accession_id id, protein
Example: accession_id SWISS:HSLV_ECOLI , hslv_ecoli
Description: The accession ID serves as a reference to look-up information
in bioinformatics services.
Providing the accession ID accellerates access to DAS services.
Otherwise BLAST searches would be performed to obtain the UNIPROT accession ID.
add_annotation selection_name, key, value
Example: add_annotation myProtein.pdb/myAnnotation1, Balloon, Another line
Description: 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.
add_xref id, protein
Example: add_xref PDB:1NED , hslv_ecoli
Description: A cross-reference can be clicked by the user to open related information in the Web-browser.
below_row row-number or protein , list of proteins
Description: This command is used to change the order of proteins in the alignment.
box protein/residue [protein/residue ... ]
Description: Drawing a box around certain residues.
The box can comprise several rows and columns.
The residues can be specified directly or a selection name can be given.
cds coding sequence expression , myProtein
Example: cds join(10 20...30) , protein
cds complement(join(10 20...30)) , myProtein
Description: The protein myProtein is given as a genomic sequence.
This command specifies, how the DNA is translated into protein.
close protein1 protein2 ...
Description: The proteins are removed from the view.
The remain on the hard disk.
cursor protein/residue
Description: The alignment cursor is set to a residue of a protein.
The name of a residue selection can be given instead.
define_protein_complex protein1 protein2 ...
Description: A multiprotein complex consists of several chains.
By default, chains of the same PDB entry form a complex.
With this command the given proteins are summarized to one complex and
will move all together when applying the command superimpose_multiprotein_complexes.
delete residue_selection1 residue_selection2 ... " :
Description: The specified residue selection is removed.
gaps x--xxxxxx-xxx-xxxxxx-xx-x , protein
Description: Gaps are inserted into the sequence.
This allows for alignments computed on the server rather than computed in the client.
icon URL of icon , protein
Example: icon http://server/path/file.gif , protein
Description: The protein icon is displayed in the alignment row at the left.
open_3D 3D-ViewID, protein1 protein2 ...
Description: The given proteins are opened in a 3D-viewer.
3D-ViewID is an identifier which allows this view to be refered to
by the commands select_3D and close_3D.
project_coordinates AUTO , protein
Example: project_coordinates AUTO , UNIPROT:P29590
Description: The most similar PDB entry is determined and the coordinates infered into the protein.
Instead of AUTO, a specific PDB-ID can be given.
rotate_translate xx xy xz yx yy yz zx zy zz translation_x translation_y translation_z , protein
Description: The protein is moved in 3D space.
This can be used to superimpose two proteins.
If a protein is given instead of a 3x3 matrix and translation vector,
then the transformation of that protein is used.
rotate_translate_protein_complex xx xy xz yx yy yz zx zy zz translation_x translation_y translation_z , protein
Description: 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 protein/residue [protein/residue ... ]
Description: The alignment is scrolled such that residues of interest come into sight.
select protein1 protein2 ... residue_selection1 ...
Description: selected proteins are highlighted in the row header.
selected residue selections are indicated by marching ants.
select_3D 3D-ViewID, protein
Example: select_3D myView , subtilisin.pdb/20-30,35
Description: With this command a 3D-view of a protein is selected.
Subsequent 3D-commands (commands starting with "3D_") are interpreted by this 3D-view.
The first argument is the viewer ID of a 3D-view created with the open_3D-command.
The second argument is a protein or a list of proteins.
Instead of referring to a particular 3D-view ID, the constant strings ANY_VIEWER or ANY_WIRE can be used.
Do not mix up "select_3D" and "3D_select".
set_annotation selection_name, key, value
Description: like add_annotation with the difference that existing entries with this key are deleted.
superimpose_protein_complexes protein1 protein2 ...
Description: For proteins that are part of a multiprotein complex, all chains of that
complex are moved together.
The relative position of the chains of complexes are sustained.
to_3D jmol, expression
Description: This command is used to send native commands to a protein viewer.
It should only be used, if none of the generic commands defined in STRAP are appropriate.
The expression is sent to the current 3D viewer (last select_3D command)
Before this, the atoms specified in the select_3D command are selected.
The first expression gives the type of 3D-viewer.
If the 3D-view given in the last select_3D command is not of this type here jmol, then the command is ignored.
to_row row-number or protein , list of proteins
Description: This command is used to change the order of proteins in the alignment.
unselect protein1 protein2 ... residue_selection1 ...
Description: deselects proteins or residue selections.
use_3D_viewer jmol
Description: Specify which 3D-viewer is used. Possible arguments: astex, pymol, jmol.
3D_biomolecule
Example: 3D_biomolecule 0x2 ANY_WIRE, PDB:1a34
Description: 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]
Description: Display the selected amino acids as spheres.
3D_center
Description: Center the view to the selected amino acids or atoms.
3D_center_amino
Description: Center the view to all peptide chains.
3D_color html-color
Example: 3D_color #ff0000
Description: 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]
Description: Draws dots around the selected atoms.
3D_label "text"
Description: Sets a text label for the selected atoms.
3D_lines [on/off]
Description: Displays the selected atoms as lines.
3D_mesh [on/off]
Description: Draws a mesh around the selected atoms.
3D_object_delete Object-name.
Description: Delets an object such as a surface.
3D_ribbons [on/off]
Description: Displays the selected amino acids as ribbons.
3D_rotate X angle
Description: Rotates angle (degree not radiant) around axis X, Y or Z.
3D_sa_surface [on/off]
Description: Creates a surface object.
The color is specified in a previous 3D_surface_color-command.
3D_script_panel
Description: Opens the native script panel of that viewer.
3D_select expression
Example: 3D_select 69.CA
3D_select NADH
Description: Selects atoms or amino acids in the active 3D view.
3D_selection_name identifier
Description: Sets the name of the selection for the following 3D_select command
3D_spheres [on/off]
Description: Display the selected amino acids or atoms as spheres.
3D_sticks [on/off]
Description: Displays the selected atoms as stick.
3D_surface [on/off]
Description: Creates a surface object.
The color is specified in a previous 3D_surface_color-command.
3D_surface_color RGB-color
Example: #77FF00FF
Description: The color is given as hexadecimal.
If 8 digits, then the first two digits are transparency.
3D_zoom percentage
Example: 3D_zoom 200%