteins which select one or more amino acid positions from the amino acid sequence. They usually have color, style attributes and a balloon message. They may be shown in the alignment (1D) and in the built in 3D-wire-frame (3D) and the scrollbar view-port (VP). Selections are created in different ways:

Annotated residue selections

[Menu-bar>Tutorials] Residue annotations, allow the assignment of information to specific amino acids or nucleotides of proteins. They are special types of residue selections. A residue annotation has a list of entries each having a name, some user typed text and a toggle button. The user can change these entries and add new entries. The entries can contain several types of information: A ResidueAnnotation can be created in different ways: Residue annotations which are highlighted in the alignment can be selected in two different ways: By CTRL left-click or by dragging a rectangular box. Selected residue annotations have Marching_ants.

Sequence Features: Features like phosporylation sites and active sites are special annotations which are retrieved from a computational service and are therefore not saved to hard disk. Their color cannot be changed.

Background Images

Image icons are a visual aid to recognize proteins and residue annotations. They are associated to proteins or annotations by Drag_and_drop. Supported formats are gif, png, bmp and jpg. Images in Web pages within the Web browser can only be dragged if they do not serve as a hyper-link. Obtaining icons:

Species Icons: Some protein files have a record of the species name. These species names can be used to set a suitable icon for the selected proteins: charite.christo.strap.StrapAlign#BUT_SPECIES_ICONS.

Structure Icons: To download the 3d-structure thumb-nails from the PDB and use them as icons for the selected proteins, press this button: charite.christo.strap.StrapAlign#BUT_PDB_ICONS.

To delete the icons of all selected proteins press this button: charite.christo.strap.StrapAlign#BUT_DEL_ICONS.

Mapping of species and icons: A table that maps species to images can be inspected: charite.christo.strap.StrapAlign#BUT_TABLE_DEFAULT_ICONS To see a list of currently loaded images press charite.christo.strap.StrapAlign#BUT_TABLE_ICONS. If you want files from a particular species be generally depicted with a certain icon you can copy the respective line to the following file: ~/.StrapAlign/speciesIcons.txt . To deactivate an icon type "NONE" instead of an image file name. ResidueSelectionPopup.html

Modifying annotations

To edit a * residue annotation The item ResidueSelectionPopup#ACTION_edit of the context menu must be activated. Alternatively, the alignment cursor can be placed on a selected residue and the tool-button StrapView#BUT_ANNOTATION clicked. The button is located below the alignment when "annotations" is activated in the UserProfile#newButton(). The annotation view contains a table. Each row is one annotation entry.
Figure: Residue annotation panel. The annotated text is displayed as a table. The left column contains the category and the right column the free text. Each row has a toggle button to activate and inactivate the entry. The user can type into the table and add new table rows.
ResidueAnnotationView#docuView()
These entries can be modified and are saved when the alignment is saved. Four obligatory fields Name,Group,Positions are unique and mandatory whereas the fields Note, Remark, Texshade and Pymol may occur zero to several times.

Export proteins

[Menu-bar>File]

Dragging proteins with the mouse

Proteins can be dragged from the alignment to the Desktop or the file browser. This requires dragging a protein label such as in the row header of the alignment with the mouse. Proteins can be dropped in other Desktop applications that support Drag_and_drop. They may also be dropped into another STRAP instance.

Usually, the protein file, i.e. the file that the protein was loaded from, is transfered. But in some cases, the user might want not this original file but a different or modified protein file: A panel with several export options is available. The button appears at the right bottom when the user attempts to drag out a protein.

Using the export dialog (file-menu)

Single protein files can be exported in various output formats. The output format is selected using a combo box.

Export PDF

[Menu-bar>File] Multiple sequence alignment alignments can be exported to PDF and PostScript with the LaTeX extension TeXshade written by Eric Beitz (see LaTeX). For simple alignment output the Export alignment ... is easier to use. Applying TeXshade requires some basic knowledge about type setting. Novices may have a look at the tiny introduction * .

Installation
A LaTeX system is required. LaTeX provides the two shell commands "latex" and "pdflatex". Windows users may use the LaTeX in Cygwin or Miktex. Macintosh users may install Texshop.

Exporting the sequence alignment to PDF
The main card of the TeXshade-Dialog has three buttons Texshade#BUT_LAB_Source, Texshade#BUT_LAB_RunTex and Texshade#BUT_LAB_Pdf which need to be pressed one after the other. On pressing Texshade#BUT_LAB_Source two files are generated: a * LaTeX-file and a multiple sequence file. As soon as both files exist the button Texshade#BUT_LAB_RunTex becomes active. When it is pressed the program pdflatex starts to work on these two files. The result is a PDF-document which will be displayed when the button Texshade#BUT_LAB_Pdf is pressed.

Including the Alignment in Text-processor documents
PDF graphics can usually not be included into MS-Word or Openoffice documents. But PostScript figures can. The check-box to toggle PDF and PostScript becomes accessible by clicking Texshade#BUT_LAB_Source with the CTRL key. STRAP will use the command latex instead of pdflatex. The output is a .ps file which needs to be converted to .eps as described in "How do I convert PostScript to EPS?" of page http://www.postscript.org/FAQs/language/ .

Annotations
Residue annotations can contain one or more fields labeled with Texshade. Those entries usually contain the variables "PROTEIN" and "RESIDUES" which are replaced by the positions and the protein number. A residue annotation can be created using the tool-button StrapView#BUT_ANNOTATION below the sequence alignment pane.
Useful TeXshade-expressions which can be added to selections 
  \feature{top}{PROTEIN}{RESIDUES}{box[Red]}{peptide}
  \feature{ttop}{PROTEIN}{RESIDUES}{box[Red]}{peptide}
  \feature{bottom}{PROTEIN}{RESIDUES}{fill:$\uparrow$}{$S_{129}$}
  \feature{bbottom}{PROTEIN}{RESIDUES}{fill:X}{cleavage}
  \fingerprint{300}
TeXshade examples with variables 
   \feature{bottom}{PROTEIN}{RESIDUES}{fill:$\uparrow$}{$$FIRST_Aaa_{$FIRST_INDEX}$}
   \feature{bottom}{PROTEIN}{RESIDUES}{fill:$\uparrow$}{$$FIRST_A_{$FIRST_INDEX}$}
A detailed description is found on the TeXshade home page.

Plotting
Numeric values computed for each residue with a class ValueOfResidue can be plotted along the sequence alignment. Classes implementing ValueOfResidue have a getValues-method which returns a numeric value for each residue. The user chooses a class in the "plotting"-card IC_PLOT. The plot has four alternative locations: top, bottom, ttop, bbottom.

Fixing LaTeX-errors
Like in any programming language PDF-LaTeX stops when the text contains syntax errors. In this case cryptic messages are written to stderr and no PDF is produced. LaTeX reports the line number where the error occurred like 1.42 meaning that an error was found at line 42. Typically the error is an incorrect TeXshade command assigned by the user to a residue annotation. The most frequent errors are unbalanced parentheses or characters that have a special syntactical meaning like underscore or "%".

Customization: In the customize dialog you can specify the command for pdflatex and for the pdf viewer.

Memory limitation: With large alignments the pdflatex-run may terminate with an ... memory exceeded ...-error. No PDF-output would be generated. If this happens the LaTeX heap size must be increased. Miktex users should set pdf_mem_size to a higher values in the file miktex.ini. For other LaTeX systems the memory settings in texmf.cnf must be increased ( e.g. multiplied by 10) and the program fmtutil run as root. Typical locations of the texmf.cnf are /etc/texmf/texmf.cnf /usr/share/texmf/web2c/texmf.cnf and /usr/local/teTeX/share/texmf/web2c/texmf.cnf. 
 # fmtutil  --byfmt=pdflatex

Publish alignment as a Web-link

[Menu-bar>File]
Figure: Generation of a Web link. The included information is specified with check-boxes and radio buttons. The link text appears in the text field from where it can be copied into the html source. A test button allows to quickly test the generated link.
new DialogPublishAlignment( )
With this dialog a Web-Link can be formed which loads the proteins from the public databases into STRAP and displays an alignment. When the link is clicked on a computer with Java, the alignment will be displayed in STRAP. Depending on the purpose of the link and on how much information should be transfered two different types are available:
  1. A compact URL
  2. A Web form
In both types, proteins that are stored in protein databases are included by database reference. This has the advantage that always the most recent version of the protein file is loaded and the current state of sequence features and cross links are available.

Single URL

Since the URL contains the information in a compact form in a single line, not all information is stored. The advantage is that the URL can not only be included in web-pages, but also in e-mails, Office-documents. The generation of the URL is conducted in two steps:
  1. DialogPublishAlignment#BUT_LAB_P The parameter String is written into the first text-field and can be modified by the user. The following table summarizes the "|"-separated fields.
    Vertical_bar separated fields of protein entries
    NoDescriptionExample
    1URL of protein file or database colon ID EMBL:M57965
    2Protein name. Optionally with exclamation mark and residue subset. b_myosin_heavy_chain
    3Icon http://www.ebi.ac.uk/thornton.../duc_temp.gif
    4Residue selections. Supported 3D-styles: sticks, spheres and dots. #00FFFF,sticks,16-20,#FF00FF,spheres,40-50
    5Coding sequence of a nucleotide sequence reverse,40-100
    The 5th field is required only for nucleotide sequence files. It contains either the index of the CDS such as "#1" for the first or "#2" for the second CDS or the CDS expression directly.
  2. DialogPublishAlignment#BUT_LAB_E From the text in the first text-field the web-link will be generated using Url_encoding and written into the 2nd text-field. The generated URL acts as a hyperlink and can be tested by clicking. A new STRAP session will be opened in web-mode and an alignment will be loaded with the specified information.

