3D_biomolecule
Example:
- ```
    3D_biomolecule 0x2  *, PDB:1a34
```
The biological units are given as a decimal or hexadecimal number which is a bit masks. For example 0x8 means the biological unit 3 since 2^3=8. -1 means the asymmetrical unit.
3D_cartoon [on/off]
Display the currently selected amino acids as spheres.
3D_center
Center the view to the currently selected amino acids or atoms.
3D_center_amino
Center the view to all peptide chains.
3D_color html-color
Example:
- ```
    3D_color #ff0000
```
The color for the selected atoms is given as a 6 digit hexadecimal number. First 2 digits Red, middle 2 digits Green and last 2 digits Blue.
3D_dots [on/off]
Draws dots around the selected atoms.
3D_highlight_selected_amino_acids [milliseconds]
Example:
- ```
    3D_highlight_selected_amino_acids 2000
```
The cAlpha atoms of the selected residues are highlighted.
3D_highlight_selected_atoms [milliseconds]
Example:
- ```
    3D_highlight_selected_atoms 2000
```
The selected atoms are highlighted.
3D_label "text"
Sets a text label for the selected atoms.
3D_label_color color
Example:
- ```
    3D_label_color #ff0000
```
Color for text labels created with 3D_label.
3D_lines [on/off]
Displays the selected atoms as lines.
3D_mesh [on/off]
Draws a mesh around the selected atoms.
3D_native viewer-type [jmol|astex|pymol] , 3D-command
Examples:
- ```
    3D_native jmol, 3D_label "This label appears only under Jmol"
```
- ```
    3D_native astex, 3D_label "This label appears only under Astex"
```
The command is send only under the condition, that the current 3D view is of the given type. This allows for native commands that are spicific to certain viewer types but not understood in other 3D-viewers.
3D_object_delete Object-name.
Delets an object such as a surface.
3D_ribbons [on/off]
Display the currently selected amino acids as ribbons.
3D_rotate X angle
Rotate angle (degree not radiant) around axis X, Y or Z.
3D_sa_surface [on/off]
Creates a surface object. The color is specified in a previous 3D_surface_color-command.
3D_script_panel
Opens the native script panel of that viewer.
3D_select expression
Examples:
- ```
    3D_select 69.CA
```
- ```
    3D_select NADH
```
Selects atoms or amino acids in the active 3D view.
3D_spheres [on/off]
Display the currently selected amino acids or atoms as spheres.
3D_sticks [on/off]
Displays the selected atoms as stick.
3D_surface [on/off/#HexColor]
Creates a surface object. The color is given as a hexadecimal number with a leading #-sign. This hexadecimal has 6 or 8 digits. If 8 digits, then the first two digits are transparency.
3D_zoom percentage
Example:
- ```
    3D_zoom 200%
```
DAS_features list of DAS services, list of proteins
Example:
- ```
    DAS_features CSA%20-%20extended uniprot cbs_total netphos netoglyc , UNIPROT:P29590
```
Position specific annotations are loaded from the DAS services and underlined in the alignment. Unfortunately, most BioDAS servers and the registry is not available any more. Also see uniprot_features
GFF file_or_GFF-line
Examples:
- ```
    GFF P25787	UniProtKB	Modified residue	24	24	.	.	.	Note=Phosphotyrosine
```
- ```
    GFF http://server/path/myGffFile.gff
```
Loads the GFF files and underlines the sequence features Fields: 1=Sequence 3=Name 4=Start-Position 5=End-Position 9=Attributes The fields are separated by tabulator character or vertical bar. A dot marks empty content. Also see DAS_features
STRAP_to_front
The application frame as top level window
aa_sequence amino acid sequence, sequence name
Example:
- ```
    aa_sequence -VLSAAERAQVKAAWGKI--QAGAHGAEALERMFLGFPTTKTYPF, Xenopus
```
Defines a protein by amino acid sequence. The sequence may have gaps "-".
accession_id id, sequence
Example:
- ```
    accession_id UNIPROT:HSLV_ECOLI , hslv_ecoli
```
The accession ID for a sequence is set. Providing the accession ID allows direct access to BioDAS services.
add_annotation attribut=value, selection_name
Examples:
- ```
