The first item in this menu - CDD Overview - is presented when a CDD is downloaded from the server, and presents a description of the CDD and buttons to activate the annotation and reference panels. The rest of this menu is for advanced users and is only available when you have loaded a CDD alignment (of a particular data type) and have turned off the CDD Read-Only option in the Preferences panel.
This is an informative panel that presents information about a CDD when downloaded from the CDD server. It shows the name and description of the domain, and if annotations and literature references are available, the buttons at the bottom will open the Edit Annotations or Edit References panels. If the CDD Read-Only option in the Preferences is checked, then both annotations and references information will be read-only, meaning you can view but not change the information.
Annotations on a CDD are linked to columns in the alignment, such as columns of conserved residues at an active site. To create a new annotation, highlight the desired columns in the sequence viewer (or highlight residues of the first sequence), and click on New in the box on the left and enter a description; available annotations will be listed above. Optionally, you may assign a general type to the annotation with the Type pulldown list. For a type beside Other, the Description pulldown list will offer some predefined descriptions for that type (read from the 'cdd_annot_types.ini' file, to which you may add custom entries). If your description matches one of the predefined descriptions, the corresponding Type will be assigned automatically. You may prepend putative to any description by checking the Is Putative? box. Clicking Edit will let you change the description of the selected annotation, modify the assigned type, and optionally change the column location of that annotation. Highlight will cause the columns of that annotation to be highlighted in the sequence viewer, and Delete removes the annotation completely.
Each annotation can have evidence associated with it - for example, a literature reference that describes in more detail the conservation of the active site. Select an annotation in the list on the left, and then click New to create a new evidence item. There are currently three types of evidence: a text comment, a literature reference (PubMed ID), or "Structure" - which can be any set of residues and molecules (including solvents and heterogens) from a single PDB that illustrate a specific case of the conserved feature annotated for the whole CDD family. Clicking Show will display the selected evidence item, Edit will let you change it, and Delete will remove it. Move up/down lets you change the ordering of the evidence items.
This command displays interactions between the master and other biomolecules using data retrieved from the Inferred Biomolecular Interactions Server (IBIS, https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi) at NCBI. It is enabled only for alignments whose master is a structure.
A table on the left side of the window summarizes the IBIS data. The possible interaction types reported by IBIS are: Protein-Protein, Protein-Nucleic Acid, Protein-Chemical, Protein-Peptide, and Protein-Ion. The type of interaction partner displayed can be restricted using the Interaction Type Filter control.
When an interaction in the table is selected, the Launch and Highlight buttons allow the user to open the IBIS web page for that interaction and highlight the interacting residues on the master in Cn3D, respectively. The Make IBIS Annotation button creates a feature annotation from the interaction, and enabled only when all interacting residues are in aligned blocks of the sequence alignment. When this condition is not satisfied, a warning message appears and the unaligned residues are listed in the Message Log.The columns in the table are as follows (see IBIS help for further details, https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis_help.shtml):
When an interaction that has a checkmark in the Annot Overlap column has been selected, the right side of the window displays information about feature annotations that overlap with IBIS interaction. One can use this information and the various Highlight buttons provided to investigate how the selected feature annotation coincides with the selected IBIS-defined interaction. The Delete IBIS Annotation button is activated only when the feature annotation appears to have been derived from an IBIS annotation using the Make IBIS Annotation button on the left side of the window.
This brings up a list of all sequences present in both alignment and import windows. You can choose to add any sequence to the CDD's reject list, which will cue the update system to not include the sequence in any subsequent updates, so use with caution! You can also optionally remove the sequence from the alignment and import windows.