Multalign Viewer

Multalign Viewer allows viewing and manipulation of sequence alignments. If any corresponding structures are open in Chimera, highlighting regions in the sequence alignment will highlight portions of the structures and vice versa. In addition, structures can be superimposed based on the sequence alignment. The state of Multalign Viewer (along with sequence alignment data) is included in saved sessions. For an informal introduction, see the Sequences and Structures tutorial.

There are several ways to start Multalign Viewer, a tool in the Structure Comparison category. Explicitly starting Multalign Viewer brings up a dialog for opening files. File formats that can be read and written are:

One of these types can be chosen from the File type: pulldown menu near the bottom of the dialog, or the type can be inferred from the suffix(es) of the chosen file(s). Once a file has been read, a sequence window containing the alignment appears; if multiple files are read, each is shown in a separate sequence window.

Multalign Viewer menu items are explained within the following sections, and a full listing with short descriptions is included at the end of this page.

Multalign Viewer sequence window

The figure shows part of the sequence window contents for the input file apoex.fa. Font size and sequence wrapping behavior can be controlled with the Layout preferences. Alignment regions (colored boxes enclosing one or more residues) are described below. The coloring of residue one-letter codes can be controlled with the Analysis preferences. One can search for occurrences of a particular string or pattern of residues in one or all of the sequences using Tools... Find Subsequence or Tools... Find PROSITE Pattern in the Multalign Viewer menu.

When the cursor is in the sequence window, the Page Down key (or space) moves the view down to start with the block below the topmost block whose beginning is currently visible; Page Up (or Shift-space) moves the view up to start with the block above the topmost block whose beginning is currently visible.

The Hide button closes the sequence window without changing the state of Multalign Viewer. The sequence window can be reinvoked using the Raise option for the Multalign Viewer instance in the Tools menu (abbreviated MAV). This is also useful when the window has become obscured by other windows. Help opens this manual page in a browser window, and Quit exits from Multalign Viewer.

By default, header lines named Consensus and Conservation are shown above the alignment in the sequence window. The consensus sequence shows the residue type most prevalent (not necessarily >50%) at each position in the alignment; highly conserved residues (80% or greater) are capitalized and shown in purple, except that the completely conserved residues are shown in red. The Analysis preferences control how consensus and conservation are determined and represented.

Arbitrary, user-defined header lines may also be shown. New header line contents can be loaded from an external header definition file (Headers... Load in the Multalign Viewer menu), while existing header line contents can be saved to the same type of file (Headers... Save in the Multalign Viewer menu). Loading values for a header with the same name as an existing header will create an additional header line, not replace the values in the existing header line.

GC (Generic per-Column) annotations in alignments in Stockholm format are also treated as headers.

The display of headers in the sequence window can be turned on and off with their respective checkboxes in the Multalign Viewer Headers menu. Clicking in a header line selects any structure residues associated with that column of the alignment.

Values of headers are available as residue attributes named mavHeader_name in any associated structures. Numerical attributes will appear in the attribute lists of Render/Select by Attribute; character attributes will be listed only in the Select by Attribute portion. It may be necessary to Refresh the attribute menus or histogram/list in these tools to update them with any changes in Multalign Viewer header information.

Alignment regions can be defined manually or by any of several operations within Multalign Viewer. A region is shown using a colored rectangle or outline in the sequence window; a single region can contain any number of disjoint and/or abutting rectangular blocks.

A region can be created manually by dragging with the left mouse button within the sequence window. Dragging downward into the following block highlights to the end of the preceding block. The initial region colors can be controlled in the Regions preferences. Shift-dragging with the left mouse button adds to the active region. Ctrl-dragging creates a new region and makes it the active region.

The active region is the region most recently created manually, clicked on in the sequence window, or designated as Active in the Region Browser. The corresponding parts of any associated structures are highlighted in the main Chimera window by becoming selected. Only one region can be active at a time. In the sequence window, the active region is indicated with a dashed outline; clicking the active region deactivates it, and clicking a different region deactivates the former active region and makes the new region active. A region with no interior color is only responsive to clicks on its borders. Where regions overlap, only the highest is responsive to clicks.

