Multiple Sequence Viewer/Editor — Toolbar

The toolbar for the Multiple Sequence Viewer/Editor Panel is described in this topic.

See Multiple Sequence Viewer/Editor Panel for an overview of the panel.

  • Features
  • Additional Resources

Toolbar Features

Load from option menu and button

Load sequences from the chosen source. The Workspace and Selected Entries choices load the structure as well as the sequence. Click the arrow button next to the menu to perform the load.

When you choose File, the button turns blue, to indicate that it should be clicked to open a file selector, in which you can navigate to a location and select one or more files. The button turns gray again when the import is done.

This feature is only present in View tabs. In the Workspace tab, it is replaced with a label.

Find / Fetch tool

Find patterns of residues in the current tab, or fetch sequences from an external source.

When finding residue patterns, the matches are selected in the residue region.

Search text box

Enter the subsequence or residue pattern to find or the list of sequences to fetch, comma-separated. Search for subsequences, PROSITE patterns, UniProt, AlphaFold PDB, Entrez, or PDB structures. Details on the extended PROSITE pattern syntax is shown below, and is also available via the Manage Saved Patterns dialog.

residue Find occurrences of the specified residue. The residue must be given as an upper case letter. For example, A finds alanine.
[list] Find occurrences of any of the residues listed. For example [AIL] finds occurrences of A, I, or L
{list} Exclude all occurrences of any of the residues listed. For example {ED} ensures that occurrences of E and D are not found.
a  Find acidic residues (D and E)
b  Find basic residues (K and R)
e  Find residues in an extended (beta-strand) region
f  Find residues in a flexible region (B-factor greater than the chain average)
h  Find residues in a helical region
o  Find hydrophobic residues (A, C, F, I, L, P, V, W, and Y)
p  Find aromatic residues (F, W, and Y)
s  Find solvent-exposed residues
x . ?  Find any residue. Any of these three characters can be used.
@number  Find the residues with the specified PDB residue number (not ruler position). Insertion codes are not recognized, so all residues with a given insertion code are found.
(m)

(m,n) 		 Find the specified number of contiguous occurrences of a residue (or residue type). The second form specifies a variable number of occurrences, e.g. o(2-4) means find two to four consecutive hydrophobic residues.

To run a simple search for a sequence of residues, just type in the sequence.

For a more complex search, in which you apply conditions at each residue position, you can combine these elements to create a search pattern, such as G-[IL]-o{AC}. There is an implied AND between contiguous elements: so in the example given, o{AC} means a hydrophobic residue that is not Ala or Cys. Each such sequence of elements that applies to a single residue must be separated from the next sequence by a - character. The search takes place when you press Enter. The patterns that are found are selected, and all other residues are deselected.

As well as typing in patterns, you can store and retrieve your own patterns from the Saved Patterns icon menu. The patterns are listed at the top of this option menu, with four default items, Deamidation Site, Glycosylation Site, Proteolysis Site, and Oxidation Site. The last item is Manage Saved Patterns, which opens the pattern, pattern-matching, pattern matching, PROSITE, pattern table, in which you can change patterns, including these default patterns, and add and delete patterns.

Saved Patterns icon menu

Select a PROSITE pattern from this menu for the search, or manage PROSITE patterns (see pattern, pattern-matching, pattern matching, PROSITE, pattern table). The menu is updated when patterns are added or removed in this dialog box.

This button is shown when you choose PROSITE pattern from the Settings button menu .

Search icon/Download icon

Click this icon to initiate the search or the fetch. You can also press Enter to initiate the search or fetch. The icon changes according to the contents of the search text box.

Previous/Next Pattern arrows

When searching for a sequence, these arrows step through the instances of the sequence pattern that were found in the sequences.

Settings button menu

Find a pattern within the sequence. The Settings button menu exposes the Saved Patterns icon menu to access & modify saved PROSITE patterns, and for creating and managing your own patterns. For finding patterns, you can choose:

  • Sequence Substring—use a sequence of single-letter residue names (upper case) as the search pattern
  • PROSITE pattern— use a pattern in PROSITE syntax. With this choice, a button menu is placed next to the search box, which you can click to choose a PROSITE pattern, or create a pattern to save. These patterns are the same as used to select residues (Select menu).

For fetching sequences, you can choose

  • PDB Structures— fetch sequences and structures from the PDB. You can append the chain name to the PDB ID to fetch a single chain. Structures are added to the Workspace and linked to the sequence.

  • UniProt or Entrez Sequences— fetch sequences from the UniProt or Entrez database by entering the sequence code. You can also use the UniProt name.

    To fetch sequences from Entrez, type the access code into the text box and press ENTER. The access code format is database|code, where database is the code for the database (gi for GeneBank, pdb for the Protein Data Bank, emb for the EMBL Sequence Database, and so on), and code is the sequence code for the database. Examples: gi|12345, pdb|2aba, emb|CAA44029.1. The sequence is retrieved from the NCBI web site and added to the project.

Multiple IDs or codes must be in a comma-separated list.

