(annotated illustration)  
As shown in the illustration above, the advanced (full feature) version of iCn3D offers a wide range of menus for retrieving structures, viewing the 3D alignment of two similar structures, opening local files, customizing the style of the structure, viewing interactions, viewing the sequence data, selecting regions of interest, sharing a link to the customized display, and more. A Toolbar beneath the menus provides quick access to a subset of commonly used controls (bypassing the need to use the menus for those actions). Shortcut keys can be used to rotate the structure, zoom in/out, and move (translate) the structure to a different position in the 3D view window. A command log lists the actions taken on the structure and enables you to move forward or backward through the actions, and/or save the state of a structure.
iCn3D's operations apply to either all atoms, or to the current selection. The selection mode toggle switch (next to the "Help" menu) specifies the portion of the structure that is to be acted upon by the "style" and "color" menus.
By default, iCn3D uses the "All atoms" selection mode and applies the "style" and "color" options to all atoms. If you select part of the structure, the selection mode toggle switch automatically changes from "All atoms" to "Selection." The "Style" and "Color" menus also become orange. Subsequent operations will apply only to the selected atoms. If you want to change the style or color for all atoms, change the selection mode toggle switch back to "All atoms."
 All - The style, color, and surface menu options will be applied to all atoms in the structure.
When the selection mode toggle switch is set to "All," the "Style" and "Color" menu labels will be displayed in black font.
 Selection - The style, color, and surface menu options will be applied only to selected atoms in the structure.
When the selection mode selection mode toggle switch is set to "Selection," the "Style" and "Color" menu labels will be displayed in orange font.
Hints: iCn3D supports picking. For example, you can use the menu option for "Select > Select on 3D" to specify the region of the structure that you want to select, such as "chain" (protein or nucleotide molecule), "strand/helix" (secondary structure, either a beta strand or alpha helix), "residue" (individual amino acid or nucleotide), or individual "atom." Then, in the 3D window (molecular graphic), use "Alt+click" to make an initial selection. If you want to continue making more selections, use "Ctrl+click" to select to select multiple, discontiguous objects in the structure, or use "Shift+click" to select a range of objects within the structure." It is also possible to select in the 2D window (interactions schematic) and the 1D window (sequences and annotations). Selections are synchronized dynamically in all displays.
Additional details about the "Selection Mode" function are provided in section 1.3 of the supplementary materials in the iCn3D paper by Wang et al. (2019).
file |
select |
view |
style |
color |
windows |
help
Menus are available only in the advanced version of iCn3D and provide a complete set of controls. (In contrast, the basic version provides a simpler interface with fewer controls.) Note that commonly used functions are available both as menu options, and as buttons that appear beneath the menus (illustration). The available menus include:
- "File" menu
- Provides a variety of input and output functions:
- Input options include:
- File > Retrieve by ID - Enter the unique identifier (UID) of a single structure to retrieve it from the database and open an interactive 3D view.
- The menu options (MMDB ID, PDB ID, OPM PDB ID, mmCIF ID, MMTF ID) determine the file format that will be loaded into iCn3D for a given structure, and are described in more detail in a separate section of this document.
- Each option accepts the structure's alphanumeric identifier (the PDB ID) as the input value. The MMDB ID option can also accept the integer assigned by NCBI (the MMDB ID) as the input value.
- The menu option you choose simply determines the file format that iCn3D will import for the structure, and therefore determines the details that will be shown by iCn3D for the 3D structure and its corresponding sequence data.
- Background information: A structure (e.g., 1hho) might have slightly different appearances in iCn3D, depending upon the file format (e.g., MMDB, PDB, mmCIF) that is loaded into iCn3D. For example, some file formats show a structure's biological unit, while others show its asymmetric unit. In addition, the MMDB file format offers an interactions schematic that displays a structure's molecular components and interactions among them.
- A separate section of this document provides illustrated examples of human oxyhemoglobin (1HHO) loaded into iCn3D in the various file formats (1HHO as an MMDB file, 1HHO as an PDB file, and 1HHO as an mmCIF file, as examples). Click on an illustration, if desired, to open a corresponding live view, or open the advanced version of iCn3D and then follow the steps shown in the table below.
- The most robust set of iCn3D features is available through the "File > Retrieve by ID > MMDB ID" menu option, or by using the mmdbid=xxxx parameter in a formatted URL. You can enter the structure's identifier either as its MMDB ID (e.g., 103701) or its corresponding PDB ID (e.g., 1TUP). It then retrieves the specified structure record from NCBI's Molecular Modeling Database (MMDB), which contains structure files that have been enhanced with features and details added by the MMDB data processing pipeline. For example, the Interactions schematic (2D view) is only available when viewing an MMDB structure. The table below describes additional differences you might see in the rendering of a structure, depending on what file format you import for that structure into iCn3D.
- File > Align - Enter the UIDs of two structures that have been found to be similar by VAST to open an interactive view of their 3D alignment. A separate section of this document provides additional details and illustrated examples.
- File > Realign selection - Realign two structures or two chains by using the iCn3D menu option for "File > Realign," if you want to view an alignment that is different than the one generated by VAST+ or by dynamic chain alignment. Specifically, the "Realign" option enables you to select residues of interest and to realign the structures or chains on those residues.