The Region Browser (Tools... Region Browser in the Multalign Viewer menu) can be used to manage the existing regions. Checkboxes reflect and control which region is Active (if any) and which are Shown in the sequence window. Clicking an entry in the Region Browser highlights the line and chooses the region. More than one region can be chosen at a time. The chosen region(s) are not necessarily active.

The Border color and Interior color of the chosen region(s) can be changed using the adjacent color wells.

The Delete button on the Region Browser deletes the chosen region(s). The region named Chimera selection cannot be deleted, but it can include zero residues. Since regions may overlap, a region can be considered higher or lower than another. Raise puts the chosen region(s) in front of any other regions in the sequence window and moves the corresponding entries in the Region Browser to the top. Lower puts the chosen region(s) behind any overlapping regions in the sequence window and moves the corresponding entries in the Region Browser to to the bottom. Copy copies the chosen region(s) and requests a new name for each copy, while Rename requests a new name for each chosen region.

Close dismisses the Region Browser and Help opens this manual page in a browser window.

Alternatively, when the cursor focus is in the sequence window, the up arrow and down arrow keys can be used to raise and lower the active region, respectively; pressing the Delete key will delete the active region.

Besides manual creation, there are several ways to generate or change the contents of regions:

• by searching for occurrences of a particular string or pattern of residues
• by reading a sequence coloring format (SCF) file or seqsel file (Tools... Load SCF/Seqsel File) generated by the program JEvTrace. The two formats are slightly different, but both contain information for coloring regions in the sequence and in any associated structures. The file reader automatically determines which format is being used. The formats are simple enough that users wishing to color residues alike in sequence and structure (for any reason) may wish to create a file manually and read it in by this route.
• as a by-product of sequence-structure association
• by selection within sequence-associated structures
• by secondary structure (actual in structure-associated sequences, predicted in sequences not associated with structures)

The active region can be moved using Ctrl-left arrow and Ctrl-right arrow. Residues cannot be added or removed, but gaps can be created, extended, reduced, or removed. To accommodate the shift, sequence flanking the active region will be pushed after intervening gaps are closed. The alignment generally cannot be restored by reversing the shift because the positions of gaps are forgotten as the gaps are closed.

Choosing File... Save As from the Multalign Viewer menu brings up a dialog for saving the sequence alignment to a file. It is possible to save just the active region to a file; the region may consist of disjoint sections, but each sequence (row) included must contain the same set of columns. The option to omit all-gap columns from the output is especially useful for saving regions with fewer sequences than the starting alignment. The formats available for saving are the same as those that can be read. An alignment saved in Stockholm format will automatically include annotations describing the secondary structure of any associated structures.

The sequence window contents can also be saved as an EPS file (File... Save EPS in the Multalign Viewer menu).

The percent identity between any pair of sequences in the alignment can be calculated. Tools... Percent Identity in the Multalign Viewer menu opens a dialog for specifying the sequences (by name from the pulldown menus labeled Compare and with) and what to divide by:

• shorter sequence length (default)
• longer sequence length
• non-gap columns in common

Apply calculates the percent identity without dismissing the dialog, while OK calculates the percent identity and dismisses the dialog. The percent identity is reported in the status area near the bottom of the sequence window and the Chimera Reply Log. Close simply dismisses the dialog, and Help opens this manual page in a browser window.

Sequence alignment files may contain various annotations.

Alignment annotations (those describing the alignment as a whole) can be viewed and altered by choosing Tools... Alignment Annotations from the Multalign Viewer menu. The dialog shows any annotations from the input file, each of which can be changed by typing in the adjacent field. Changes are not assessed for correctness.

Each annotation in the top section of the panel has two parts, a name and a value (generally text). For example, MSF length is a name and 366 is a possible associated value. A new annotation can be added by clicking New and specifying a name. The name will appear in the top section of the panel, and a value can be entered by typing in the adjacent field. Values can have multiple lines even though only one is shown; hitting return when typing into a value field retains the previous information and starts a new line. Clicking Delete and then choosing an annotation name removes the corresponding annotation. Multiple lines of free-form text can be placed in the Comments area in the lower section of the panel.

