Menu Bars

• File menu
  • New MSV Project
  • Open MSV Project
  • Import MSV Project
  • Save
  • Save As
  • Get PDB
  • Fetch Sequences
  • Import Sequences
  • Paste In New Sequence Text
  • Load from Maestro
  • Export Sequences
  • Save Image
  • Exit
• Edit menu
  • Undo
  • Redo
  • Edit Sequence In Place
  • Copy Selected Residues
  • Save as Entry Property
  • Delete
  • Move Sequence
  • Duplicate Sequences
  • Set as Reference Sequence
  • Rename Sequence
  • Sort Sequences by
  • Get PDB Structures
  • Get AlphaFold PDB Structures
  • Translate DNA / RNA Sequence
  • Replace Selection with Gaps
  • Renumber Residues
  • Edit Sequence as Plain Text
  • Settings and Defaults
• Select menu
  • Sequences by Feature
  • Residues/Columns with Structure
  • Pattern-Matching Residues
  • Identities
  • Aligned Residues
  • Binding Site Residues
  • Antibody CDRs
  • Expand Along Columns
  • Expand Reference Selection Only
  • Update Workspace Selection
  • Link Sequences to Entries
• View menu
  • Hide Selected Sequences
  • Show Workspace Sequences Only
  • Show All Sequences
  • Find Sequence in List
  • Expand
  • Collapse All
  • Show/Hide Colors
  • Show/Hide Annotations
  • Configure
  • Reset to Defaults
• Align menu
  • Align Sequences
  • Align Structures
  • View Dendrogram
  • Set Constraints
  • Clear Constraints
  • Reset Alignment Settings
  • Anchor Selection
  • Clear Anchoring
• Help menu

File menu

This menu provides tools for creating, opening, and saving Multiple Sequence Viewer/Editor projects; importing and exporting sequences; saving images, and closing the panel.

New MSV Project

Create a new Multiple Sequence Viewer/Editor (MSV) project. Opens a file selector, in which you can navigate to and select the project.

Open MSV Project

Open an existing Multiple Sequence Viewer/Editor (MSV) project. Opens a file selector, in which you can navigate to and select the project.

Import MSV Project

Import the contents of an existing Multiple Sequence Viewer/Editor (MSV) project into the current project. Opens a file selector, in which you can navigate to and select the project.

Save

Save the current MSV project. If the project has not yet been saved, a file selector opens, in which you can navigate to a location and name the project. If the project has been saved previously, the project is simply saved.

The current project is automatically saved after major changes such as sequence addition, edits, and alignments. If the MSV project has not previously been saved, it is saved within the current Maestro project. As Maestro scratch projects are deleted when you quit Maestro, you may need to save your MSV project to a location outside the Maestro project, or save the scratch project.

An MSV project consists of the contents of the View tabs, but does not include the Workspace tab.

Save As

Save the current MSV project with a new name. Opens a file selector, in which you can navigate to a location and name the project. After saving, the current project is the one with the new name.

Get PDB

Import sequences from the PDB, along with structures. Opens the Get PDB File Dialog Box to specify the sequences.

Fetch Sequences

Fetch sequences from the UniProt or Entrez (NCBI) databases. Opens the Fetch Sequences dialog box to specify the sequences.

Import Sequences

Import sequences into the project. Sequences can be imported from a range of file formats: FASTA, CLUSTAL, SWISSPROT, GCG, PIR, EMBL, as well as PDB, Maestro, and seqd (see .seqd, ResID, ResName for the format of this file type). Opens a file selector, in which you can choose the file type, navigate to and select the file.

Structural data (ATOM records), B-factors, and secondary structure assignments are also imported if the data are in the PDB file. A nonstandard version of FASTA format is accepted, in which a residue can be preceded by its residue number; numbering is otherwise sequential, starting from 1.

