Multiple Sequence Viewer/Editor — Shortcut Menus

This topic describes the shortcut menus available in the display area of the Multiple Sequence Viewer/Editor.

  • Features
  • Additional Resources

Features

Sequence shortcut menu

This menu has items that apply to a selection of sequences. Many of the items are also on the Edit menu.

Set as Reference

Make the selected sequence the reference sequence. The sequence is moved to the top of the list, as the reference sequence is always the first sequence in the list. Only available when a single sequence is selected. If the sequence is in an alignment set, the entire set is moved to the top, with the selected sequence first, then the rest of the set in the same order as previously.

Rename

Rename the selected sequence. Opens a dialog box in which you can specify a name and a chain. Only available when a single sequence is selected.

Duplicate

Duplicate the selected sequences, and place each duplicate according to the choice from the submenu.

  • In Place—Place the duplicate sequence immediately below the original.
  • At Bottom—Place the duplicate sequence at the end of the sequence list.
  • At Top—Place the duplicate sequence at the top of the non-reference sequence list, immediately below the reference sequence.
  • As Reference Sequence—Make the duplicate the reference sequence. Not available when duplicating the reference sequence.
  • Into New Tab—Create a new tab and place the duplicates in the new tab.
  • Into Existing Tab—Place the duplicate sequences at the end of the list in an existing tab, which you choose from the submenu. The duplicated sequences are selected in the destination tab.
Move To Top

Move the sequence to the top of the list of non-reference sequences, immediately below the reference sequence.

Move Up

Move the sequence up one row.

Move Down

Move the sequence down one row.

Move To Bottom

Move the sequence to the end of the sequence list.

Sort All by

Sort all sequences to place them in a chosen order. The selection is ignored, but retained.

Ascending
Descending

Sort the sequences by the value of a given property, in ascending or descending order. The properties that can be used are Name, Chain ID, Number of Gaps,Length, Identity %, Similarity %, Conservation %, and Overall Score. Conservation is calculated as the percentage of residues with identical side-chain chemical properties (as defined for the Side-Chain Chemistry color scheme).

Alignment Set

Set or change the assignment of the selected sequences to an alignment set, by choosing from the submenu. When an alignment is done, the sequences in each set remain in the same relative alignment. The set membership is marked with an annotation (Alignment set) that contains an icon and the set name and is colored differently for each set. Changing the sequences in a set moves the sequences in the set up so that they are all together (contiguous).

Sequences in alignment sets cannot be edited; to perform edits, you must first move the sequences out of the set (or dissolve the set), do the edits, and then move the sequences back in or create a new set. Editing may change the alignment of the sequences relative to one another. You can perform an alignment within the set, however, and alignment to other sequences or sets can create gaps, which are added to all sequences in the set.

If the sequences are not in a set, the submenu items are:

  • Create Set—create a new set with the selected sequences. Opens a dialog box to name the set. An Alignment set annotation is added to the sequences.
  • Add to Set—add the selected sequences to the set chosen from the submenu. Not available if there are no sets.

If the sequences are already in a set, the submenu items are:

  • Remove from Set—remove the selected sequences from the alignment sets they are assigned to. The Alignment set annotation is removed from the sequences. If you remove all sequences from the set, the set itself is removed. Not available if there are no sets.
  • Move to Set—move the selected sequences to the set chosen from the submenu or to a a new set.

See sequence alignment, force alignment, superposition, superimpose, constraints for more information on alignment.

Get Structure from PDB/AlphaFold PDB

Download structural information (secondary structures, B-factors, coordinates) for any of the selected sequences that came from the PDB/AlphaFold PDB, such as in a BLAST search. The database type will change automatically based on the structure selected. The information is obtained from a local copy of the PDB, or the RCSB or AlphaFold PDB websites. The sequence is replaced by the sequence from the PDB/AlphaFold PDB.

Translate DNA / RNA

Translate DNA and RNA sequences into the sequence for the proteins they code for, using standard genetic code. The protein sequence replaces the nucleic acid sequence if the sequence is in a View tab; if the sequence is in the Workspace tab, the protein sequence is added as a new sequence in a new tab.

Unlink from Entry

Unlink the selected sequences from their Maestro project entries. Opens the Link Sequences to Entries dialog box with the sequences selected in the Linked Sequences tab. When an entry is unlinked, the icon is removed from the left of the sequence name in the sequence list.

Select All Residues

Select all residues in the selected sequences.

Deselect All Residues

Deselect all residues in the selected sequences.

Export

Export sequences from the project to a file in FASTA, CLUSTAL, or CSV format, or as a plain text file. Opens the preserve relative indices, in which you can set export options, navigate to a location and name the file.