Web form

Since the web form has no size limitation, the entire information for the alignment can be included. The draw-back is that it can only be included in web-pages, but not in office documents or e-mails. A minimal html-page including the web link for the selected proteins is generated on pressing DialogPublishAlignment#BUT_LAB_W. For testing it is loaded into the web browser upon pressing DialogPublishAlignment#BUT_LAB_B. From this html code the text between the opening and closing and <body> tags can be used in any html-page. An overview of the STRAP scripting commands is given in http://3d-alignment.eu/strap_script.html.

The following commands are available:

accession_id ,add_annotation ,add_xref ,align ,align_bg ,below_row ,biomolecule ,box ,cds ,close ,close_jmol ,close_pymol ,close_wire ,cursor ,deiconify,delete ,gaps ,hide ,icon ,iconify,jmol ,load ,new_nucleotide_selection ,new_residue_selection ,plugin ,pymol ,remove_xref ,rotate_translate ,scroll_to ,select ,seqvista ,jalview ,spice ,set_annotation ,superimpose ,superimpose_bg ,to_row ,to_structure_viewer ,tree ,unhide ,unselect ,wire

Start STRAP from command line

STRAP starts on clicking strap.jar or strap2.jnlp. It may also be started from the command line using the command "java" in the bin/ directory of the Java installation: 
java -jar STRAP.jar
In case of the error message "java: command not found" the complete path should be provided like: 
/local/jdk1.5.0/bin/java -jar STRAP.jar

Options:
Examples with protein files: 
java -jar strap.jar a1_Homo.seq a1_Saccharomyces.seq
starts STRAP and loads two protein files.

Example with sequence grouping: 
java -jar strap.jar \{ a*.swiss \} \{ b*.swiss \}
loads all files starting with an "a" into one line and all files starting with "b" into the other line. (See Stacking proteins into a single line ...).

Example with grep: 
java -jar strap.jar $(grep -l -i '^OS.*human'  *.swiss)
loads all Swissprot files with the organism human. The option -i makes the search case insensitive.

Example with pdb chain identifier: 
java -jar strap.jar pdb1ryp.ent:A
loads only chain A of the proteasome.


Example with pdb chain identifier using underscore: 
java -jar strap.jar pdb1ryp_A.ent
loads only chain A of the proteasome.


Example with residue subset: 
java -jar strap.jar 'pdb1ryp.ent!20-30,50-66'
loads only the given residue ranges of the proteasome.


Example with the at-sign: 
java -jar strap.jar  @list
loads all files found in file list. The text file "proteins.list" contains the previously loaded files.

Example with PDB-id: 
java -jar strap.jar -pdb=1sbc
loads the PDB:1sbc from the PDB-server.

Exceptions and the streams stdout and stderr

The standard streams Standard_streams stdout and stderr are pre-connected output channels of computer program. Stdout and stderr are collected in files residing in "./strapTmp" unless STRAP was started with the command line parameter "-stderr" and "-stdout". They can be viewed in the menu "errors" of the option menu. Alternatively, the program ControlPanel in /local/java/jdk1.6.0_13/jre/bin/ can be used to switch the so-called Java-console on. In case of runtime errors like division by zero the Java machine throws so-called exceptions in stderr.

STRAP on Windows

Windows32 is the world's most widely applied operation system.
Windows differs to conventional OS with respect to Always-On-Top attribut of a window: This is one of the essential features the Windows desktop is still lacking. Fortunately there are free and shareware programs to install the Stay-on-Top attribut of a windows on the desktop: AlwaysOnTopMaker (recommended, because it is very small) or Acer-GridVista (free) or WindowSpace.

Some important Windows tips for STRAP users



Cygwin: STRAP uses the Gnu-compiler in Cygwin to install Bioinformatics programs if no other is specified.

The directory for program settings: Dot_files are used for files that store settings of application programs. Since there had been problems on some Windows versions with file names starting with a dot, the dot is omitted. Consequently the settings directory is "%HOMEPATH%\StrapAlign\" rather than ~/.StrapAlign/". But if %HOMEPATH% contains white space then "C:\StrapAlign\" is used instead. An alternative directory can be provided in the file %HOMEPATH%\.location_of_StrapAlign.ini.

Macintosh

The computer mouse of classical Macs had only one mouse button which is ergonomically better. The right mouse button can be simulated in STRAP by holding ALT and CTRL while clicking.
Classical software installation of additional Bioinformatics tools requires Compilers for C++ and Fortran. The compilers are unfortunately not present and must be installed from the DVD.