Not all formats can accommodate annotations. Thus, saved files may not include this information or reflect any changes that have been made. Only the Stockholm format accommodates arbitrary annotations, whereas both Stockholm and RSF formats can include comments. When an alignment in Stockholm format is read into Multalign Viewer, any GF (Generic per-File) markups are interpreted as alignment annotations and GC (Generic per-Column) markups are treated as headers: they can be shown above the alignment and are available as residue attributes in any associated structures.

When an alignment is saved in Stockholm format, the saved file will automatically include GR (Generic per-sequence and per-column) markup lines describing the secondary structure of any associated structures. The GR markup line for a sequence and its associated structure starts with

#=GR seq-name Chimera_actual_SS_struct-name

If a sequence did not have a GR SS markup in the original input file and is associated with only one structure, another markup line with the same contents but named SS instead of Chimera_actual_SS_struct-name will also be included. GR markups are not displayed by Multalign Viewer.

A sequence in the alignment will be associated automatically with a structure chain if their sequences can be aligned without too many mismatches. The allowable number of mismatches is user-specified as a proportion of the total number of residues in the structure chain (1/10 by default; see the Structure preferences). For automatic association, gaps in the structure sequence relative to the sequence in the alignment file can only occur where residues are missing from the structure (for example, a flexible loop with insufficient density for coordinates to be determined). The order in which the sequence and structure files are opened does not matter. Associations are reported in the status area near the bottom of the sequence window and the Chimera Reply Log. A structure (even if it has multiple chains) cannot be associated with more than one sequence, but a single sequence can be associated with more than one structure. If more than one sequence matches a given structure chain, the single best-matching sequence is associated.

The names of structure-associated sequences are shown in bold over a box indicating the model-level color of the structure. For example, APE_HUMAN in the sequence window figure is associated with a structure whose model-level color is white. If multiple models are associated with the same sequence, the box is shown as a dark green dashed outline. When the cursor is placed over the name of a sequence, information on the sequence and any associated structure(s) is shown in the status area near the bottom of the sequence window. When the cursor is placed over a sequence residue that is associated with a residue in one or more structures, information on the structure residue(s) is given. Association information can be saved to a file.

Sequence-structure association may create new regions. If all residues of a sequence are matched, no region is created. Otherwise, by default

• the matched part(s) of a sequence become(s) a region named matches of... with a black border and no interior color
• any gap(s) in the structure relative to the sequence become(s) a region named gaps... with a red border and no interior color
• any mismatch(es) become(s) a region named mismatches... with a red interior and no border

Association enables several types of sequence-structure crosstalk:

• Clicking/dragging on sequence → structure selection. Clicking within a header line in the sequence window will select any structure residues associated with that column of the alignment. Structure residues associated with the active region (that most recently clicked on or created by dragging within the sequence window) are selected.
• Structure selection → sequence region. By default, making a selection within one or more structures creates a region named Chimera selection in any associated sequences. Each residue with at least one atom or bond selected will be included in the region. Whether selection creates a region and the colors of the resulting region can be controlled in the Regions preferences. The region is not created when the structure selection merely reflects the current active region.
• Focusing the view. Clicking with the right mouse button on a structure-associated residue in the sequence window will focus the view in the graphics window on the corresponding structure residue (or residues, since there could be more than one structure associated with the sequence). Shift-right-clicking within a region (or right-clicking within the region but not on a residue) will focus the view on all of the structure residues associated with the region, if any.

Apply performs the indicated association(s) without dismissing the panel. OK performs the indicated association(s) and dismisses the panel, Close dismisses the panel without changing the associations, and Help opens this manual page in a browser window.

Automatic Structure Loading

Structure... Load Structures in the Multalign Viewer menu can be used to open structure files corresponding to sequences that are not already structure-associated. The corresponding structure files are determined from the sequence names using the rules given in the Structure preferences, then retrieved and opened (as described for Fetch by ID). If Automatically load Structures is turned on (also in the Structure preferences), this will occur as soon as an alignment is read.

Regions Defined by Secondary Structure

Regions can be defined within structure-associated sequences based on helices and sheets in the corresponding structures. Structure... Secondary Structure... show actual in the Multalign Viewer menu creates regions named structure helices and structure strands colored goldenrod and lime green (see the named colors), respectively. Helices and strands are defined by HELIX and SHEET records in the input file, or if these are not present, using ksdssp. (Regardless of whether the regions exist, however, an alignment saved in Stockholm format will automatically include annotations describing the secondary structure of any associated structures.)