Paste In New Sequence Text

Insert entire sequences into the sequence viewer either as letter codes for the residues or in FASTA format. Opens the Paste In New Sequence Text dialog box, in which you can choose whether to enter text or a FASTA alignment, paste the sequences and edit them as text, and name the sequence. Lines beginning with a > character are treated as a sequence header. These lines also separate one sequence from the next. Multiple sequences thus delineated are saved as separate sequences.

This feature is useful for copying an alignment from a web site and adding it directly to the MSV without having to save a file. You can also add sequences by importing a file (see above).

Load from Maestro

Load sequences from the Maestro project. The submenu allows you load sequences from the Workspace or from the selected entries.

Export Sequences

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.

Save Image

Save an image of the sequence viewer. Available formats are PNG and PDF. Opens a file selector, in which you can navigate to a location and name the file. The Include menu allows you to choose what to export, from Entire alignment region (default), Visible alignment region (what you can see in the sequence display area of the panel), or Sequence Logo only. You can also set the image resolution, in DPI, from a choice of values.

Exit

Close the panel. The current Multiple Sequence Viewer/Editor (MSV) project is also closed.

Edit menu

From this menu you can choose to undo or redo actions, edit sequences, and delete sequences. Many of these items are also on the Sequence shortcut menu.

Undo

Undo the last editing operation. The operation is appended to the menu item text, for example Undo - Change Residue Selection.

Redo

Redo the last undone editing operation. The operation is appended to the menu item text, for example Redo - Change Residue Selection.

Edit Sequence In Place

Edit the selected sequence in place (instead of in a dialog box). The Edit toggle is selected, and the Sequence editing tools are displayed in the toolbar in place of the homology modeling tools. A cursor is displayed in each sequence at the current insertion point, which is to the left of the current residue selection.

Changes can only be made to residues without associated structure. All the editing capabilities are available for unlinked sequences. For linked sequences you can add residues in the View tabs, but there is no structure associated with these residues. You can always add or delete gaps in any sequence, regardless of whether it is linked or not.

You can insert, replace, or delete residues or gaps by character code. When you click a toolbutton to perform an action that requires residue input (insertions or replacements), a small text area is displayed below the selected residues. Only the 20 standard amino acid codes, X (unknown residue), and - and ~ (gap symbols) are recognized. To add gaps at the insertion point, you can use the Spacebar.

You can slide the selection to the left or the right. Sliding to the left can only be done if there are gaps to the left of the selection, and only slides the selection as far as the next residue. Sliding to the right fills any gaps immediately to the right of the selection, and then slides all residues and gaps to the right of the selection as well as sliding the selection.

The selection can be extended by using Shift+Arrow. The arrow key shifts the current residue to the next position in the arrow direction, and when an unselected residue or gap is encountered, it adds the residue or gap to the selection. You can also move the selection with the arrow keys, if it is a single residue; if it is multiple residues, the current residue becomes the selection (deselecting any other residues), and the selection moves with the arrow keys.

To finish editing, click the X button in the editing tool set, or click the Edit toggle.

Copy Selected Residues

Copy the selected residues. These can be pasted wherever needed, e.g. when editing a sequence.

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.

Delete

Delete the objects chosen from the submenu.

• Selected Residues—Delete the selected residues.
• Selected Gaps—Delete the selected gaps.
• All Gap-Only Columns—Delete gaps from all sequences in columns that only have gaps.
• Selected Sequences—Delete the selected sequences.
• Redundant Sequences—Delete sequences that are duplicates of another sequence. The first of the identical sequences is kept.
• All Predictions—Delete the results of all predictions made with ... .
• This Tab—Delete the current View tab. This removes all the sequences in the tab from the MSV project, and any related data.
• All View Tabs—Delete all View tabs. The MSV project remains open, and any project-level data is kept, but all sequences and their data are removed from the project.

Move Sequence

Move the selected sequence according to the choice from the submenu.

