The plot's appearance can be changed via the settings menu, which opens upon right-clicking in the map field.
The top field enables the change of the Title of the map.
The fields in the Design section can be used to set the number of amino acids per line, band height and border, font, colors. Several color palettes are pre-set, but full customization is also possible. Further settings of the map appearance are under section Advanced - sequence gaps, peptide sorting (N-terminal first / the longest first), numbering style.
Section Numbering allows setting numbering step or adjusting the numbering in case of protein constructs - add N- or C-terminal tags, and start numbering with a number corresponding to a native protein sequence.
Field Data series is used to sort the order of the analysis, renaming, and removal.
The Structure and Domains allow the user to add structural elements (alpha helix, beta sheet or “other”) and name them. Domains can be added to highlight other structural elements - domains, tags. These appear further above the sequence and structural elements.
Structural elements can be imported from a file using the format described below. Users should be aware of potential mismatches between the numbering in their input file and the residue numbering shown in the DigDig visualization. For example, if you define a His-tag as residues 1-10 in the Structure-Domain file but load it into a map where the sequence numbering was shifted by 8 residues and the native sequence is set to start at residue 2, then the domain 1-10 cannot be matched, because residue 1 does not exist in the visualization.
To avoid such issues, it is recommended to upload the Structure-Domain file before applying any residue shift or custom numbering. The domain and structure annotations will then be automatically adjusted to match the updated residue numbering.
The structure/domain file must contain headers as defined here.
Structure Name Type Start End
Three types of structural elements are recognized: helix, sheet, and other.
For domains, the section must begin with the header:
Domains Name Start End Colour
All columns must be tab-separated. The domain color must be specified using a hexadecimal color codes, including the leading # symbol (e.g., #FF0000).
An example Structure-Domain file shown here will generate image below.
Structure Name Type Start End A1 helix 15 25 S1 sheet 30 40 O1 other 45 55 A2 helix 60 80 S2 sheet 90 99 Domains Name Start End Colour HisTag 1 8 #9b9b9b Domain A 15 50 #FF0000 Transmembrane 60 85 #006400
Structural elements (helix, sheet, other) must not overlap. In contrast, domains may overlap. However, when placing multiple domains over the same region, the order of appearance in the input file matters: domains listed later will be drawn on top of earlier ones. Therefore, longer domains should be listed first, followed by shorter or nested domains. If the “CLC-ec1” domain is placed in the last position, it will cover smaller domains.
The file must then adjusted to this:
Structure Name Type Start End A1 helix 15 25 S1 sheet 30 40 O1 other 45 55 A2 helix 60 80 S2 sheet 90 99 Domains Name Start End Colour CLCec1 1 100 #FFEA00 HisTag 1 8 #9b9b9b Domain A 15 50 #FF0000 Transmembrane 60 85 #006400
Please note that domain colors are rendered semi-transparently. As a result, overlapping regions will appear as a blend of the overlapping colors.
This behavior is also reflected in the Domains field, which is not sorted by N-to-C terminal sequence order but rather by domain length, with longer domains listed first.
An example structure-domain file that pairs with the CLCec1 test data can be downloaded HERE.