- File > Open File - Open a local structure file. A separate section of this document provides details about each option.
- Output options include:
- File > 3D Printing - This option exports both Stereolithography (STL) and Virtual Reality Modeling Language (VRML) files for 3D printing. It also includes options for adding stabilizers and for specifying the thickness for 3D printing.
- File > Save Files
- iCn3D PNG Image - To save a custom display of the 3D structure, it is recommended to save the image using the option "Save File > iCn3D PNG Image" in the File menu. This PNG image is of high quality, has a transparent background, and contains the sharable link at the end of the file. It can be also be imported into iCn3D at a later time in order to reproduce the display, using the option "Open File > iCn3D PNG Image" in the File menu. Thus, this saved iCn3D PNG Image contains both the static image display and the commands to reproduce the dynamic display.
- State File - captures the sequence of commands, from the command log, that were used to customize the image of the structure, so the same view can be opened at a later time
- Selection File - a text file that lists the selections that you have made in the structure
- Residue Counts - an HTML file that lists the residue and atom count for each protein sequence, nucleotide sequence, and ligand in the structure.
- Interaction List - an HTML file, formatted as a two column table:
- Each row represents an interaction between two molecules of the structure
- Column 1 contains the label of the first molecule, along with the residue numbers within the molecule that interact with the second molecule
- Column 2 contains the label of the second molecule (e.g., 1TUP_B, which represents protein chain B in the 1TUP structure)
- A separate row will show the inverse relationship (that is, it will list the specific residues in the second molecule that interact with the first molecule)
- As an example, the interactions file (1TUP_interactions.html) for structure 1TUP: Tumor Suppressor P53 Complexed With DNA, includes: One row that lists the specific residues in protein chain A (1TUP_A: .A:72 or .A:74-75) that interact with nucleotide chain E. A separate row shows the inverse relationship, listing the specific residues in nucleotide chain E (1TUP_E: .E:14-15) that interact with protein chain A. Additional rows for each interaction identified in the structure. (The method for identifying interactions is described in the MMDB help document.)
- File > Share Link - after customizing the display of a 3D structure to your desired specifications (e.g., select regions of interest, render them in the desired style, highlight and label biological features), you can use the "File > Share Link" menu option to generate a URL that you can share with others
- "Select" menu
Defined Sets |
All |
By Distance |
Inverse |
Side Chains |
Advanced |
Select on 3D |
Save Selection |
Clear Selection |
Highlight Color |
Highlight Style |
Toggle Highlight
- Select > Defined Sets - opens a "Select Sets" window that allows you to select a specific structure (if you are viewing an alignment of two structures), a specific molecule (e.g,. individual protein or nucleotide chain), or a category of objects (e.g., proteins, nucleotides, ions) in the structure. To select multiple items from the "Select Sets" window, press Ctrl+Click to select discontiguous items, or Shift+Click to select a range of items.
- Initially, the "Select Sets" window lists the PDB ID of the structure (choosing this will select all), each chain within the structure (i.e., each protein, DNA, and/or RNA molecule, enabling you to select one or more molecules of interest), and each 3D domain within each protein molecule. The selected molecules will then be highlighted in the 3D (molecular graphic) and 2D (Interactions) windows. The 1D (Sequences and Annotations) windows will display only the molecules you have selected.
- It also lists the broad categories of molecule types that compose the structure (e.g., ions, nucleotides, proteins, water). Selecting a category will highlight all molecules of that type, in all three windows (3D, 2D, and 1D).
- Additional items will appear in the "Select Sets" window if you use the "Select > Advanced" menu option to select and name a custom set (in that case, the name you applied to your custom set will appear in the "Select Sets" window).
- Additional items will also appear if you use the "Windows > Interactions" menu option to open the 2D window and click on an interaction line beteen two molecules to highlight the specific residues taking part in the interaction. For example, if you double click on the line in the 1TUP interaction schematic that connects proteins B and C (specifically, if you click on the part of the line that is closer to protein B), iCn3D will select/highlight all of the residues in protein B that are interacting with protein C. A new item, listed as "inter_B_C" will then appear in the "Select Sets" window.
- Select > All - selects the complete structure
- When a structure is first loaded into iCn3D, the complete structure is selected by default. Therefore, choosing the option for "Select > All" doesn't initially change the view.
- To display the highlighting on the full structure after choosing "Select > All", click on "Show Toolbar," then click the "Toggle Highlight" button. The complete structure highlighted in the 3D window. Click the "Toggle Highlight" button in the ToolBar again to toggle the highlight off (or choose the "Select > Toggle Highlight" menu option).
- If you later select specific objects in the structure (e.g., specific chains, secondary structures, residues, or atoms using the "Select > Select on 3D" option), only those objects will be selected, and the Selection Mode toggle switch automatically moves from "All atoms" to "Selection."
- If you then choose the "Select > All" menu option again, the Selection Mode toggle switch slides back to "All atoms" and removes the highlights from the objects selected in the previous step.
- However, iCn3D remembers the selection you made (in its command log), and you can view it again by simply moving the toggle switch back to "Selection."
- Select > By Distance - highlights residues/atoms that are within a certain distance of a selected object (e.g., select a ligand and the use the "Select > By Distance" option to highlight all amino acids that are within 5 Angstroms of the ligand).