• To Top—Move the sequence to the top of the list of non-reference sequences, immediately below the reference sequence.
• Up—Move the sequence up one row.
• Down—Move the sequence down one row.
• To Bottom—Move the sequence to the end of the sequence list.
• Set as Reference—Make the sequence the reference sequence.

Duplicate Sequence

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.

Set as Reference Sequence

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 Sequence

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.

Sort Sequences by

Sort sequences to place them in a chosen order.

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).

Reverse Last Sort

Reverse the order of the sequences as placed by the last sort.

Get PDB Structures

Download structural information (secondary structures, B-factors, coordinates) for sequences that came from the PDB, such as in a BLAST search. The information is obtained from a local copy of the PDB or from the RCSB website. If sequences are selected, information is obtained for these sequences, otherwise it is obtained for all sequences. The sequences are replaced by the sequences from the PDB.

Get AlphaFold PDB Structures

Download structural information (secondary structures, B-factors, coordinates) for sequences that came from the AlphaFold PDB, such as in a BLAST search. The information is obtained from a local copy of the AlphaFold PDB or from the AlphaFold PDB website. If sequences are selected, information is obtained for these sequences, otherwise it is obtained for all sequences. The sequences are replaced by the sequences from the AlphaFold PDB.

Translate DNA / RNA Sequence

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.

Replace Selection with Gaps

Replace the selected residues with gaps.

Renumber Residues

Renumber the residues in one or more sequences. Opens the standard increments, template-based, antibody CDRs, where you can either renumber the selected sequences so that residues at the same position in the sequence viewer have the same residue number; or import and align a template for a single sequence, and apply the numbering of the template to the selected sequence.

Edit Sequence as Plain Text

Edit the selected sequence as plain text. Opens a dialog box in which you can specify a display title and perform the editing.

Settings and Defaults

Specify settings by choosing from the submenu.

Reset Remote Server Confirmations

If you checked the "do not ask again" box when prompted to confirm access to a remote server, change this setting so that you receive prompts again.

Autosave

Specify how often the MSV project should be saved automatically: Regularly and After Edits, Only After Edits, or Never.

• Regularly and After Edits: automatically saves the MSV project every few minutes and when changes such as sequence addition, edits, and alignments are made.
• Only After Edits (default): automatically saves the MSV project when changes such as sequence addition, edits, and alignments are made.
• Never: the MSV project will not be saved automatically. The MSV project is saved only if and when File → Save or File → Save As is chosen.

Use Light Theme

Use a light-colored background for the sequence display area.

Select menu

This menu allows you to select sequences and residues, according to various criteria. Many of the items are self-explanatory; those that may need some explanation are listed below.

You can drag to select multiple residues, both within a row and across rows, except in Edit mode, where dragging slides the selection. You can use Shift with arrow keys to expand the selection in the direction of the arrow. You can click on the Alignment set annotation for a sequence to select (or deselect) all the sequences in the set.

Sequences by Feature

Select sequences that have specific features. The submenu offers these features:

• With Structure—the sequence has a corresponding 3D structure
• By Identity—select sequences that have matching residues with the reference sequence according to a specified matching criteria. Opens the reference sequence.
• Antibody Heavy Chain—the sequence has the heavy chain for an antibody
• Antibody Light Chain—the sequence has the light chain for an antibody

Residues/Columns with Structure

Select sequences or residues that have a corresponding 3D structure.

Pattern-Matching Residues

Select residues that match a pattern of residues. The submenu has four standard patterns, corresponding to sites in the protein. You can also define and modify your own patterns, by choosing Manage Saved Patterns, which opens the pattern, pattern-matching, pattern matching, PROSITE, pattern table. The submenu is updated when patterns are added or removed in this dialog box.

Identities

Select columns in which the residue is the same for all sequences.

Aligned Residues

Select residues in any sequence that match residues in the reference sequence, i.e. the same residue in the same column (identities). This is not the same as selecting identities (see above), where all sequences must have the same residue in the same column.