In sequences not associated with any structures, Structure... Secondary Structure... show predicted in the Multalign Viewer menu creates regions named predicted helices and predicted strands colored gold and light green (see the named colors) that correspond to helices and strands, respectively, predicted using GOR.

Structure residues associated with residues in a sequence alignment shown by Multalign Viewer are assigned attributes:

• mavPercentConserved - the value for a residue is the percent conservation of the most prevalent residue type at the corresponding position in the alignment.
• mavHeader, where Header is the name of any header line - the value for a residue is the character or number (shown with bar height in a histogram) in the header line at the corresponding position of the alignment. If Conservation is shown as a histogram, for example, there will be a mavConservation attribute with numerical values; if it is shown with characters, the attribute values will be characters.

Structure... Select (or Render) by Conservation in the Multalign Viewer menu opens the corresponding portion of Render/Select by Attribute, set to the residue attribute mavPercentConserved.

Numerical attributes will appear in the attribute lists of Render/Select by Attribute; character attributes will be listed only Select by Attribute portion. It may be necessary to Refresh the attribute menus or histogram/list in these tools to update them with any changes in Multalign Viewer header information.

Structure... Match in the Multalign Viewer menu allows structures to be superimposed based on the alignment of their associated sequences. The dialog contains two subpanels, each listing the structures associated with sequences in the alignment. One reference structure should be chosen in the left side, but any number of structures to be matched (superimposed) with it can be chosen in the right side. Residues in each Structure to match are paired with the aligned (in the sequence alignment) residues of the Reference structure. If both structures are associated with the same sequence, the correspondence is even more obvious. One point per residue is used for the least-squares fitting: CA in amino acid residues and C4' in nucleic acid residues. The number of atom pairs fitted and the resulting RMSD are reported in the Chimera Reply Log and the status area near the bottom of the sequence window.

Match highly conserved residues only causes only the well-conserved (at least 80%) positions in the alignment to be used for the least-squares fit. These are the positions shown as capital letters in the consensus sequence.

Match active region only causes only the positions in the current active region of the alignment to be used for matching.

Use pseudobonds to show matched atoms indicates that lines (pseudobonds) should be drawn between the matched atoms. For each matched pair of structures, a pseudobond group is created and colored uniquely (in order, the named colors dark green, dodger blue, sienna, yellow, spring green, purple, gray, and coral are used). Each group is named matches of..., where the rest of the name indicates the structures and chains that were matched. The PseudoBond Panel can be used to change the appearance of or delete the pseudobonds.

Create region showing matched residues indicates that the residues paired to generate the fit should be shown as a region named matched residues.

Iterate by pruning long atom pairs until no pair exceeds [x] angstroms refers to an iterative fitting procedure: in each cycle, atom pairs are removed from the match list and the remaining pairs are fitted, until no matched pair is more than x angstroms apart (x=2.0 by default). The atom pairs removed are either the 10% farthest apart of all pairs or the 50% farthest apart of all pairs exceeding the cutoff, whichever is the lesser number of pairs. The result is that the best-matching "core" regions are maximally superimposed; conformationally dissimilar regions such as flexible loops are not included in the final fit, even though they may be aligned in the sequence alignment.

Apply performs the matching (superposition) without dismissing the dialog. OK performs the matching and dismisses the dialog, Cancel dismisses the dialog without performing a match, and Help opens this manual page in a browser window.

Structure... Assess Match in the Multalign Viewer menu opens a dialog for evaluating how well the sequence-aligned residues of structures are superimposed in space. A Reference structure should be chosen from the pulldown menu of structures associated with sequences in the alignment. One or more Structures to evaluate should be chosen from the list of remaining structures. The structures should already be superimposed, but the superposition can have been generated in any way, including manually (not necessarily using Structure... Match).