- Select > Inverse - When you select an object or region within a struture, it will become highlighted. If you then use the "Select > Inverse" option, iCn3D will remove the highlight from the orignally selected region and will highlight the remaining region of the structure. Using the "Select > Inverse" option again will cause the highlight to toggle back to the originally selected region.
- Select > SideChains - By default, side chains are hidden in the 3D display. They can be revealed in the 3D window by using the "Style > Side Chains" menu option to choose the style in which you would like them rendered. Once the side chains are visible, you can take other actions on them, such as selecting them. Therefore, be sure to use the "Style > Side Chains" menu to change from "hide" to some other style before using the "Select > Side Chains" option. If those actions are done in reverse order, the connection between the side chain and the backbone won't be visible.
- Select > Advanced - opens a dialog box where you can use command language to specify the selection of structures, chains (molecules), or residues (individual nucleotides, amino acids, ligands, ions, or water). The dialog box includes specification tips (hints) about command syntax and examples of advanced selection. In the command syntax, various symbols are used to specify what type of molecule you want to select. For example:
- Dollar sign ($) is used to select a structure. If you are viewing the alignment of two similar structures and want to select one of them, you can use the dollar sign followed by the PDB ID of the structure you want to select (e.g., if you are viewing an alignment between 1HHO and 4N7N, you can enter $1HHO in the "Select" text box if you want to highlight that structure).
- Period (.) is used to select a chain, or molecule, within a structure (e.g., enter .B,E in the "Select" text box if you want to highlight molecules B and E within the structure
- Colon (:) is used to:
- select residues (amino acids or nucleotides) at specific positions within a molecule (e.g., enter numerical values such as :5-10 in the "Select" text box if you want to highlight the fifth through tenth residues in the selected molecule).
NOTE: If you do not specify a given molecule, then iCn3D will highlight the specified residues in each molecule of the structure. For example, if you are viewing the 1TUP structure and select :5-10, then the fifth through tenth residues in each of the biopolymers (protein chains A, B, C, and nucleotide chains E, F) will be highlighted. To view a span of residues on a given biopolymer, include its chain identifier (e.g., .B:5-10 will select chain B, residues 5-10).
- select all of a given type of residue (e.g., enter the one IUPAC abbreviation of an amino acid, such as :K for Lysine, in the "Select" text box if you want to highlight all Lysine residues in the structure). You can also highlight multiple types of residues; for example, you can enter :KRDE in order to find all instances of Lysine-Arginine-AsparticAcid-GlutamicAcid sequence in the structure, or you can enter :K,R,D,E (where the IUPAC abbreviations are separated by commas) to select all instances of those individual residues in the structure (i.e., to select all Lysine, Arginine, Aspartic Acid, and Glutamic Acid in the structure, regardless of whether they occur together).
- select all of the objects in the structure that fall into the specified category, where the categories can be "proteins", "nucleotides", "chemicals", "ions", and "water" (e.g., enter :chemicals in the "Select" text box if you want to highlight all of the chemicals in the structure).
- select any combination of the objects noted above (e.g., enter :5-10,KRDE,chemicals (or :5-10,K,R,D,E,chemicals) uses the colon ":" to indicate residue selection. Residue selection could be residue number (5-10), one-letter IUPAC abbreviations, or predefined names: "proteins", "nucleotides", "chemicals", "ions", and "water". IUPAC abbreviations can be written either as a contiguous string (e.g., :KRDE), in order to find all instances of that sequence in the structure, or they can be separated by commas (e.g., :K,R,D,E) to select all residues of a given type in the structure (in the latter case, select all Lysine, Arginine, Aspartic Acid, and Glutamic Acid in the structure).
- The at symbol (@) is used to select an atom within a structure. It can be followed by a numerical value that represents the atom's position in a structure, or by the symbol for a specific element (e.g., enter @Ca,C in the "Select" text box if you want to highlight all of the calcium and carbon atoms within the structure).
- Partial definition is allowed. It is not necessary to provide a complete definition of the structure, chain (molecule), residues, and atoms. Rather, you can define only one of those items, or a subset of them, if desired. For example, if you only specify the positions of residues, but you don't specify the desired molecule, iCn3D will highlight the specified residues in each molecule of the structure (e.g., :1-10 selects all residue IDs 1-10 in all molecules).
- "Save Selection to Defined Sets" button can be used to give a name to your selection and to save it. The saved set will then be listed in the Select Sets window that appears when you choose the "Select > Defined Sets" menu option.
- Select > Select on 3D - allows you to select a chain (protein molecule or nucleotide molecule), strand/helix (beta strand or alpha helix secondary structure), residue (amino acid or nucleotide), or atom of interest on the 3D structure:
- Use "Alt+click" to make an initial selection.
- By default, that action selects a single residue (amino acid or nucleotide).
- You can use the "Select > Picking with Alt+Click" menu options to change the type of object that is selected upon clicking (e.g., chain (protein molecule or nucleotide molecule), strand/helix (beta strand or alpha helix secondary structure), residue (amino acid or nucleotide), or atom.