    add_annotation Balloon=My text, myProtein.pdb/myAnnotation1,
```
- ```
    add_annotation Balloon="<HTML><BODY>My text with <b>bold</b> or <u>underline</u></BODY></HTML>", myProtein.pdb/myAnnotation1,
```
An entry consisting of a key such as "Remark" or "Balloon" and a value such as a free text is added to the named selection. Only the following attributes are supported for the HTML-output: - Balloon (Free text or HTML), - Color (e.g. #FF0000), - Style (UNDERLINE or BACKGROUND), - 3D_view (A 3D-command), Atoms (dot - PDB atom name like .CA or .CB or .N) .CA.CB means C-alpha or C-beta. .C* means means any Carbon.
add_compound hetero-compound or nucleotide-chain , protein1 protein2
Example:
- ```
    add_compound  PDB:1gd2_A PDB:1gd2_B, 1gd2_E.pdb
```
Hetero-compounds or nucleotide chains are added. For HTML output only nucleotide chains of the same PDB id are regarded.
add_xref reference, sequence
Example:
- ```
    add_xref PDB:1NED, hslv_ecoli
```
Adding a sequence ID for that sequence. While a sequence has only one accession ID, it can have several cross references e.g. from the RefSeq, UniProt and PDB.
align sequences
Example:
- ```
    align *
```
Aligns the sequences
ants residues
Example:
- ```
    sequence1/20-30  sequence2/22-40
```
Draws a rubber band rectangle around all given residue selections
balloon_text Text , list of sequences and residue selections
Example:
- ```
    balloon_text bla bla , sequence1
```
Defines the mouse-over text HTML code is assumed, if lower case tags are found. In this case greater-than, less-then and ampersand characters need to be HTML encoded.
below_row row-number or sequence , list of sequences
Change the order of sequences in the alignment.
bg_color residue-set=hex-color residue-set=hex-color, sequence
Examples:
- ```
    bg_color 20-30=#00FF00, sequence1
```
- ```
    bg_color 20:-30:=#00FF00, sequence2
```
The color of individual residues is set. PDB residue numbers can be refered to by appending a colon to the position number.
box residue
Same as ants
clip_C_term sequence-slash-position
See clip_N_term
clip_N_term sequence-slash-position
Examples:
- ```
    clip_N_term sequence1/100
```
- ```
    clip_N_term sequence1/nameOfResidueSelection
```
- ```
    clip_N_term sequence1
```
The entire alignment is truncated left at the specified position. If slash and position number are omitted, the first residue of that sequence is used. Residue selections can be given by name. If more than one object is specified, then the most left one is used.
close sequence1 sequence2 ...
The sequences are removed from the view. The remain on the hard disk.
close_3D view ID , proteins
Removes the proteins from the 3D view. If no proteins are given, the 3D view is closed.
close_wire proteins
Closes the 3D backbone representations
cursor sequence/residue
The alignment cursor is set to a residue of a sequence. The name of a residue selection can be given instead.
define_protein_complex protein1 protein2 ...
A multiprotein complex consisting of several chains is formed. By default, chains of the same PDB entry form a complex. See superimpose_multiprotein_complexes.
delete residue_selection1 residue_selection2 ... " :
The specified residue selection is removed.
echo bla bla bla
Example:
- ```
    echo Hello world
```
The text is printed to standard output (console) or to a file specified with -scriptOutput=filePath
feature_colors name=color1,color2 name=color
Example:
- ```
    feature_colors Modified_residue=#FF2222,#FF0000 Phosphorylated_residue=#AAaa00 Glycosylated_residue=#00ffFF
```
Assignment of colors to sequence feature names. The first color is for black background and the other optional color is for white paper. All residue selections with one of those names will be treated as sequence features.
gaps x--xxxxxx-xxx-xxxxxx-xx-x, sequence
Gaps are inserted into the sequence.
hide sequences
The sequences are removed from the current alignment but remain in memory.