Binding Site Residues

Select residues that are in contact with any ligand, i.e. residues with any heavy atom within 5 Å of a ligand heavy atom (by default). The distance can be changed in the Annotations panel (button above Annotations toggle or View → Configure → Annotations) by selecting Binding Site then choosing the distance from the menu that is displayed.

Antibody CDRs

If the sequence is an antibody, select the residues in the variable loops (CDRs). The numbering scheme used to determine the CDRs is the Chothia scheme by default. You can change the scheme in the Annotations panel (button above Annotations toggle or View → Configure → Annotations) by selecting Antibody CDRs then choosing the scheme from the menu that is displayed.

Expand Along Columns

Expand the selection to include the corresponding residues in all sequences, i.e. expand the selection up and down the columns.

Expand Reference Selection Only

Expand the residue selection in the reference sequence to include the corresponding residues in all other sequences, i.e. expand down the columns from the reference. Selected residues in other sequences remain selected.

Update Workspace Selection

Update the atom selection in the Maestro Workspace from the residue selection in the linked sequences. This item is available when the Workspace selection doesn’t correspond to the selection in the linked sequences.

Link Sequences to Entries

Link sequences to the corresponding chains in Maestro entries, or unlink linked sequences. Linking allows you to merge edits in Maestro into the MSV, and perform operations on the sequence that are reflected in the Workspace. For example, middle-clicking a residue zooms the Workspace structure to that residue. Sequence editing is disabled for linked sequences.

Choosing this item opens the unlinked, in which you can choose an entry chain from the Workspace (table on the left) and an MSV sequence (table on the right), and click Set Link to link the sequence to the entry. The sequence identity for the selected pair is shown below the tables. The residues that do not match the entry sequence are marked as structureless in the MSV by using a less intense color. This facility is useful if the sequences are imported into the MSV and the structures are independently imported into Maestro. (The linking is done without adding new sequences, modifying the alignment, or importing structures into the MSV.)

Sequences are automatically linked when copied from the Workspace tab, imported from the Maestro project, downloaded with a structure, updated with a PDB structure. Deleting a linked entry unlinks the sequence.

View menu

This menu allows you to show or hide various objects and features.

Hide Selected Sequences

Hide the selected sequences, so that they are no longer shown in the display area.

Show Workspace Sequences Only

Show only the sequences for the structures in the Workspace, and hide all others.

Show All Sequences

Display all sequences. Use this when you have hidden sequences to show them again.

Find Sequence in List

Find a sequence in the list of sequences, by sequence name. The Load from tool on the toolbar is replaced with a search field. As you type, the list of sequences is temporarily trimmed to those that match, with red lines at the left marking where the hidden sequences are.

Expand

Expand sequences so that the associated data, such as secondary structure assignment, is displayed. You can choose which group of sequences to expand from the submenu: Selected, Unselected, Displayed (if sequences are hidden), All (if all sequences are displayed).

Collapse All

Hide the associated data for all sequences. You can choose which group of sequences to expand from the submenu: Selected, Unselected, Displayed (if sequences are hidden), All (if all sequences are displayed).

Show/Hide Colors

Show or hide the sequence coloring. Synchronized with the Color toggle.

Show/Hide Annotations

Show or hide annotations of the sequences. Synchronized with the Annotations toggle.

Configure

Configure various aspects of the display. The items on the submenu are:

• Annotations—choose the kinds of annotations of sequences or alignments to display. Same as clicking the ... button above the Annotations toggle.
• Color—choose the color schemes for sequences and highlighting schemes for residues. Same as clicking the ... button above the Color toggle.
• View—set options for alignment and sequence display. Same as clicking the View Options toggle.

Reset to Defaults

Reset all view settings to their default values.

Align menu

This menu provides tools for alignment of sequences with or without constraints, and alignment of structures. The Align Pane contains more features for alignment.