- If you want to continue making more selections:
- Use Ctrl+Click to select multiple, discontiguous objects
- Use Shift+Click to select a range of objects
- Selections are synchronized dynamically in all displays. For example, if you have the 1D window ("Sequences and Annotations") window open as well, the object(s) you selected will be highlighted in both the 3D structure window and the 1D Sequences and Annotations window.
- To save your selections, use the Select > Save Selection menu option. A small dialog box will appear that allows you to give a customized name to your selection, if desired. That name will then appear in the Select Sets window that appears when you choose the "Select > Defined Sets" menu option.
- To clear your selections, use the Select > Clear Selection menu option.
- Note: Separate sections of this document describe how selections can be made in the 2D (Interactions schematic) and 1D (Sequences and Annotations) windows.
- Save selection
- Selections will be temporary unless you use on the "Select > Save Selection" menu option. (Another option for saving a selection is to click on the "Save" button in the "Details" tab of the "Sequence and Annotations" window).
- The "Select > Save Selection" menu option adds your selection to the command log (and therefore to the state file).
- The "Select > Save Selection" menu option will also add the selection to the "Select Sets" window that appears when you choose the "Select > Defined Sets" option.
(The "Select Sets" window also lists, and therefore enables you to select, some predefined data sets such as all proteins, all nucleotide sequences, all ions, and all ligands.)
- Clear selection
- The "Clear Selection" button will clear the highlights in all views (i.e., in the sequence window (1D view), interactions schematic (2D view), and structure window (3D view)).
- However, if you have pressed the "Save Selection" button, your selection will remain listed in the "Select Sets" window that appears when you choose the "Select > Defined Sets" option. Therefore, you can choose it from that menu to highlight that selection again.
- Select > Highlight Color
- by default, selected regions of the structure are highlighted in yellow, or can be changed to green or red
- Select > Highlight Style
- by default, selected regions of the structure are highlighted with an outline (in whatever highlight color you have selected), or can be changed to 3D objects (cubes rendered in whatever highlight color you have selected)
- Select > Toggle Highlight
- turns highlighting on/off for the objects you most recently selected
- "View" menu
- choose which portion of the structure to display (the complete structure or only the region you have selected). For example, some options include:
- View Only Selection - shows only the objects that you have selected
- Zoom in Selection - zooms into the selected region of the structure
- Center on Selection - centers the view of the structure on your selection
- View Full Structure - displays the full structure once again (if you you have previously viewed only the selection) and retains the highlights on your selection
- analyze the structure. For example, some options include:
- Chemical Binding: show the hydrogen bonds (as green dashed lines) between biopolymers and chemicals in the structure
- H-bonds and Interactions: show each hydrogen bond, contact/interaction, and/or salt bridge in 3D; a dialog box appears that allows you to select the objects in the structure that you want to examine, and to specify the distance threshold of the hydrogen bonds, salt bridges and contacts/interactions.
- Disulfide bonds between objects appear as yellow cylinders and can be shown or hidden, as desired. Disulfide bonds are shown by default in the iCn3D 3D window.
- Cross-linkages between objects appear as green cylinders and can be shown or hidden, as desired, and often represent bonds that have formed between chemicals and proteins (read more about cross-linkages).
Cross-linkages are hidden by default in the iCn3D 3D window. If you choose to show them, the style of protein molecules will automatically change from ribbons to lines in order to increase the visibility of the green cylinders that represent the cross-linkages. The 1GPK structure provides an example, in which cross-linkages can be seen as small green cylinders that show the connection between the protein and chemicals, and in one instance, between a pair of chemicals.
- Distance: measure the distance between two atoms; pick two atoms in the 3D view while holding the "Alt" key, and use the "View > Distance" dialog box to specify the color
- Label: can be used to label either the full structure (if the Selection Mode toggle switch is set to "All atoms"), or the regions you have selected (if the Selection Mode toggle switch is set to "Selection"). The option to "Label > By Picking Atoms" enables you to pick atoms in the 3D view while holding the "Alt" key; a line/connection will be drawn between them and you can apply a label to the line). Labels can be applied per atom, per residue, per chain, etc.
- side by side display:
- Use the "View > Side by Side" option to display the same structure in two views. Each view has the same orientation, but can have an independent 3D display. Use the menu icon in the upper left corner of either view to customize the style, color, etc. of the structure in that view.
- adjust the position of the structure and details of the display. For example, some options include:
- Rotate - the option to Rotate 90 degrees rotates the structure along the selected axis (x, y, or z). Auto Rotation provides an animated view of the structure, spinning it continuously in the specified direction (left, right, up, down); click anywhere on the structure to stop the spinning.
- Camera - sets the view of the structure as either perspective or orthographic
- Fog - turns fog on or off; fog blurs everything behind the center (tip: when viewing chemical binding, it can be helpful to combine fog and slab, which produces a sphere of about 20 Å)
- Slab - turns slab on or off; slab removes from view everything in front of the center (tip: when viewing chemical binding, it can be helpful to combine fog and slab, which produces a sphere of about 20 Å)
- X-Y-Z axes - show or hide the X-Y-Z axes
- additional viewing options include:
- Reset - reloads the original view of the structure
- Undo - moves back to the previous step you took in viewing/customizing the structure (back to the previous step that is recorded in the command log).