Homologs button

Find homologs for the reference sequence, using BLAST. Opens the Search for Homologs dialog box, where you can make settings for the BLAST search, choose the full PDB database or the nonredundant (NR) database, and select an option to allow multiple chains from the same structure. When the search is done, the BLAST, algorithm, opens, so you can select the homologs to import. The homolog sequences are added to the sequence list and the structures are imported into Maestro and linked. For more information on working with BLAST and the PDB, see BLAST, basic local alignment search tool, protein data bank, PDB, local, environment variables, PSP_BLASTDB, SCHRODINGER_PDB.

You might want to select Align → Auto-Align New Sequences before you find the homologs, to perform an alignment of the homologs to the reference when they are imported.

Align button

Align sequences or structures. The sequence alignment, force alignment, superposition, superimpose, constraints is displayed below the button with tools for doing the alignment.

Other Tasks button

Select a task to perform. Opens a pane in which the tasks are listed in various categories.

Structure and Property Predictions

Run All Predictions

Run all the predictions listed below.

Secondary Structure

Run the secondary structure programs to obtain a prediction of the secondary structure of the selected sequences, or for all sequences if no sequence is selected.

Solvent Accessibility

Predict accessibility of each residue to solvent. If more than 25% of total residue surface area is predicted to be exposed to the solvent, the residue is colored blue, otherwise it is colored yellow.

Domain Arrangement

Predict the arrangement of domains. Residues marked gray are likely to form a domain. Residues marked red are likely to be in linker (inter-domain) regions.

Disordered Regions

Calculate a disorder score and classify residues by this score The score is normalized to a 0 to 1 range. If a residue has a disorder score less than 0.5, it is marked light gray. If the score is between 0.5 and 0.9, the residue is marked orange. If the score is greater than 0.9, the residue is marked red.

Disulfide Bonds

Predict disulfide bonds between cysteines. Predicted bonds are drawn as lines connecting cysteine residues, colored from black (strongest prediction) to light gray (weakest prediction).

Family Features Calculations

Align by Family (Beta)

Opens the Align by Family Dialog Box, where you can select the family to use for aligning the sequences. The highlights made can be toggled on and off from the annotations, calculated attributes, family features, predictions, sequence annotation.

Identify Family Features.

Opens the Identify Family Features Dialog Box, where you can select and compute family features for the specified sequences.

Homology Modeling and Analysis

Find Homologs (BLAST)

Find homologs for the reference sequence, using BLAST. Opens the Search for Homologs dialog box, where you can make settings for the BLAST search, choose the full PDB database or the nonredundant (NR) database, and select an option to allow multiple chains from the same structure. When the search is done, the BLAST, algorithm, opens, so you can select the homologs to import. The homolog sequences are added to the sequence list and the structures are imported into Maestro and linked.

You might want to select Align → Auto-Align New Sequences before you find the homologs, to perform an alignment of the homologs to the reference when they are imported.

Homologs Search Results

Show the output of the latest BLAST search for each tab, in the Homolog Search Results dialog box. The dialog box allows you to select homologs, sort results by some properties, download PDB structures for the homologs, and incorporate selected homologs into the project. See BLAST, algorithm, for more information.

Build Homology Model

Open a panel that takes you through the steps for building a homology model. The panel has links to other tools that may need to be used to complete a step.

Analyze Binding Sites

Open the ligand, conservation, distance, export, to perform an analysis of binding sites and display statistics of the binding site.

Compare Sequences

Compare all sequences or the selected sequences, by identity, similarity, or conservation. The percentage is displayed in a table, like a heat map, with cells color-coded by the percentage value. Opens the save grid, compare, in which you can choose the comparison measure to display, switch between all or selected sequences, and refresh the display after changing the alignment.

Property Calculations

Compute Sequence Descriptors

Compute descriptors for the sequences, selected from a wide range of properties. Opens the protein sequence descriptors,, where you can select the descriptors you want to compute.

Aggregate Residue Properties

Aggregate a residue property over all residues in each of a specified set of sequences, and add the results to the sequences as a descriptor. Opens the display results.

Sequence editing tools

Edit the current sequence in place. These tools are displayed when you choose Edit → Edit Sequence In Place or click the Edit toggle, and they replace the Homologs and Align buttons in the toolbar. For more information, see Edit Sequence In Place.

Insert a gap at the cursor position in the sequence. Each click adds a single gap residue. You can also use the Spacebar to insert a gap at the cursor position.
Delete the selected gaps. You can also use the Delete key.
Insert residues at the cursor position. A text box opens below the position so you can type or paste in the one-letter residue codes. Press Esc to cancel, Enter to accept changes.
Delete the selected residues. You can also use the Delete key.
Change the selected residue to a different residue. A text box opens over the residue so you can enter a new one-letter residue code. Press Esc to cancel, Enter to accept changes. You can also press Enter to open the text box.
Replace the selected residues with a new set. A text box opens below the selection so you can type or paste in the one-letter residue codes for the new residues. Press Esc to cancel, Enter to accept changes. You can also press Enter to open the text box.
Exit Edit mode.
Find sequence in list tool

Find a sequence in the list of sequences in the tab by matching the title. This tool is displayed by choosing View → Find Sequence in List, and replaces the Load from option menu when it is activated.

Set constraints banner

This banner covers the Find / Fetch tool when constraints are being set (Align → Set Constraints).

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