Auto-Align New Sequences

Align new sequences to existing sequences in the tab. A multiple alignment is performed if the tab that contains just a single sequence (treated as the reference); otherwise, it does a pairwise alignment with locked gaps for each added sequence, to minimize changes to the reference sequence. Gaps are inserted into the existing alignment to preserve the residue matching.

This option may be useful when importing the results of a BLAST search for a reference sequence.

Align Sequences

Align new sequences with a query sequence without changing the existing alignment. Gaps are inserted into the existing alignment to preserve the residue matching.

Multiple Alignment

Align the selected sequences simultaneously using ClustalW or MUSCLE. If there are columns (residues) selected, the alignment is performed only on the selected residues. You can run an alignment on several discontinuous selected regions at the same time.

Pairwise Alignment

Align the selected sequences pairwise using a Smith-Waterman algorithm.

Pairwise with Secondary Structure Prediction

Align the selected sequences pairwise taking into account secondary structure matching as well as profile-sequence matching. See sta—Single Template Alignment for more information.

Profile Alignment

Align the selected sequences when the selection involves an alignment set that contains the reference sequence and another sequence or another alignment set. Alignment sets are sets of sequences in which the alignment between the sequences is preserved. This means that aligning one member of the set aligns them all.

Profile alignment cannot be performed with combined chains. Select Split chains in the View Options Pane to enable the alignment.

Align Based on Structure Superposition

Align sequences according to the geometric proximity of their residues. The structures for the sequences must be already superimposed. The alignment is done by calculating the matrix of Cα–Cα distances for each sequence pair, then using these matrices for scoring to determine the alignment.

Align Structures

Align (superimpose) structures with various methods. A results dialog box shows some statistics for the alignment and allows you to add the RMSD of the atoms to the aligned structures as an entry property.

Protein Structure Alignment

Run the Prime Protein Structure Alignment program on the selected (or all) protein structures and return the alignments. The sequences you select must have structures associated with them. See Protein Structure Alignment Panel and Multiple Template Alignment: structalign for more information.

Align Binding Sites

Run the Prime Align Binding Sites program to align the binding sites of the selected (or all) proteins and return the alignments. The sequences you select must have structures with ligands associated with them. See Align Binding Sites Panel andStructure Alignment: align_binding_sites for more information.

Align Based on Sequence Alignment

Superimpose structures based on their sequence alignment. Uses the Superposition Panel, with sequence identities selected as the atoms for superposition. If the reference sequence does not have a structure, the first sequence in the set for alignment that has a structure is used as the reference for the superposition.

View Dendrogram

View a sequence alignment dendrogram. Opens the tree, similarity matrix, relationship matrix.

Set Constraints

Apply constraints on pairwise alignments, so that the constrained residues are in the same position (same column) after the alignment.

When you select this option, a constraint row is displayed between the reference sequence and the other sequences, and the constraints banner is displayed in the toolbar, with instructions. To add a constraint, click on a residue in the reference sequence and then on a position in one of the other sequences. The constraints are displayed as blue lines connecting the constrained residue pair. To remove a constraint, click on the constrained residue pair again.

This option is currently only available for a single pairwise alignment. If the tab contains multiple non-reference sequences, you must select the desired sequence, and set Selected only in the Align pane. The sequence is moved to the top and the Constraints annotation row is added below the reference sequence.

To remove all constraints, choose Align → Clear Constraints.

Clear Constraints

Remove all constraints on the alignment.

Reset Alignment Settings

Reset the alignment settings to their default values. The settings are made with the Align tool.

Anchor Selection

Set an anchor on the selected residues. 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.

Clear Anchoring

Remove the anchoring on the residues, so that they are permitted to move.

Help menu

This menu provides access to the help topics for the main panel and a few of the major panes or panels. It also provides access to the Getting Started Guide and the Tutorials that introduce features of the Multiple Sequence Viewer/Editor panel.