Modifying annotations

Figure: The left column gives the type and the right column the annotation text. Each row has a toggle button to activate and inactivate the entry.

• The most important entry is Positions which defines the the selected sequence positions. Here are some examples of valid entries
  1. The expression "1,3,4,6,101-103,110-112" selects the residue indices 1,3,4,6,101,102,103,110,111,112. Instead of the commas, spaces can by used.
  2. The expression "+2 1 3 4" selects the residues 3,5, and 6 because the preceding +2 adds an offset of 2 to all positions. The "+"-sign is the first character in this expression. For the user interface the first residue has the index "1" whereas internally STRAP starts counting at zero. A negative offset of "2" is achieved by a leading "+-2".
  3. The expression "1:G-3:G 5:G" selects the residues with the pdb-numbers 1,2, 3 and 5 of the chain G. If the protein has only one chain the chain identifier can be omitted like "1:-3: 5:"
  4. Referring to nucleotide positions: When the toggle button is pressed (default state) the indices refer to amino acid positions. Otherwise the positions indicate nucleotides in case the protein is translated from a nucleotide sequence.
  5. To any group an atom specification can be appended. This allows to select certain atoms before changing their style in the 3D-viewers. Even though protein 3D viewers usually have a specific language for atom selection, the atom expression used here is defined by STRAP and works for all 3D-viewers.
     for example "10:-20:.CA.CB" narrows the selection to the atoms CA and CB for the residues 10 to 20. A later command such as "3D_spheres" would affect only c-alpha and c-beta atoms. There may be more than one "Atoms"-entries. Each "Atoms" specification take effect only on the following 3D-style commands but not on the previous. Asterisk can be used as a wild card like "*.CA" or "10:-20:.C". For the proper atom identifiers have a look at the PDB file.
• Atoms Certain Atoms can be specified by an expression like ".CB.CA" which means only Cα and Cβ atoms. The next 3D-command will act on these rather than on all atoms of the amino acid. When sending the commands to a 3D-program, the rows are processed sequentially. If there comes yet another Atoms-row, the previous atom-specification is replaced by the new one.
• Name Each selection has a name. Un-checking the check box deactivates the residue annotation.
• Group Several selections may be bundled in one group e.g. "active site"
• : TeXshade commands. See menu Export in the file menu.
• Note, Remark: Free text. URLs are clickable. Supports cross-links like PDB:1ryp, PUBMED:0815. The list of databases can be changed by Ctrl-click the cross-link.
• Balloon: The balloon text appears when the mouse is over the highlighted residues.