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 iCn3D Help
 
 
 
 

BRIEF TABLE OF CONTENTS
 
  What is iCn3D?
Overview
Examples of use
gallery with live examples (separate file)
Two versions: basic, advanced (illustrations)
Where to access iCn3D
MMDB structure summary pages
Direct access via URL, examples of URLs
Download source code from GitHub
Input options
UID for single structure
Two UIDs for alignment
Open local file
Display controls
Annotated illustration
Selection Mode (toggle switch) (all, selection)
Menus
Toolbar
Shortcut Keys
3D view: Molecular Graphic
2D view: Interactions Schematic
(illustrations)
1D view: Sequences and Annotations
Command Log (illustration)
Examples of structures (illustrations)
Single structure in various file formats
Align two structures
Chemical structure
Web API
URL format
URL examples
Log of changes to iCn3D
References
Citing iCn3D
Additional references
 
 
 


BASIC VERSION of iCn3D
designed for easy integration into your own website
Thumbnail image showing the basic (simple) version of iCn3D, featuring the structure for 1HHO, human oxyhemoglobin. Click on the image to read more.
 


ADVANCED VERSION of iCn3D
many controls for viewing structures and sequences
Thumbnail image showing the advanced (full feature) version of iCn3D, featuring the structure for 1HHO, human oxyhemoglobin. Click on the image to read more.
 

 
What is iCn3D? back to top

overview | examples of how iCn3D can be used | two versions: basic & advanced

Overview back to top


iCn3D ("I see in 3D") is a WebGL-based viewer for interactive viewing of three-dimensional macromolecular structures and chemicals on the web.

There is no need to install a separate application in order to use iCn3D; you just need to use a web browser that supports . If your browser doesn't support WebGL, you might need to modify the settings in the browser to enable WebGL, or update your web browser to a newer version that supports WebGL. (See the site for more information about compatibility with various web browsers.)

iCn3D can be accessed in several ways: iCn3D has a feature-rich user interface and allows users to visualize macromolecular complexes in 3D, 2D and 1D, synchronizing user selections among the various representations. iCn3D also allows users to define custom atom sets, display custom labeling, show highlights, go back and forth to different a stage, show the 3D alignment of similar structures, share a link to their customized display, and more. A gallery with live examples demonstrates a variety of ways in which iCn3D can be used to view and analyze structures.

Although iCn3D was developed for use on the web, without the need to install a separate application, the source code is available for those who would like to run the program locally, and for those who would like to customize the code or contribute to it (read more...).


Examples of how iCn3D can be used back to top



Two versions of iCn3D back to top


iCn3D is available in two versions: basic and advanced, illustrated below (click on either image to open the corresponding live view).

Both widgets can be easily added to web pages, if desired. The basic interface has the minimum javascript code for the interface and is easy to understand. It has the basic features to change color and styles. The advanced interface has a library for the interface, many features, and is more complicated to understand. The iCn3D API documentation provides instructions for incorporating either view.

Illustrated example of the basic version of iCn3D, featuring the structure for human oxyhemoglobin, 1HHO  
  • The basic version of iCn3D provides an interactive view of a 3D structure.

  • It has the minimum javascript code for the interface and basic features such as changing color and styles.

  • Can be opened directly with a formatted URL that uses the filename "index.html" and includes the PDB ID or MMDB ID of the desired structure

  • Has a "Tools" tab, which provides basic controls for customizing the style and color of the structure

  • Designed for easy integration into your own website (instructions on how to do this are provided in the iCn3D Web API help document)

  • As an example, open a live view of the human oxyhemoglobin structure (1HHO) in the basic version of iCn3D, featured in the illustration shown here. (You can also click on the illustration to open the live view.)


Illustrated example of the advanced version of iCn3D, featuring the structure for human oxyhemoglobin, 1HHO  
  • The advanced (full feature) version of iCn3D provides an interactive view of a 3D structure and its corresponding sequence data, if desired.

  • It has a library for the interface. This version is recommended, since it has many features. It can also be implemented with a simple user interface, using URL parameters such as

  • Can be accessed by clicking the "full-featured 3D viewer" button in the "Molecular Graphic" of an MMDB structure summary page

  • Can also be opened directly by entering a formatted URL that uses the filename "full.html" and includes the PDB ID or MMDB ID of the desired structure

  • Or, you can open the advanced iCn3D home page:
    http://foodzines.com/Structure/icn3d/full.html,
    where you can use the "File" menu to retrieve a structure or open a local file

  • Has menus and buttons, which provide extensive controls for rendering the structure, viewing corresponding sequence data, and for making selections in either one

  • Enables examination of the sequence-structure relationship

  • Enables you to share the link to a customized view of a structure

    • after rendering the structure as desired, use the File > Share Link menu option to open the view in another browser tab, where which shows the complete URL to the customized view
    • from there, you can copy the complete URL and share it with others

  • Includes a command log that lists the actions you've taken on the structure

    • allows you to use the previous and next arrows beside the "File" menu to move backward and forward through the views
    • the command log can also be edited directly, acting as a command dialog box

  • Can be integrated into your own website (instructions on how to do this are provided in the iCn3D Web API help document)

  • As an example, open a live view of the human oxyhemoglobin structure (1HHO) in the advanced version of iCn3D, featured in the illustration shown here. (You can also click on the illustration to open the live view.)

 
Where to access iCn3D back to top

access iCn3D via MMDB structure summary pages | direct access via URL | download source code from GitHub

Access iCn3D via MMDB structure summary pages back to top


iCn3D can be accessed from the structure summary page for any record in the Molecular Modeling Database (MMDB).
As an example, open the MMDB summary page for human oxyhemoglobin (1HHO).
  • By default, the "molecular graphic" section of the page shows a static image of the structure
  • To view the interactive display, you can either:
  • The interactions schematic that appears beside the molecular graphic is clickable, as noted in the illustration below
    • if you load the basic version of iCn3D into the structure summary page, you can click on a molecular component in the interactions schematic to highlight the corresponding molecule in the molecular graphic

Illustrated of the molecular graphic section of the MMDB Structure summary page for human oxyhemoglobin, 1HHO. Click on the image to open the live structure summary page, where you can click the spin icon in the molecular graphic to load an interactive view of the hemoglobin structure.

The MMDB help document provides additional information about the structure summary page.


Direct access to iCn3D via URL back to top

URL to the home page for Advanced iCn3D
To open iCn3D directly, you can connect to the home page for the advanced version of iCn3D:
http://foodzines.com/Structure/icn3d/full.html
where you can use the "File" menu to retrieve a structure or open a local file.

Web API: URL format for opening structures directly in Basic or Advanced iCn3D
It is possible to directly open a structure of interest in either the basic version or advanced version of iCn3D, or to open an 3D alignment of two similar structures in the advanced version of iCn3D.

To do this, enter a URL that is formatted according to the instructions in the Web API section of this document into a web browser supports WebGL.

The URL format for opening structures directly requires that you include a base URL, specify the desired iCn3D version (basic or advanced), specify the file type you will load into iCn3D and the UID of the structure(s), and include any desired optional parameters.

The Web API section of this document also includes examples of properly formatted URLs.

A separate iCn3D Web API help document provides complete details on using the API.

Download iCn3D source code from GitHub back to top


iCn3D is WebGL-based 3D viewer that uses Three.js and jQuery. It is based on the 3D styles of and , and the surface generation of .

Although iCn3D was developed for interactive viewing of three-dimensional macromolecular structures on the web, without the need to install a separate application, the source code is available from GitHub for users who would like to install the program on their local computer, and for developers who want to customize iCn3D and/or contribute code:
  • The complete distribution copy of iCn3D can be obtained for use on your local computer from: http://foodzines.com/Structure/icn3d/icn3d-0.9.6-dev.zip. That file includes the code written by NCBI as well as the corresponding third party JavaScript libraries such as jQuery and Three.js.

  • The development version of iCn3D is available for developers who want to customize and/or contribute code to the iCn3D program. Click on the "Download ZIP" button in the upper right corner of the page to download that version, which includes only the code written at NCBI but not the corresponding third party javascript libraries like jQuery or Three.js.

 
Input Options back to top

iCn3D can accept several types of input. Details about each input option are provided below:

UID for single structure record | Two UIDs for sequence-structure or structure-structure alignment | Open a local file

Input UID for single structure record back to top


If you have the unique identifier (UID) of a publicly available structure, you can load the structure directly into iCn3D. You can do this either by:
iCn3D can retrieve and load the following types of structures, and details about each are provided below:

Loading a macromolecular structure into iCn3D:

The "File > Retrieve by ID" menu allows you to 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 data source or file format that will be loaded into iCn3D for a given structure, and are described in more detail below.

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.

Select the menu option for: For example, enter: Result:
File > Retrieve by ID > MMDB ID 1HHO (alphanumeric identifier)
or
1183 (integer assigned by MMDB)
iCn3D will load a structure record from NCBI's Molecular Modeling Database (MMDB), which shows the default biological unit of the structure.

The MMDB file format also provides the option of displaying an interactions schematic, which shows the molecular components of the structure and the interactions among them. This schematic is available only when a structure is loaded in MMDB file format because it is generated as part of MMDB data processing.

As an example, see the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an MMDB file. You can click on the illustration to open the live view of the MMDB file in iCn3D.

File > Retrieve by ID > PDB ID 1HHO (alphanumeric identifier) iCn3D will load the record from the , in , which shows the asymmetric unit of the structure, where xxxx is the structure's UID.

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

As an example, see the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an PDB file. You can click on the illustration to open the live view of the PDB file in iCn3D.
File > Retrieve by ID > OPM PDB ID 1HHO (alphanumeric identifier) iCn3D will display membranes for transmembrane proteins using data from .

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

As an example, see the iCn3D display for 6JXR (Structural basis of assembly of the human T cell receptor-CD3 complex).
File > Retrieve by ID > mmCIF ID 1HHO (alphanumeric identifier) iCn3D will load the record from the , in , which shows the asymmetric unit of the structure, where xxxx is the structure's UID. (mmCIF is the abbreviation for macromolecular crystallographic information file.)

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

As an example, see the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an mmCIF file. You can click on the illustration to open the live view of the mmCIF file in iCn3D.
File > Retrieve by ID > MMTF ID 1HHO (alphanumeric identifier) iCn3D will load the record from the , in , which is a new compact binary format to transmit and store biomolecular structural data quickly and accurately. The MMTF format shows the asymmetric unit of the structure, and xxxx represents the structure's UID.

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

As an example, open the live view of the MMTF file in iCn3D for 1HHO (human oxyhemoglobin) and its corresponding sequence data.
Loading a macromolecular structure that contains a specific protein sequence as a component into iCn3D:

The "File > Retrieve by ID > gi" menu option allows you to specify the unique identifier (GI number) for any protein or nucleotide sequence present in a structure. iCn3D then loads the MMDB file for that structure. For example, open the advanced version of iCn3D, and then:

Select the menu option for: Enter: Result:
File > Retrieve by ID > gi 229985
or
229986

(protein sequence identifier, in the form of an integer, for any protein that is a component of a 3D structure record. The protein GIs shown in this example are components of the human oxyhemoglobin structure, 1HHO)
iCn3D will load the MMDB file for the structure that contains the protein you specified, which displays the biological unit of the structure.

In this case, iCn3D will load the structure for human oxyhemoglobin, 1HHO. Protein A of that structure has GI number 229985, and protein B has GI number 229986.

See the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an MMDB file. You can click on the illustration to open the live view in iCn3D.
Loading a chemical or other small molecule (e.g. peptide) into iCn3D:

The "File > Retrieve by ID > CID" menu option allows you to specify the unique identifier () of a chemical or other small molecule (e.g., peptide) from the the PubChem Compound database. For example, open the advanced version of iCn3D and then:

Select the menu option for: Enter: Result:
File > Retrieve by ID > CID 2244
(PubChem compound identifier for aspirin)
iCn3D will load the 3D structure of aspirin (CID 2244), from the PubChem Compound database.

See the annotated illustration of aspirin loaded into iCn3D. You can click on the illustration to open the live view in iCn3D.

Input two UIDs to view a sequence-structure or structure-structure alignment back to top


If you have the PDB IDs or MMDB IDs of two structures that have been found to be similar by VAST, you can load their precomputed 3D alignment directly into iCn3D. You can do this either by: Separate sections of this document: (1) describe other types of alignments that can be loaded into iCn3D using the "File > Align" menu options (e.g., Sequence to Structure, Chain to Chain), and (2) provide additional details about viewing the alignment of two simlar structures.

Loading an alignment of two similar structures into iCn3D:

For example, open the advanced version of iCn3D, and then:
Select the menu option for: Enter: Result:
File > Align > Structure to Structure 1HHO
and
4N7N (PDB IDs)

or

1183
and
118837 (MMDB IDs)
iCn3D will load the 3D alignment of two macromolecular structures, which was precomputed by VAST.

Note that buttons in the dialog box allow you to specify which type of alignment to display: all matching molecules superposed (the initial alignment calculated by VAST+), or the invariant substructure superposed (the refined alignment calculated by VAST+).

A separate section of this document provides illustrated examples of each type of alignment, using the structures shown here: 1HHO (human oxyhemoglobin) and 4N7N (human deoxyhemoglobin). You can click on either illustration to open the corresponding live view in iCn3D.

The VAST+ help document provides additional details about the algorithm used to generate 3D alignments, describes the differences between the initial alignment (all matching molecules superposed) and the refined alignment (invariant substructure superposed), along with links to examples of each.


Open local file back to top


To display a 3D structure that is stored as a file on your local computer, open the advanced version of iCn3D (http://foodzines.com/Structure/icn3d/full.html) and use the "File > Open File" menu option. iCn3D can open the types of files listed below.

Note that a single structure might have slightly different appearances in iCn3D, depending upon the file type that is loaded into iCn3D. For example, some file types show a structure's biological unit, while others show its asymmetric unit. See the annotated illustrations of human oxyhemoglobin (1HHO) loaded into iCn3D in 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 the corresponding live view.

For example, open the advanced version of iCn3D, then:
Select the menu option for: Select file type: Comments:
File > Open File PDB File The traditional , by the , used for representing macromolecular structures.

As an example, see the annotated illustration of the human oxyhemoglobin structure (1HHO) and its corresponding sequence data loaded into iCn3D as an PDB file. You can click on the illustration to open the live view in iCn3D.
mmCIF File , used for representing macromolecular structures.

As an example, see the annotated illustration of the human oxyhemoglobin structure (1HHO) and its corresponding sequence data loaded into iCn3D as an mmCIF file. You can click on the illustration to open the live view in iCn3D.
Mol2 File A Mol2 file (.mol2) is a "complete, portable representation of a SYBYL molecule. It is an ASCII file which contains all the information needed to reconstruct a SYBYL molecule," and is a representation of small molecule such as a chemical.

SDF File "SDF" stands for "spatial data file" or "structure-data file" It is one of a family of chemical-data file formats intended especially for structural information.

Chemical records from the PubChem Compound database can be saved on your computer in SDF format.

Details of the PubChem Data Specifications for SDF files are provided in files on the PubChem FTP site:
SD Field Descriptions (PDF file)
SD Field Descriptions (text file)

See the annotated illustration of aspirin (CID 2244) loaded into iCn3D as an SDF file. You can click on the illustration to open the live view in iCn3D.
XYZ File An is a plain text format for storing molecular coordinates. It is mainly used for chemicals, but can also be used for macromolecular structures such such as proteins.

URL (Same Host) loads a structure record from a URL in the same host into iCn3D. URLs in different hosts may be accessible, depending on the setting of the hosts.

This feature is useful, for example, if you have files with your own annotations on your own server, and you want to view them in iCn3D hosted in your pages.

Use the "File > Open File > URL (Same Host)" menu option to open a dialog box that allows you to:
  • select a file type:
    pdb, sdf, mol2, or xyz.
    If you don't specify a type, iCn3D will assume the file type is pdb (default).

  • enter a URL, for example:

    to obtain that file from the specified web server and load it into iCN3D.

Note:

If you open a blank window of the advanced version of iCn3D by connecting to http://foodzines.com/Structure/icn3d/full.html, and then select the "File > Open File > URL (Same Host)" menu option, the URL can be entered without encoding (as in the example URL above: http://files.rcsb.org/view/1gpk.pdb).

However, if you use the iCn3D Web API and input the URL as a parameter, then the URL of the web server that contains the file you want to load must be encoded with encodeURIComponent. For example, you would use %2F to represent each forward slash in the URL of the web server that contains the desired structure file, e.g., http://foodzines.com/Structure/icn3d/full.html?type=pdb&url=https%3A%2F%2Ffiles.rcsb.org%2Fview%2F1gpk.pdb
(read more...)

State/Script File A "State/Script" file is a plain text file that is saved by iCn3D when you use the menu option for "File > Save File > State File" in the advanced version of iCn3D. You can save a state file while viewing any type of structure (macromolecular structure or chemical) in the advanced version of iCn3D.

The "File > Save File > State File" function captures, into a plain text file, all of the lines from the iCn3D command log that were used to display the structure. It therefore allows you to open the same view of the structure at a later time.

This function is particularly useful if you have customized the display of the structure. For example, if you have rendered the structure using colors/styles of your choosing, labeled and/or highlighted selected regions of the structure, etc., simply use the menu option for "File > Save File > State File" to capture the commands you used. Then, you can open the same view at a later time by using the menu option for "File > Open File > State/Script File."

Because the state file captures all of the steps you took in customizing the display of the structure, you can use the "previous" and "next" arrows to step backward and forward through the steps you took, once you have opened the file in iCn3D.

A sample state file, for human Abl2 kinase with Gleevec bound (3GVU), is provided here. It is a plain text file that contains commands that were used to customize the molecule's display, highlighting the residues that are associated with ATP-binding (according to CDD annotation of conserved sites). If you save the file to your computer, you can then open advanced version of iCn3D and use the menu option for "File > Open File > State/Script File" to interactively view the 3D structure, and to further customize the display, view corresponding sequence data, etc.

Selection File A "Selection" file is a plain text file that is saved by iCn3D when you use the menu option for "File > Save File > Selection File" in the advanced version of iCn3D. You can save a selection file while viewing any type of structure (macromolecular structure or chemical) in the advanced version of iCn3D.

This function is particularly useful if you have selected/highlighted regions of interest the structure, and want to preserve those selections. For example, after selecting molecules/atoms/ligands/etc. in a structure of interest, simply use the menu option for "File > Save File > Selection File" to capture the commands you used. Then, you can open the same view at a later time by using the menu option for "File > Open File > Selection File."

A sample selection file, for Rhodobacter capsulatus porin(2POR), is provided here. It is a plain text file that contains commands that were used to select all calcium ions (by opening the "Custom" menu and selecting "ions"), and then to select all amino acids within 5 Angstroms of the calcium ions (by choosing the menu option for "Select > By Distance > sphere with a radius of 5 Angstroms"). If you save the file to your computer, you can then open advanced version of iCn3D and use the menu option for "File > Open File > Selection File" to interactively view the 3D structure, and to further customize the display, view corresponding sequence data, etc.


 
Display Controls back to top

Display Controls in the advanced version of iCn3D (annotated illustration) back to top


Annotated illustration of the controls available in the advanced (full feature) version of iCn3D, featuring 1HHO (human oxyhemoglobin) as the example structure


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.


Selection Mode (toggle switch): "all" or "selection" back to top

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."

  • When the selection mode toggle switch in the upper left corner of iCn3D is set to All, the style, color, and surface menu options will be applied to all atoms in the structure. 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.

  • When the selection mode toggle switch in the upper left corner of iCn3D is set to Selection, the style, color, and surface menu options will be applied only to selected atoms in the structure. 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).

Menus (complete set of controls) back to top

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 back to top

    • 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.

      • 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.

        • Sequence to Structure - Enter (1) the UID of a protein sequence (or enter the protein's sequence data in FASTA format), and (2) the UID of a protein sequence that has been identified by as having a similar sequence to your query and being present in a resolved 3D structure record.
          (For example, display the iCn3D alignment of the query protein NP_001108451.1 against the sequence-similar protein 1TSR_A (1TSR structure, protein chain A). To see additional examples, use Protein BLAST to enter a query protein sequence of interest and search it against the Protein Data Bank proteins (pdb) database.)

        • Structure to Structure - 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.

        • Chain to Chain - Enter the UIDs of two structure-based proteins that have been found to be similar by VAST to open an interactive view of their 3D alignment. For example, display the .

      • 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 back to top
    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 back to top
    • 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 ().
        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 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 back to top
    • 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 back to top
    • 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 back to top
    • 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 back to top
    • 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
    • - 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


Toolbar (shortcuts to a subset of common controls) back to top

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.)

Shortcut Keys back to top

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


3D view: Molecular Graphic back to top

file format affects appearance | condensed view for very large structures | customize appearance | save state | share link
  • File format affects appearance of molecular graphic


  • 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


2D view: Interactions Schematic back to top

 
An interactions schematic shows the molecular components of the structure and the interactions among them (illustrated examples are below). This schematic is available only when a structure is loaded in MMDB file format because it is generated as part of MMDB data processing. The method by which the schematic is generated is described in the MMDB help document.
(Structures that only have alpha carbons, and no side chains, do not show interactions. In those cases, the schematic just shows the structure's molecular components (proteins, nucleotide sequences, and ligands) as free floating (disconnected) icons.)
Interactions schematic for human oxyhemoglobin (1HHO)  
  • Molecular components of the structure can include the following

      Proteins, if present, are shown as circles: example of circle icons used to depict proteins  etc.  
      Nucleotide sequences (DNA, RNA), if present, are shown as squares: example of square icons used to depict nucleotide sequences  etc.  
      Chemicals, if present, are shown as diamonds: example of diamond shaped icons used to depict chemicals etc.  
      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.)
    example of parallelogram icons used to depict non-standard biopolymers  etc.  
      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, Example of circle icons with alphanumeric labels used to depict protein molecules generated by applying transformations from crystallographic symmetry. or Example of square icons with alphanumeric labels used to depict nucleotide sequences generated by applying transformations from crystallographic symmetry.), 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.

  • 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.

Structure of 1HHO (human oxyhemoglobin) loaded into iCn3D in MMDB file format, with protein A selected in the interactions schematic, highlighting that protein all three views: structure, interactions schematic, and sequence window.


Structure of 1HHO (human oxyhemoglobin) loaded into iCn3D in MMDB file format, highlighting the residues in protein B that interact with protein A. These residues were selected by clicking on the line in the interaction schematic that connects the two proteins, with the click action taking place on the half of the line that is closest to protein B.


1D view: Sequences and Annotations back to top

file format affects sequence data displayed | select on sequence data | save selection | clear selection | add track | custom color
  • File format affects sequence data displayed


  • 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.


Command Log back to top

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.

Illustration showing the structure of 1HHO (human oxyhemoglobin) loaded into the advanced version of iCn3D, which includes a command log that records the steps you have taken on the structure. The File/Save File/State File menu option can be used to save the set of commands that were used to customize the view of the structure, so the same view can be opened at a later time.


 
Examples of Structures back to top

Single structure loaded in various file formats back to top


When a single structure is viewed in iCn3D, the data that are displayed in the 3D structure window and corresponding sequence window depend on the file format that is loaded into iCn3D, as described and shown in the illustrations below.

You can specify the desired file format by using the "File > Retrieve by ID" menu option in the advanced (full feature) version of iCn3D, or by formatting a URL that includes the desired file type.

It is also possible to open a local structure file that you have stored on your computer in any one of several file formats.

As an example, the structure of human oxyhemoglobin (1HHO) is shown in various file formats in the illustrations below:

MMDB file example MMDB is the abbreviation for Molecular Modeling Database. MMDB contains experimentally determined three-dimensional structures from the . The data processing procedure at MMDB results in the addition of a number of features which facilitate computation on the data and link them to many other types of data in NCBI's Entrez retrieval system.

When a structure in loaded in MMDB file format, iCn3D displays the default biological unit of the structure and an interactions schematic. The corresponding sequence view window includes sequence data provided by the author, as well as those generated by applying transformations from crystallographic symmetry (if the asymmetric unit represents only a portion of the biological unit) and bound chemicals.
As an example, see the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an MMDB file. You can click on the illustration to open the live view of the MMDB file in iCn3D.
PDB file example PDB is the abbreviation for . The displays the asymmetric unit of the structure. The corresponding sequence view window includes sequence data provided by the author
As an example, see the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an PDB file. You can click on the illustration to open the live view of the PDB file in iCn3D.
mmCIF file example mmCIF is the abbreviation for macromolecular crystallographic information file. The displays the asymmetric unit of the structure. The corresponding sequence view window includes sequence data provided by the author, as well as bound chemicals.
As an example, see the annotated illustration of 1HHO (human oxyhemoglobin) and its corresponding sequence data loaded into iCn3D as an mmCIF file. You can click on the illustration to open the live view of the mmCIF file in iCn3D.
MMTF file example MMTF is the abbreviation for file format, which is a new compact binary format to transmit and store biomolecular structural data quickly and accurately. The displays the asymmetric unit of the structure. The corresponding sequence view window includes sequence data provided by the author, as well as bound chemicals.
As an example, open the live view of the MMTF file in iCn3D for 1HHO (human oxyhemoglobin) and its corresponding sequence data.


Example of a single structure, 1HHO (human oxyhemoglobin), imported into iCn3D in MMDB file format, which shows the default biological unit, along with an interaction schematic and corresponding sequence data. Click on the image to open the live view in iCn3D.




Example of a single structure, 1HHO (human oxyhemoglobin), imported into iCn3D in PDB file format, which shows the asymmetric unit, along with corresponding sequence data. Click on the image to open the live view in iCn3D.




Example of a single structure, 1HHO (human oxyhemoglobin), imported into iCn3D in mmCIF file format, which shows the asymmetric unit, along with corresponding sequence data. Click on the image to open the live view in iCn3D.




Alignment of two similar structures back to top


iCn3D can show the alignment of similar 3D structures by providing two PDB IDs or MMDB IDs, whose alignment has been pre-calculated at NCBI by the VAST algorithm.

As an example, the illustrations below show the:
initial alignment of 1HHO (human oxyhemoglobin) and 4N7N (human deoxyhemoglobin): all matching molecules superposed
refined alignment of 1HHO (human oxyhemoglobin) and 4N7N (human deoxyhemoglobin): invariant substructure superposed

You can open an alignment in any of the following ways:
  • open a blank window of the advanced version of iCn3D by connecting to http://foodzines.com/Structure/icn3d/full.html, and use the "File > Align" menu option to specify the PBD IDs or MMDB IDs of two structures that have been found to be similar by the VAST algorithm.

  • format a URL to open the desired structures directly, specifying "align=xxxx,xxxx" as the file type, where xxxx,xxxx are the PBD IDs or MMDB IDs of two structures that have been found to be similar by the VAST algorithm. If desired, use the optional parameter of "atype" to indicate the alignment type you would like to view: initial alignment (invariant substructure superposed) or the refined alignment (all matching molecules superposed).

  • use VAST+ to enter the PDB ID or MMDB ID of a query structure. On the VAST+ results page, click on the "+" to the left of any matching structure to open a detailed view of the hit. In the detailed view, click on the "Visualize 3D structure superposition" button, and select "iCn3D (Web)". By default, iCn3D will show the refined alignment (invariant substructure superposed). To view the initial alignment (all matching molecules superposed), you can either use the "File > Align" menu option to open a dialog box that gives you a choice of superposition, or you can change the value of the "atype" parameter in the URL from "1" to "0".
The VAST+ help document provides additional details about the algorithm used to generate 3D alignments and describes the differences between the initial alignment (all matching molecules superposed) and the refined alignment (invariant substructure superposed).


Example of a 3D alignment of two similar structures in iCn3D, featuring the initial alignment of 1HHO (human oxyhemoglobin) and 4N7N (human deoxyhemoglobin), with all matching molecules superposed. Click on the image to open the live view in iCn3D.




Example of a 3D alignment of two similar structures in iCn3D, featuring the refined alignment of 1HHO (human oxyhemoglobin) and 4N7N (human deoxyhemoglobin), with an invariant substructure superposed. Click on the image to open the live view in iCn3D.




Chemical structure back to top


In addition to displaying macromolecular structures, iCn3D can also display chemical structures, as shown in the illustrated example below, which shows the 3D structure of the PubChem Compound record for aspirin (CID 2244).

To load a chemical structure into iCn3D:

Example of the three-dimensional structure of a PubChem Compound, CID 2244 (aspirin), displayed in iCn3D. Click on the image to open the live view in iCn3D.




 
Web API: URL format for displaying structures in iCn3D back to top

URL format for opening structures directly | base URL | specify iCn3D version | specify file type and UID | optional parameters
Examples of properly formatted URLs
URL Format for opening structures directly in Basic or Advanced iCn3D back to top

It is possible to directly open a structure of interest in either the basic version or advanced version of iCn3D, or to open an 3D alignment of two similar structures in the advanced version of iCn3D.

To do this, enter a URL that is formatted according to the instructions below into a web browser supports WebGL.

The URL format for opening structures directly requires that you include a base URL, specify the desired iCn3D version (basic or advanced), specify the file type you will load into iCn3D and the UID of the structure(s), and include any desired optional parameters.