One point per residue is used for the comparison: CA in amino acid residues and C4' in nucleic acid residues. The distance between each reference-evaluation pair of residues aligned in the sequence alignment (or corresponding to the same residue, if the reference and evaluation structures are associated with the same sequence) is measured. The distances are assigned as a residue attribute of the evaluation structure(s), named matchDist by default. After attribute values have been assigned, Select by Attribute will appear, set to the new residue attribute.

OK performs the comparison and dismisses the dialog, while Close just dismisses the dialog. Help opens this manual page in a browser window.

The Preferences section of the Multalign Viewer menu controls preferences specific to Multalign Viewer; settings are saved with other preferences in the Chimera preferences file. Multalign Viewer preferences are grouped together in sections shown as index cards:

• Layout
• Structure
• Analysis
• Regions

Close dismisses the Multalign Viewer preferences tool, and Help opens this manual page in a browser window.

Note that a typed-in value will not be applied until Apply, OK (which also dismisses the preferences tool), or the Enter (return) key has been pressed. Other types of settings take effect right away.

The Layout section of the Multalign Viewer preferences controls the font and arrangement of text in the sequence window.

• Alignment wrapping - whether the alignment should be continuous from left to right or automatically wrap to successive blocks; there are three mutually exclusive settings:
  • Wrap to new line every [n]0 residues - wrap every 10n positions in the alignment no matter how many sequences are aligned (n=5 by default)
  • Never wrap
  • Wrap if [k] or fewer sequences (the default) - wrap every 10n positions in alignments that contain k or fewer sequences (n=5 and k=8 by default)
• Font - font size and type
  • Use [m] point (Courier/Helvetica/Times) (m=12 by default)
• Spacing
  • Column separation (pixels) (0 by default)
  • Line separation (pixels) (1 by default)
• Sequence names
  • Use ellipsis for names longer than [j] (j=30 by default)

The Structure section of the Multalign Viewer preferences allows adjustment of criteria for automatic sequence-structure association and automatic loading of structures corresponding to the sequences in an alignment.

• Auto-association - criteria for automatic sequence-structure association
  • Allow one mismatch per [n] structure residues (n=10 by default)
• Structure loading - whether/how sequence names relate to the names of the corresponding structure files; whether to retrieve and open such files (as described for Fetch by ID) as soon as a sequence alignment is read. No more than one structure per sequence will be loaded. If a sequence name corresponds to both a SCOP file and a PDB file, the SCOP file will be loaded (unless the Load SCOP... option is turned off).
  • Load SCOP file for each unassociated sequence whose name appears to be a SCOP ID (sid) (on by default)
  • Load PDB file for each unassociated sequence whose name...
    • is < pdb code >
      (e.g."1gcn")
    • starts with < pdb code >
      (e.g."1k6w_A")
    • contains "pdb|" + < pdb code >
      (NCBI-style; e.g. "gi|1421399|pdb|1FTZ")
    • starts with [string] + < pdb code >
      where string is user-specified
    These correspondence rules are not mutually exclusive; all but the last are on by default.
  • Automatically load structures (off by default) - whether to retrieve and open structures as soon as a sequence alignment is read; if not, the procedure can still be invoked with Structure... Load Structures in the Multalign Viewer menu
  • Do not autoload if more than [N] structures would load (on and N=10 by default)

The Analysis section of the Multalign Viewer preferences controls how the Consensus and Conservation headers are determined and represented, and how residue one-letter codes are colored.

• Consensus style (majority in column including gaps/majority in column ignoring gaps) - contents of the header line named Consensus. If several residue types are equally the most prevalent, one is chosen at random to appear in the consensus sequence. When gaps are included, however, the consensus will show a gap at positions where a gap is the most prevalent or equally the most prevalent as one or more residue types.
• Show consensus initially (true/false) - whether to show the Consensus header line when an alignment is opened
• Conservation style (AL2CO/Clustal histogram/Clustal characters/identity histogram) - contents of the header line named Conservation. Note: the usefulness of such measures depends on whether the sequence alignment contains sufficient representatives. Conservation values can be saved to a file.

  AL2CO refers to the program described in:

  J. Pei and N.V. Grishin, "AL2CO: calculation of positional conservation in a protein sequence alignment" Bioinformatics 17:700 (2001).

