R3DAID Server Help Page

R3DAID, pronounced "Red Aid" takes two chains from PDB representing the same molecule, aligns them using cmalign from Infernal and covariance models from Rfam, and displays the alignment visually by listing each pair of aligned nucleotides next to each other. Between the nucleotides is a bar that is colored according to the number of conserved basepairs made by the two nucleotides. Basepairs are indicated by colored arcs to the left and right of the alignment. Symmetrical arcs indicate that the alignment quality is good. After clicking Submit, the PDF may download directly to your computer, where it can be visualized using a tool like Adobe Acrobat Reader.

Table of Contents

Input page

Enter PDB ID or multiple chain IDs

Choose your preferred color scheme

Helix numbers

Choose interaction arcs to show, dim or hide - future

Submit

Direct URL requests

Output

Examples

Example 1:

Input page

Enter two chain IDs

To begin using the R3DAID server, enter two chain identifiers from PDB.  The format is pdb|model|chain for example 8GLP|1|L5 for PDB identifier 8GLP, model 1, chain L5.  

To find chain IDs, consult the current RNA Representative Set release.

Choose your preferred color scheme - future

In the second box, labeled "Choose the color scheme," you can select from several color formats to represent different types of interactions. The default format uses specific colors to indicate various interactions:

• Blue for nested Watson-Crick base pair interactions
• Red for non-nested Watson-Crick base pair interactions, occurring between nucleotides in different chains
• Cyan for nested non-Watson-Crick base pair interactions
• Green for non-nested non-Watson-Crick base pair interactions
• Yellow for stacking interactions
• Magenta for base-phosphate interactions
• Orange for base-ribose interactions
• Gray for near interactions

Additionally, there is a "Wong format" designed for accessibility, particularly for individuals with color blindness. More information about this format can be found at Color blindness article. There is also a grayscale format available, which uses shades of gray to represent the interactions.

Helix numbers - always on, at the moment

Some chains are annotated with helix numbers. This option allows you to adjust the display size of these numbers within the diagram. Simply enter 0 if you do not want the helix numbers to be displayed.

Choose interaction arcs to show, dim or hide - future

In this section, you can choose to show, hide, or dim specific interaction arcs. The 'show' option displays the arcs using the selected color scheme. The 'hide' option allows you to remove certain arcs from view. The 'dim' option reduces the visibility of selected arcs, making them appear lighter so you can focus on others. Note that regardless of the option you select, the list of interactions outside the diagram will remain unchanged. Below are descriptions of each group of interactions you can customize using the show, hide, or dim options.

• “nested Watson-Crick basepairs” Interactions: This corresponds to nucleotides forming Watson-Crick interactions.
• “non-nested Watson-Crick basepairs” interactions : This corresponds to nucleotides forming Watson-Crick interactions that cross more than three other Watson-Crick interaction arcs; these are also called long-range interactions.
• “nested non-Watson-Crick basepairs” interactions :  This corresponds to nucleotides forming interactions other than Watson-Crick interactions.
• “non-nested non-Watson-Crick basepairs” :  This corresponds to nucleotides forming interactions other than Watson-Crick interactions so that the arcs cross more than three other Watson-Crick interaction arcs.
• “stacking interactions”
• “base-phosphate interactions”
• “base-ribose interactions”
• “near interactions”  : This corresponds to interaction arcs not listed above.

Submit

After pressing the Submit button, the server will process your request and generate a PDF with the diagram reflecting all your selected options. Additionally, a link will be created to save your choices for that specific diagram. The link can also be generated separately from the input page, using the settings described in the following section.

Direct URL requests

The base URL is:

• https://rna.bgsu.edu/correspondence/r3daid 

List the two chains to request a diagram:

• https://rna.bgsu.edu/correspondence/r3daid?chains=5J7L|1|DA,4WF9|1|X 

Output

The output is a PDF that gets downloaded after submission on the input page.

Examples

Example 1: