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.


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.


Description: Center the view to the selected amino acids or atoms.


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.


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%