Hide

Hide the selected sequences, so they are no longer shown in the display area. You can show them again from the View menu.

Delete

Delete the selected sequences.

Residue/gap selection shortcut menu

This menu has items that apply to a selection of residues and gaps. The items available depend on the content of the selection: residues only, residues and gaps, gaps only.

Expand Selection

Expand the selection by one of the following methods:

  • To Same Annotation Values—When you right-click on an annotation, expand the residue selection in the sequence to those that have the same value of the annotation property. (This includes gaps with the same annotation on both sides). For example, if the selection is in a helix and you right-click on the secondary structure annotation (anywhere) and choose this item, the selection expands to all helices.You can expand the selection to a single secondary structure by double-clicking the secondary structure annotation.

    Only available when you right-click on an annotation.

  • Between Gaps—Expand the selection of residues (horizontally) in both directions up to the next and previous gaps. The selection must contain residues.

  • Along Gaps—Expand the selection of gaps (horizontally) in both directions up to the next and previous residues. The selection must contain gaps only.

  • Along Columns—Expand the selection in all sequences to include the corresponding residues or gaps, i.e. expand the selection vertically up and down the columns. The expansion is done regardless of what is selected, residues or gaps. If no sequences are selected, the residue selection is expanded to cover all sequences.

  • From Reference Sequence—Expand the residue selection in the reference sequence along columns to all other sequences.

Invert Selection

Invert the selection of residues: select the unselected residues and deselect the selected residues.

Copy Selection to New Tab

Copy the selected residues and gaps as new sequences to a new tab. Selections from a given sequence are placed in the same sequence in the new tab. No gaps are added for unselected parts of a sequence. The new sequences do not have any associated structures.

This feature can be useful for copying CDR loops for sequence alignment, for example.

Save as Entry Property
In the dialog that appears, choose the option to write a New Property or select an Existing property to write the residue information for the selected chain(s). If multiple chains are selected in the residue block, all selected residues are saved with commas separating the chains. All chains (in the order of the alignment) in the selection associated with each property will have their selected residue saved as that entry property. When Existing property is selected there are two additional options, Replace value and Append new value, which replaces the existing value or adds to the value, respectively.
Search for Matches

Search for matches in all sequences for the selected residue pattern, and add the hits to the selection.

Copy

Copy the selected residue sequence into the paste buffer, so it can be pasted into other locations. The residues selected for copying must be from the same sequence and must be contiguous.

Delete

Delete the selected residues and gaps. Not available when the sequence has a linked structure.

Delete Gaps Only

Delete only the gaps from the selection.

Delete Selected Gaps

Delete the selection when it contains only gaps.

Replace with Gaps

Replace the selected residues with gaps.

Edit Sequence in Place

Edit the current sequence directly (rather than in a dialog box). This item does the same as the one on the Edit menu. See Edit Sequence In Place in the Menu Bar topic for more information.

Highlight Selection

Highlight the selected residues with a chosen color. This color overrides the current color scheme.

Remove Highlights

Clear highlighting of the selected residues.

Hide Columns

Hide the selected columns.

Anchor and Clear Anchoring

Set or clear an anchor on the selected residues. The menu item changes between the two when the action is performed. The anchor is applied to the whole column, ensuring that these residues remain aligned and contiguous. Thus, when an alignment is done, these residues are not permitted to move out of the columns, and gaps cannot be inserted between contiguous anchored columns. An anchor symbol is placed above each end of the selection, and the selection color is faded across all columns.

Alignment set shortcut menu

This menu is displayed when you right-click on an alignment set row in the left pane of the sequence viewer.

Select All in Set

Select all sequences in the alignment set, and deselect sequences that are not in the set.

Deselect All in Set

Deselect all sequences in the alignment set. This does not affect sequences not in the set.

Rename Set

Rename the alignment set. Opens a dialog box to specify the new name.

Dissolve Set

Remove the alignment set annotation from all the sequences in the set, so that they are no longer in a set, and delete the set.

Gather All Sets

Reorder the sequences so that each alignment set is a contiguous set of sequences. Each set is gathered under the topmost sequence in the set, in the current order in the sequence list. This may be necessary if you move sequences so that they are no longer grouped with their sets.

Annotations shortcut menu

This menu is displayed when you right-click on an annotation row in the left pane of the sequence viewer.

Clear Annotations

Clear the annotations of the type that you right-clicked on from all sequences.

Select Associated Residues

For the binding site annotation, select the residues in the binding site of the ligand whose annotation you right-clicked on.

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