- Redo - moves forward to the next step you took in viewing/customizing the structure (forward to the next step that is recorded in the command log).
- Full Screen - displays the 3D window in your full screen (press the "ESC" key to exit full screen)
- "Style" menu
- style by molecule type: choose the style in which you would like to render each type of molecule. For example, some options include:
- protein molecules can be rendered as ribbon, strand, cylinder and plate, C alpha trace, B factor tube, lines, stick, ball and stick, or sphere
- side chains are hidden by default and can be displayed, if desired, as lines, stick, ball and stick, or sphere
- nucleotide molecules can be rendered as cartoon, 03' trace, schematic (similar to 03' trace, with the addition of small labels that represent each nucleotide in the sequence), lines, stick, ball and stick, or sphere
- chemicals can be rendered as lines, stick, ball and stick, schematic, or sphere
- ions can be rendered as sphere or dot
- Tip: To easily select an individual ion by using ALT+Click in the 3D structure view, display the ions as "dot."
- When ions are rendered as spheres, you need to click on the center of the sphere in order to highlight the ion. If you click elsewhere in the sphere, it is possible that an atom from another component of the structure might be highlighted instead of the ion. This happens if your click was closer to the atom than to the center of the ion's sphere. Rendering ions as "dot," on the other hand, makes it easy to precisely select one or more ions. (Use Ctrl+Alt+click to select multiple ions.)
- Alternatively, individual ions can also easily be selected by clicking on the interactions schematic, or the complete set of ions can be selected from the "Select Sets" window that appears when you choose the "Select > Defined Sets" menu option.
- water molecules are hidden by default and can be rendered as dots or spheres
- surface rendering options include:
- choose the type of surface to display (Van der Waals, molecular surface, solvent accessible), and the degree of opacity (in increments of ten percent, ranging from 0.5 to 1.0)
- selection mode:
- Note that the styles you select will be applied to "all atoms" or to the "selection" you have made, based on how you have set the selection mode toggle switch near the upper left corner of the iCn3D window.
- The "Style" menu label will appear in black font if the switch is set to "all atoms" and will appear in orange font if the switch is ste to "selection."
- "Color" menu
- choose the color in which you would like to render the structure. For example, some options include:
- spectrum, secondary, charge, hydrophobic, chain, residue, atom, or unicolor
- "custom" opens dialog box appears beneath structure, where you can enter the hexidecimal code of the desired color, e.g., #FF0000, then press "Apply."
- selection mode:
- Note that the color you select will be applied to "all atoms" or to the "selection" you have made, based on how you have set the selection mode toggle switch near the upper left corner of the iCn3D window.
- The "Color" menu label will appear in black font if the switch is set to "all atoms" and will appear in orange font if the switch is ste to "selection."
- "Windows" menu
- View Sequences & Annotations - a 1D view of the structure, showing the sequence data and annotations for the biopolymers (proteins, DNA, RNA) that compose the structure (read more)
- View Interactions - a 2D view of the structure, represented as a schematic that shows the interactions among the structure's molecular components (read more)
- Links - follow links to related data:
- Structure Summary - the Structure Summary page, in the Molecular Modeling Database (MMDB), for your structure of interest
- Similar Structures - other structures in MMDB that are similar in 3D shape to the selected structure, as determined by the original VAST (Vector Alignment Search Tool), and by VAST+, during MMDB data processing. (The similar structures are sometimes referred to as VAST or VAST+ "neighbors," and the VAST help document and VAST+ help document provide additional details about those tools.)
- Literature - PubMed records for the reference(s) cited in the structure record.
- Protein - sequence records for the proteins that compose the structure.
- "Help" menu
- About iCn3D - a brief overview of the program, including an example of iCn3D embedded into a browser window, and links to files that provide additional details about how to use iCn3D
- Help doc - this file, which provides details about the iCn3D web interface
- Web APIs - links to an iCn3D gallery with live examples, information on how to embed iCn3D in your web page, URL parameters, and commands
- iCn3D source code- available from GitHub
- Transform hints - tips on how to rotate, zoom in/out, and translate
- Selection hints - tips for selecting on 3D structure, 2D interactions, and 1D sequences
save iCn3D PNG image |
defined sets |
view sequences & annotations |
view interactions |
view chemical binding |
view only selection |
toggle highlight |
remove labels
An option to "Show Toolbar | Hide Toolbar" is provided at the top of an iCn3D window. When shown, the toolbar displays buttons beneath the menus, providing quick access to a subset of commonly used controls (illustrated example). Those controls are also accessible from the menus (as noted in italics, below). The toolbar simply bypasses the need to use the menus for these commonly used actions:
- Save iCn3D PNG Image
- The "Save iCn3D PNG Image" function is recommended for saving a custom display of the 3D structure. (This function is also available from the "File > Save Files > iCn3D PNG Image" menu option.) The PNG image is of high quality, has a transparent background, and contains the sharable link at the end of the file. It can be also be imported into iCn3D at a later time in order to reproduce the display, using the option "Open File > iCn3D PNG Image" in the File menu. Thus, this saved iCn3D PNG Image contains both the static image display and the commands to reproduce the dynamic display.