  Several AL2CO parameters can be adjusted:

  • Frequency estimation method (unweighted/modified Henikoff & Henikoff/independent counts) - whether/how to weight the sequences
  • Conservation measure (entropy-based/variance-based/sum of pairs) - which of the formulas available in AL2CO to use for conservation
  • Averaging window (1 by default) - how many alignment positions to average over in a sliding window
  • Gap fraction (0.5 by default) - alignment positions in which at least gap fraction of the sequences have gaps will be given a conservation value of "None"
  • Sum-of-pairs matrix [choices: BLOSUM-30, BLOSUM-35, BLOSUM-40, BLOSUM-45, BLOSUM-50, BLOSUM-55, BLOSUM-60, BLOSUM-62 (default), BLOSUM-65, BLOSUM-70, BLOSUM-75, BLOSUM-80, BLOSUM-85, BLOSUM-90, BLOSUM-100, BLOSUM-N, identity, PAM-40, PAM-120, PAM-150, PAM-250] - which amino acid similarity matrix to use with the AL2CO sum of pairs Conservation measure
  • Matrix transformation (none/normalization/adjustment) - whether/how to modify the matrix used with the AL2CO sum of pairs Conservation measure

    normalization:     S'_ab = S_ab / (S_aaS_bb)^½

    adjustment:     S''_ab = 2S_ab – ½(S_aa + S_bb)

  The AL2CO paper should be consulted for further details and cited if the results are used in a publication. The conservation values from AL2CO are in standard deviations from the mean (sometimes called Z-scores) and can range from –∞ (least conserved) to +∞ (most conserved). Z-scores are converted into histogram bar heights ranging from 0 to 1 according to:

  for Z-scores ≥ 0,    1 – ½(e^–score)

  for Z-scores < 0,    ½(e^score)

  Thus, a Z-score of zero (mean level of conservation) is shown with a half-height bar. However, the Z-score values (not the values used for display purposes) are used for the mavConservation attribute and written out when conservation values are saved.

  In a Clustal histogram, full bar height indicates complete identity, 2/3 bar height indicates Clustal strong group conservation, and 1/3 bar height indicates Clustal weak group conservation.

  Clustal characters are the characters used in Clustal format to indicate conservation: "*" for complete identity, ":" for strong group conservation, and "." for weak group conservation.

  An identity histogram shows what proportion of the sequences have the most prevalent nongap character per alignment column. Histogram bar heights are proportional to (M-1)/(N-1), where M is the number of occurrences of the most prevalent residue type at a position in the alignment and N is the number of sequences in the alignment. Thus, if every sequence has a different residue at a given position, the bar height is zero, not 1/N. However, M/N values (not the values used for display purposes) are used for the mavConservation attribute and written out when conservation values are saved.

  None means that the row marked Conservation will not be shown.

• Show conservation initially (true/false) - whether to show the Conservation header line when an alignment is opened
• Residue letter coloring (black/Clustal X/Kyte-Doolittle hydrophobicity/custom_file1/custom_file2...) - how one-letter residue codes are colored in the sequence window. The Clustal X coloring scheme depends on both residue type and the pattern of conservation within a column. The Kyte-Doolittle hydrophobicity coloring scheme ranges from red for the most hydrophobic amino acids to blue for the most hydrophilic, with black in the middle. Custom coloring schemes can be described in the Clustal X parameter file format and loaded with Tools... Load Color Scheme.

The Regions section of the Multalign Viewer preferences controls whether a selection will be shown as a region and sets initial region colors.

• Show Chimera selection as region (true/false) - whether to show a selection within structures as a region named Chimera selection within associated sequences (if any); a residue will be included in the region if any of its atoms are selected
• Chimera selection region border color (a color well, forest green by default) - initial border color for the region showing the Chimera selection
• Chimera selection region interior color (a color well, No color by default) - initial interior color for the region showing the Chimera selection
• New region border color (a color well, No color by default) - initial border color for manually created regions
• New region interior color (a color well, white by default) - initial interior color for manually created regions
• Use ellipsis for names longer than [j] (j=25 by default)