icon URL_or_absolute_file_path, sequence
Examples:

    icon http://www.bioinformatics.org/strap/images/dog.png , protein

```
    icon NULL , protein
```

    icon data:image/gif;base64,R0lGODlhGgAaAIABADMzM////yH5BAEKAAEALAAAAAAaABoAAAI5jI+py+0Po0SgWmpry9nwq3yimIwmh51nqo5s+71wd8yuPIc2Xe7AZnvkIK3JauJBIVlLXfMJjUIKADs= , 4 5

The protein icon is displayed in the alignment row at the left.

iconify
The application frame is iconfied
let $variable=Text which may contain white space and any printable ASCII character
Examples:
- ```
    let $x=protein/selection
```
- ```
    new_selection 20-30, $x
```
- ```
    color #00ff00, $x
```
Variable declaration similar as in programming languages like BASIC. Quotes are not required.
load list of URLs or database IDs or absolute file paths
The sequences are loaded
new_nucleotide_selection nucleotides, rotein/selectionName
Same syntax as new_selection. Positions refer to the nucleotide sequence that the protein was translated from.
new_selection residues, sequencName/selectionName
Examples:
- ```
    new_selection 1-20, my_protein/N-terminus
```
- ```
    new_selection 10:-20: 30:, my_protein/a_selection
```
A residue selection for the given sequence is created. The name of the selection is given after the slash. The residue subset can use the natural numbering starting at 1 or the PDB resn. The PDB resn is recognized by the colon according to the Rasmol convention.
nt_sequence [coding] nucleotide sequence , sequence name
Defines a nucleotide sequence. Syntax like aa_sequence. Only if the alignment type has been specified with either command set_alignment_type_N or set_alignment_type_CN, the sequence is not translated to amino acids.
open_3D ViewID, protein1 protein2 ...
The given proteins are opened in a 3D-viewer. ViewID is an identifier which allows this view to be refered to by the commands select_3D and close_3D.
print_3D_transformation proteins
Prints the 3x3 rotation matrix and translation vector of the given proteins.
print_selections sequences
Prints a list of all residue selections of the sequences
print_sequences
Prints a list of all sequences to standard output (console) or to a file specified with -scriptOutput=filePath
project_coordinates PDB ID, protein
Examples:
- ```
    project_coordinates PDB:1BOR_A , UNIPROT:P29590
```
- ```
    project_coordinates AUTO , UNIPROT:P29590
```
- ```
    project_coordinates NULL , UNIPROT:P29590
```
The 3D coordinates are infered into the protein. With AUTO, the most similar PDB entry is determined automatically.

put_property key=value , sequences
Examples:

    put_property NOT_USE_STRUCTURE_FOR_ALIGNMENT=true ,  *

    put_property NOT_USE_STRUCTURE_FOR_ALIGNMENT=NULL ,  *

remove_xref reference, sequence
rotate_translate xx xy xz yx yy yz zx zy zz translation_x translation_y translation_z , protein
Examples:
- ```
    -0.51  -0.69   0.50   0.22   0.45   0.86  -0.82   0.55  -0.80     91.15 25.13  55.68 , protein
```
- ```
     NULL, protein
```
The protein is moved in 3D space. If a protein is given instead of a 3x3 matrix and translation vector then the transformation of that protein is used. Also see command "superimpose".
rotate_translate_protein_complex xx xy xz yx yy yz zx zy zz translation_x translation_y translation_z , protein
Works similar as rotate_translate. In addition, if protein is part of a multiprotein complex, then also all peptide chains of the complex are rotated and translated.
scroll_to sequence/residue [sequence/residue ... ]
The alignment is scrolled such that residues of interest come into sight.

secondary_structure character-sequence , protein
Example:

    secondary_structure ---HHHHHH---HHHHH---EEEEEEEEEE----EEEEEE , Xenopus

select sequence1 sequence2 ... residue_selection1 ...
selected sequences are highlighted in the row header. selected residue selections are indicated by marching ants.
select_3D 3D-ViewID, proteins or residue selections
Examples:
- ```
    select_3D  ViewID
```
- ```
    select_3D  ViewID , subtilisin
```
- ```
    select_3D  ViewID , subtilisin/100-200
```
Subsequent commands starting with "3D_" such as "3D_select" act on the selected 3D-view, protein (and residue selection). The first argument is the identifier of a 3D-view (See open_3D). The second argument is optional and is one or several proteins in this view or residue selections. Instead of referring to a particular view ID, the constant strings, an asterisk "*" can be used. Note that the command "select_3D" and "3D_select" are different.
sequence_group NameOfGroup, list of sequences H Defines sequence groups. H They can be used in the menu "Sequence groups" of the HTML output. E sequence_group Alpha, HBA.* E sequence_group Beta, HBB.* H Also see taxonomy_group
set_alignment_type_CN
The alignment type is explicitely set to coding nucleotide sequences
set_alignment_type_N
The alignment type is explicitely set to nucleotide sequence alignment This affects following "nt_sequence" commands such that the coding sequence is not translated.
set_alignment_type_P set_alignment_type_P
The alignment type is explicitely set to amino acid sequence alignment. "P" stands for peptide. See set_alignment_type_N
set_annotation key=value, selection_name
like add_annotation but already existing entries with this key are deleted.
set_characters_per_line number
Example:
- ```
    set_characters_per_line 60
```
Number of letters per line for non-interactive mode with command line export options -toHTML, -toClustal and -toMSF.
set_color hash-sign-hex-rgb, sequences or residue selections
Examples:
- ```
    color #00FF00 , sequence1
```
- ```
    color #00FF0066 , sequence1
```
The color of residue selections or sequences can be changed. The color of a protein is used for the rendered 3D view. If the color has 8 instead of 6 hexadecimal digits, the last two digits are the transparency.
set_color_mode color-type
Example:
- ```
    set_color_mode hydropathy
```
Residue colors. white|black|charge|hydropathy|chemical|nucleotide|zappo|taylor
set_conservation_threshold number
Example:
- ```
    set_conservation_threshold 70
```
Number is in the range of -100 to 100. Positive numbers the threshold in percent up from where conserved residues are emphasized. Negative numbers define the minimal diversity.
set_nucleotide_index_offset number , protein
Change the numbering of coding nucleotides in an amino acid sequence A positive value shifts all nucleotide selections to the left
set_residue_index_offset number , sequence
Change the numbering of residues
set_ruler_secondary_structure theProtein
The protein should have secondary structure information. A ruler is drawn above or below the alignment. Helices are red and beta sheets are yellow.
set_taxonomy , list of sequences
Examples:
- ```
    Eukaryota;Metazoa;Craniata;Vertebrata;Euteleostomi;Mammalia;Primates;Hominidae;Homo,  sequences1
```
- ```
    taxonomy_group Primates, *
```
The taxonomy data is assigned to the given sequences. It is umportant for taxonomy_group commands which create respective sequence groups.
superimpose proteins
Example:
- ```
    superimpose *
```
Superimposes the proteins. The reference protein is the one that is most similar to all others
superimpose_protein_complexes protein1 protein2 ...
Multiprotein complexes as whole are superimposed upon each other. See define_protein_complex
taxonomy_group list of groups, list of sequences
Example:
- ```
    taxonomy_group Vertebrata Viruses Eukaryota Bacteria Archaea Fungi Mammalia, *
```
Defines sequence groups according to taxonomy. They can be used in the menu "Sequence groups" of the HTML output. Also see sequence_group
to_row row-number or sequence , list of sequences
Change the order of sequences in the alignment.
translate_cds coding sequence expression , myProtein
Examples:
- ```
    cds join(10 20..30) , protein
```
- ```
    cds complement(join(10 20..30)) , myProtein
```
- ```
    cds 1.. , myProtein
```
- ```
    cds 2 , myProtein
```
The protein myProtein is given as a genomic sequence. This command specifies, how the DNA is translated into protein. Either it takes a CDS expression (which is recognized by the dot dot) or a number or range of numbers which refer to the n-th CDS expression[s] in the Embl or GB file.
tree sequences
Example:
- ```
    tree *
```
Displays a phylogenetic tree
unhide sequences
Sequences previoulsly hidden with hide are put back into the alignment
uniprot_features proteins
Examples:
- ```
    find_uniprot_id *
```
- ```
    uniprot_features *
```
Loads the GFF files and underlines the sequence features. The UniProt ID may be defined in the sequence file. It can be searched automatically (find_uniprot_id) or set explicitely (accession_id) Also see DAS_features and GFF
unselect sequence1 sequence2 ... residue_selection1 ...
deselects sequences or residue selections.
url_alias alias1=url1 alias2=url2 ...
Examples:
- ```
    alias_for_url WIKTIONARY:=http://en.wiktionary.org/wiki/
```
- ```
    balloon WIKTIONARY:happy , sequence
```
Aliases for URLs to be used in balloon texts for sequences and annotations
use_3D_viewer jmol
Set jmol as the default 3D-viewer. Possible arguments: astex, pymol, jmol.
use_aligner t_coffee
Set t_coffee as the default aligner. Possible arguments: clustalw, t_coffee, amap, clustalw, dialign, dialignt, kalign, mafft, muscle, probcons2
use_aligner3D mapsci
Set mapsci as the default aligner. Possible arguments: ce, mapsci, matt, mustang, native_ce, smolign, tm_align
use_aligner_p t_coffee
Set t_coffee as the default aligner allowing profiles. Possible arguments: clustalw, t_coffee
wait_for command
Examples:
- ```
    bg align *
```
- ```
    ... some script lines ...
```
- ```
    wait_for align
```
waits for the command to be finished which has been previously started with bg
wire protein1 protein2 ...
Show 3D protein trace