- Defined Sets
- Opens a "Select Sets" window that allows you to select a specific structure (if you are viewing an alignment of two structures), a specific molecule (e.g,. individual protein or nucleotide chain), or a category of objects (e.g., proteins, nucleotides, ions) in the structure. To select multiple items from the "Select Sets" window, press Ctrl+Click to select discontiguous items, or Shift+Click to select a range of items.
(This function is also available from the "Select > Defined Sets" menu option.)
- Initially, the "Select Sets" window lists the PDB ID of the structure (choosing this will select all), each chain within the structure (i.e., each protein, DNA, and/or RNA molecule, enabling you to select one or more molecules of interest), and each 3D domain within each protein molecule. The selected molecules will then be highlighted in the 3D (molecular graphic) and 2D (Interactions) windows. The 1D (Sequences and Annotations) windows will display only the molecules you have selected.
- It also lists the broad categories of molecule types that compose the structure (e.g., ions, nucleotides, proteins, water). Selecting a category will highlight all molecules of that type, in all three windows (3D, 2D, and 1D).
- Additional items will appear in the "Select Sets" window if you use the "Select > Advanced" menu option to select and name a custom set (in that case, the name you applied to your custom set will appear in the "Select Sets" window).
- Additional items will also appear if you use the "Windows > Interactions" menu option to open the 2D window and click on an interaction line beteen two molecules to highlight the specific residues taking part in the interaction. For example, if you double click on the line in the 1TUP interaction schematic that connects proteins B and C (specifically, if you click on the part of the line that is closer to protein B), iCn3D will select/highlight all of the residues in protein B that are interacting with protein C. A new item, listed as "inter_B_C" will then appear in the "Select Sets" window.
- View Sequences and Annotations
- Displays the sequence data from the structure record, including protein and nucleotide sequences, as well as chemicals (if present). (This function is also available from the "Windows > View Sequences & Annotations" menu option.)
- Use your mouse to select sequence regions of interest: drag your mouse over a sequence region to select it; drag again to deselect. The selected region will be highlighted in the sequence view as well as in the 3D structure.
- Multiple selections are allowed in the sequence window, without the need to use the CTRL key.
(In contrast, selecting on the 3D structure requires the use of ALT+click to pick, CTRL+click to select multiple discontiguous regions; and Shift+click to select a range.)
- A separate section of this document provides additional details about the structure's 1D view (sequences and annotations) and its features and functions.
- View Interactions
- Displays an interactions schematic of the structure, showing the structure's molecular components and the interactions among them. (This function is also available from the "Windows > View Interactions" menu option.)
- This function is available only when a structure is loaded into iCn3D in MMDB file format because the schematic is generated as part of MMDB data processing. (The "View Interactions" button will be visible in the Toolbar only if you open a structure by either: (a) clicking the "full-featured 3D viewer" button in the molecular graphic shown on a MMDB structure summary page, or (b) loading a structure into iCn3D by using the "File > Retrieve by ID > MMDB ID" menu option.)
- A separate section of this document provides additional details about the structure's 2D view (interactions schematic) and its features and functions.
- View Chemical Binding
- Shows the hydrogen bonds (as green dashed lines) between biopolymers and chemicals in the structure.
- (This function is also available from the "View > Chem. Binding" menu option.)
- View Only Selection
- If you have selected a region(s) of interest, this button will display only the selected region(s) in the molecular graphic (3D view), and will hide the other regions of the structure from view. (This function is also available from the "View > View Only Selection" menu option.)
- Tip: To revert to a view of the full structure, use the "View > View Full Structure" menu option. The highlights on your selected region(s) will be preserved as you switch between the two views.
- Toggle Highlight
- Turns highlighting on/off for the objects you most recently selected. (This function is also available from the "Select > Toggle Highlight" menu option.)
- Remove Labels
- If you have used the "View > Label" menu option to display labels in the 3D window, the "Remove Labels" button can be used to turn them off. (This function is also available from the "View > Label > Remove" menu option.)
Rotate |
Zoom |
Translate
A structure can be rotated, zoomed in/out, or translated (moved) with your mouse, or with the following key combinations:
- Rotate
- Left mouse button can be used to rotate the structure
- Key L - left
- Key J - right
- Key I - up
- Key M - down
- Zoom
- Middle mouse button can be used to zoom
- Left Mouse + Shift can be used as an alternative to the middle mouse button
- Key Z - zoom in
- Key X - zoom out
- Translate
- Right mouse button - can be used to translate (slide) the structure to a different location within the 3D window
- Left Mouse + Control can be used as an alternative to the right mouse button
- Arrow Left - left
- Arrow Right - right
- Arrow Up - up
- Arrow Down - down
file format affects appearance |
condensed view for very large structures |
customize appearance |
save state |
share link
- File format affects appearance of molecular graphic
- Structure records are available in various file formats. The "File > Retrieve by ID" menu options for macromolecular structures (MMDB ID, PDB ID, mmCIF ID, MMTF ID) determine the file format that will be loaded into iCn3D for a given structure. Each of those menu options accepts the structure's alphanumeric identifier (the PDB ID) as the input value. The MMDB ID option can also accept the integer assigned by NCBI (the MMDB ID) as the input value.
Note that a single structure might have different appearances in iCn3D, depending upon the file format that is loaded into iCn3D. For example, some file formats show a structure's biological unit, while others show its asymmetric unit. In addition, the MMDB file format offers an interactions schematic that displays a structure's molecular components and interactions among them.
A separate section of this document provides illustrated examples of human oxyhemoglobin (1HHO) loaded into iCn3D in the various file formats (1HHO as an MMDB file, 1HHO as an PDB file, and 1HHO as an mmCIF file). Click on an illustration, if desired, to open a corresponding live view.
- Consensed view for very large structures
- Some very large structures are loaded into iCn3D in a condensed view, in which proteins are shown as bricks and cylinders, and DNA and RNA molecules are shown as atoms. An example of this is 1FFK: Crystal Structure of the Large Ribosomal Subunit From Haloarcula Marismortui at 2.4 Angstrom Resolution (open the MMDB structure summary page for 1FFK, open 1FFK in the advanced version of iCn3D). The "style" menu can then be used, if desired, to render various subsets of the structure in greater detail.
- Customize appearance of molecular graphic
- The advanced version of iCn3D provides menus that enable you to select regions of interest, and apply a desired style and color to either the whole structure or to the selected region (as determined by the selection mode toggle switch that alternates between "all" and "selection"). In addition, the view menu enables you to label atoms or selected regions in the structure, and to show H-bonds or disulfide bonds, if desired.
- Use the "Alt" key in combination with a mouse click to select objects of interest in the molecular graphic (3D view) window. The "Select > Select on 3D" menu enables you to specify what will be selected upon the click action (residue (default), strand/helix, or atom).
- The interactions schematic and sequence view windows can also be used to select objects or regions of interest in the structure. The selections will then be highlighted in all three views (molecular graphic (3D view), interactions schematic (2D view), and sequence window (1D view)).
- Save state
- Use the "File > Save File > State File" menu option to save your customized view of the structure. The state file will capture the sequence of commands (from the command log) that were used to customize the image, so the same view can be opened at a later time.
Note: You can also save a custom display by using the option "Save File > iCn3D PNG Image" in the File menu. This PNG image is of high quality, has a transparent background, and contains the sharable link at the end of the file. It can be also be imported into iCn3D at a later time in order to reproduce the display, using the option "Open File > iCn3D PNG Image" in the File menu. Thus, this saved iCn3D PNG Image contains both the static image display and the commands to reproduce the dynamic display.
- Use the "File > Open File > State File" menu option to open the file at any time, and use the forward and back arrows near the upper left corner of the iCn3D window to move through the sequence of steps you took to generate the customized view of the structure.
- Share link
- Use the "File > Share Link" menu option to generate a URL to your customized view of the structure, which you can then share with others
- For example, the structure for human Abl2 kinase with Gleevec bound was customized to highlight the residues that are associated with ATP-binding (according to CDD annotation of conserved sites), and the "File > Share Link" menu option generated the following URL, which captures the selections and styles that have been applied to the structure:
/Structure/icn3d/full.html?mmdbid=3gvu&command=select .A:38-40 or .A:42 or .A:45 or .A:61 or .A:63 or .A:77-78 or .A:82 or .A:91 or .A:107-108 or .A:110 or .A:114 or .A:162 or .A:172-173; style proteins stick; color atom; set surface Van der Waals surface; add label ATP-binding Site | size 18 | color #0000ff | background #cccccc | type custom; select .STI; color green; toggle highlight
The Share Link can be shortened, e.g. to
https://icn3d.page.link/2rZWsy1LZmtTS3kBA
This opens a custom display of tumor suppressor P53 interacting with DNA (PDB ID 1TUP). As noted in the iCn3d paper by Wang et al. (2019), "iCn3D highlights key residues involved in the interaction: arginine 175, 248-249, 273 and 282, and glycine 245 (Cho, et al., 1994). The residue Arg 248 at chain B inserts into the major groove of the DNA double-helix. Other highlighted residues are also involved in protein-DNA interactions or protein-protein interactions. Mutations of these key residues may affect the interaction of P53 with DNAs and are associated with cancer (Vogelstein, et al., 2000). These mutations and are shown on ClinVar (the variants associated with clinical diseasesClinVar) (Landrum, et al., 2018) and SNP sequence annotation tracks (Figure 1D)." Additional details about the "Share link" function are provided in section 1.11 of the supplementary materials in Wang et al. (2019).
- Molecular components of the structure can include the following
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Proteins, if present, are shown as circles: |
 etc. |
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Nucleotide sequences (DNA, RNA), if present, are shown as squares: |
 etc. |
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Chemicals, if present, are shown as diamonds: |
 etc. |
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Non-standard biopolymers, if present, are shown as parallelograms:
(These are molecules such as nucleotide or protein sequences that contain a large percentage of non-standard residues.) |
 etc. |
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If any protein or nucleotide molecules in the structure were generated by applying transformations from crystallographic symmetry, their labels are shown as alphanumeric combinations (for example,  or  ), indicating the source molecule from which they were generated (to the left of the underscore bar) and the copy number (to the right of the underscore bar). Chemicals that interact only with such molecules were also generated by applying transformations from crystallographic symmetry; their icon labels also include an underscore bar, with a number on either side of the underscore bar to indicate the source chemical and the copy number, respectively.
The protein and nucleotide icons are scaled to show the relative sizes of those molecular components, so they are roughly comparable to each other based on molecular weight. All chemical icons are the same size.
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- Interactions among components are shown as lines, and an interaction is displayed only if there are at least 5 contacts at a distance of 4 Å or less between the heavy atoms of the molecules.
- There is no meaning to the length of the lines in the interaction schematic. After the interactions are drawn, the diagram is flattened out to fit into the square, lengthening or shortening lines as needed.
- Because of the latter thresholds, ions that are part of the biological unit may be missing from the interaction diagram, but they will be listed in the table of molecular components and interactions on the corresponding MMDB structure summary page.
Interactions for short peptides, or for molecule types other than protein, DNA/RNA, and chemical, are not calculated. Molecules, such as crystallization agents, etc., that are not part of the biologically active molecule are absent from both the interaction schematic and the molecular components list.
- Features and functions
- Mouse over the icon for any molecular component to see its description
- Select/highlight molecular components: Click the icon for any molecular component to select it. Once selected, the component will be highlighted in al three views (molecular graphic (3D view), interactions schematic (2D view), and sequence window (1D view)). Below is an illustrated example of human oxyhemoglobin (1HHO), showing protein A highlighted in this way.
- View interaction interfaces: Click on half of a line to highlight the residues in the nearest molecule that are involved in the interaction, and to view the interaction interface. Below is an illustrated example of human oxyhemoglobin (1HHO), showing residues in protein B that interact with protein A. The highlighted molecules can then be rendered with the desired style, color, and surface.
- Customize display of interaction interfaces: If a single molecule interacts with several others, each interaction interface can be selected and rendered in a different way (for example, with different types or colors of surface), making it possible to visualize the various interaction surfaces simultaneously.
file format affects sequence data displayed |
select on sequence data |
save selection |
clear selection |
add track |
custom color
- File format affects sequence data displayed
- Structure records are available in various file formats. The "File > Retrieve by ID" menu options for macromolecular structures (MMDB ID, PDB ID, mmCIF ID, MMTF ID) determine the file format that will be loaded into iCn3D for a given structure. Each of those menu options accepts the structure's alphanumeric identifier (the PDB ID) as the input value, and the MMDB ID option can also accept the integer assigned by NCBI (the MMDB ID) as the input value.
- Some file formats, such as PDB, mmCIF, and MMTF, display only the sequence data that was supplied by the submitter of the structure (i.e., the sequence data that corresponds to the asymmetric unit).
- The MMDB file format displays the sequence data for the biological unit, including sequence data that was generated by applying transformations from crystallographic symmetry.
- A separate section of this document provides illustrated examples of human oxyhemoglobin (1HHO) loaded into iCn3D in the various file formats (1HHO as an MMDB file, 1HHO as an PDB file, and 1HHO as an mmCIF file, as examples), showing the corresponding sequence data for each. Click on an illustration, if desired, to open a corresponding live view.
- Select on sequence data
- To select sequence regions of interest, drag your mouse over a sequence region to select it; drag again to deselect. The selected region will be highlighted in all views (sequence window (1D view), interactions schematic (2D view), and molecular graphic (3D view))
- Multiple selections are allowed in the sequence window, without the need to use the CTRL key
(In contrast, selecting on the 3D structure requires the use of ALT+click to pick, Ctrl+Alt+click to select multiple discontiguous regions; and Shift+Alt+click to select a range.)
- Save selection
- Selections will be temporary unless you click on the "Save Selection" button at the top of the sequence view window
- The "Save Selection" button adds your selection to the command log (and therefore to the state file).
- The "Save Selection" button will also add the selection to the the "Select Sets" window that appears when you choose the "Select > Defined Sets" menu option.
(The "Select Sets" window also lists, and therefore enables you to select, some predefined data sets such as all proteins, all nucleotide sequences, all ions, and all ligands.)
- Clear selection
- The "Clear Selection" button will clear the highlights in all views (i.e., in the sequence window (1D view), interactions schematic (2D view), and structure window (3D view)).
- However, if you have pressed the "Save Selection" button, your selection will remain listed in the "Custom" menu, and therefore you can choose it from that menu to highlight that selection again.
- Add track
- The "Add track" button that appears beside each protein in the "Sequences and Annotations" window enables you to add a multiple sequence alignment as a track.
- Custom color
- The "Custom color" button that appears beside each protein in the "Sequences and Annotations" window enables you to add custom colors when aligning a sequence to a structure.
list of actions taken |
previous & next arrows |
save state file |
open state file
- List of actions taken
- A command log appears in the bottom grey area of the advanced iCn3D window, as shown in the illustration below. It lists the actions you have taken on the structure and can be edited directly.
- Previous & next arrows
- The "previous" and "next" arrows that appear to the left of the "File" button enable you to step forward or backward through the actions
- Save state file
- The "File > Save File > State File" menu option saves the set of commands that were used to customize the image, so the same view can be opened at a later time.
- Open state file
- Use the "File > Open File > State File" menu option to open the file at any time, and use the forward and back arrows near the upper left corner of the iCn3D window to move through the sequence of steps you took to generate the customized view of the structure.
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to load a 
to open the 