• File
• Structure
• Headers
• Tools
• Preferences

• Save As... bring up a dialog for saving the sequence alignment to a file. It is possible to save just the active region to a file; the region may consist of disjoint sections, but each sequence (row) included must contain the same set of columns. The option to omit all-gap columns from the output is especially useful for saving regions with fewer sequences than the starting alignment. The formats available for saving are the same as those that can be read. An alignment saved in Stockholm format will automatically include annotations describing the secondary structure of any associated structures.
• Save EPS... bring up a dialog for saving an Encapsulated PostScript file of the sequence window contents. Options:
  • color mode - (color/grayscale/black & white)
  • rotate 90 - (true/false)
  • extent - (visible region/entire alignment)
  If the alignment is wrapped (or would wrap if it were longer), one EPS file will be saved with the specified name. Otherwise, the sequence names and alignment will be saved in two separate EPS files with "-names" and "-alignment" appended to the specified name (before the ".eps" suffix, if present).
• Save Association Info... save a text file that states which structure is associated with which sequence and lists the correspondences between alignment positions and structure residues. The Residue naming style option controls how residues will be specified in the file.
• Hide - close the sequence window without changing the state of Multalign Viewer (the window can be reopened using the Raise option for the Multalign Viewer instance in the Chimera Tools menu, abbreviated MAV)
• Quit - exit from Multalign Viewer

• Load Structures - for sequences not already associated with a structure, retrieve and open the corresponding structure files (as described for Fetch by ID); correspondence is determined from sequence names according to the rules given in the Structure preferences
• Match... open a dialog for superimposing structures based on the sequence alignment
• Assess Match... open a dialog for evaluating how well the sequence-aligned residues of structures are superimposed in space
• Associations... open a dialog for adding or changing associations between structures and sequences
• Secondary Structure
  • show actual - create regions named structure helices and structure strands colored goldenrod and lime green (see the named colors) and corresponding to residues in associated structures that are in helices and strands, respectively. Helices and strands are defined by HELIX and SHEET records in the input file, or if these are not present, using ksdssp.
  • show predicted - create regions named predicted helices and predicted strands colored gold and light green (see the named colors) in sequences without associated structures. Helices and strands in these sequences are predicted using GOR.
• Select by Conservation... open the Select by Attribute tool to select residues in sequence-associated structures by conservation
• Render by Conservation... open the Render by Attribute tool to color or otherwise change the appearance of residues in sequence-associated structures by conservation

• Save... save a header definition file containing alignment positions and header values. Header values are the characters or numbers (shown with bar heights in a histogram) in a header line such as Conservation in the sequence window. No-value positions (for example, when the AL2CO Conservation style is used, positions with a gap in more than gap fraction of the sequences) can be omitted from the file.
• Load... read a header definition file to show a new header line and have its values available as residue attributes in any associated structures

• Consensus
• Conservation
• another_header_name
• (etc.)

• Find Subsequence... find occurrences of a string of residues in one or all sequences and make them into a region named search result
• Find PROSITE Pattern... find all matches to a pattern specified with PROSITE pattern syntax in one or all sequences and make them into a region named search result (residue codes must be capitalized; extended syntax involving an asterisk, e.g. <{C}*>, is not supported)
• Percent Identity... calculate the percent identity between a pair of sequences in the alignment
• Region Browser - manage the existing regions
• Alignment Annotations... show alignment annotations from the sequence alignment file, allow changes and additions
• Load SCF/Seqsel File... read a JEvTrace file; color sequence regions and the corresponding parts of any associated structures accordingly
• Load Color Scheme... read a parameter file to set the coloring of residue codes in the sequence window. When a scheme is loaded, the residue codes are colored accordingly and the name of the custom coloring file is added to the list of choices for Residue letter coloring in the Analysis preferences. The dialog for loading the file includes an option to Make this scheme the default. The location of each custom coloring file is saved in the preferences file. If a custom coloring file is later renamed, moved, or deleted, trying to load the corresponding scheme will generate an error.

• Layout - control the font and and arrangement of text in the Multalign Viewer sequence window
• Structure - adjust criteria for automatic sequence-structure association and automatic loading of structures corresponding to the sequences in an alignment
• Analysis - control how Consensus and Conservation are determined and represented, and how residue one-letter codes are colored
• Regions - control whether a selection will be shown as a region; set initial region colors