Examples of properly formatted URLs are included within the table below, and also listed beneath the table (for convenience).

A separate iCn3D Web API help document provides complete details on using the API.

Base URL http://foodzines.com/Structure/icn3d/
iCn3D version
Specify which version of iCn3D you would like to open, followed by question mark:
index.html? opens the basic version of iCn3D
full.html? opens the advanced version of iCn3D
File type and
unique identifier (UID)
of the desired structure.
Structure records are available in various file types, and iCn3D can read the file types below. After you specify which version of iCn3D you want to open (basic or advanced), indicate the type of file you would like to load (by specifying mmdbid, pdbid, mmcifid, gi, cid), followed by the UID of the desired structure.

Note that a single structure might have slightly different appearances in iCn3D, depending upon the file type that is loaded into iCn3D. For example, some file types show a structure's biological unit, while others show its asymmetric unit. See the annotated illustrations of human oxyhemoglobin (1HHO) loaded into iCn3D in different 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.
mmdbid=xxxx loads a structure record from NCBI's Molecular Modeling Database (MMDB), which shows the default biological unit of the structure, where xxxx is the structure's UID.

Structures in MMDB are derived from the and go through a data processing pipeline to enhance the records with value-added features such as explicit chemical graphs, computationally identified 3D domains (compact substructures), links to similar 3D structures (as determined by the Vector Alignment Search Tool (VAST) algorithm), as well as links to literature, similar sequences, information about chemicals bound to the structures, and more.

The UID can be entered as the MMDB ID (an integer assigned by NCBI) or the PDB ID (an alphanumeric string assigned by PDB).

For example:

http://foodzines.com/Structure/icn3d/index.html?mmdbid=1183 or
http://foodzines.com/Structure/icn3d/index.html?mmdbid=1hho
will open the MMDB file for the human oxyhemoglobin structure (1HHO) in the basic version of iCn3D.

and:

http://foodzines.com/Structure/icn3d/full.html?mmdbid=1183   or
http://foodzines.com/Structure/icn3d/full.html?mmdbid=1hho
will open the MMDB file for the human oxyhemoglobin structure (1HHO) in the advanced version of iCn3D.

A separate section of this document provides an annotated illustration of the structure and its corresponding sequence data loaded into advanced iCn3D as an MMDB file. You can click on the illustration to open the live view in iCn3D.

pbid=xxxx loads a record from the , in , which shows the asymmetric unit of the structure, where xxxx is the structure's UID.

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

For example:

http://foodzines.com/Structure/icn3d/full.html?pdbid=1hho

will open the PDB file for the human oxyhemoglobin structure (1HHO) in the advanced version of iCn3D.

A separate section of this document provides an annotated illustration of the structure and its corresponding sequence data loaded into iCn3D as an PDB file. You can click on the illustration to open the live view in iCn3D.

mmcifid=xxxx loads a record from the , in , which shows the asymmetric unit of the structure, where xxxx is the structure's UID. (mmCIF is the abbreviation for macromolecular crystallographic information file.)

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

For example:

http://foodzines.com/Structure/icn3d/full.html?mmcifid=1hho
will open the mmCIF file for the human oxyhemoglobin structure (1HHO) in the advanced version of iCn3D.

A separate section of this document provides an annotated illustration of the structure and its corresponding sequence data loaded into iCn3D as an mmCIF file. You can click on the illustration to open the live view in iCn3D.

mmtfid=xxxx loads a record from the , in , which is a new compact binary format to transmit and store biomolecular structural data quickly and accurately. The MMTF format shows the asymmetric unit of the structure, and xxxx represents the structure's UID.

The UID should be entered as the PDB ID (the alphanumeric string assigned by PDB).

For example:

http://foodzines.com/Structure/icn3d/full.html?mmtfid=1hho
will open the MMTF file for the human oxyhemoglobin structure (1HHO) in the advanced version of iCn3D.

url=xxxx loads a structure record from a URL in the same host into iCn3D. URLs in different hosts may be accessible, depending on the setting of the hosts.

This feature is useful, for example, if you have files with your own annotations on your own server, and you want to view them in iCn3D hosted in your pages.

Be sure to include the "type" parameter, which indicates the type of file you will load, before specifying the URL of the server from which you want to obtain the structure file.

Values for "type" can be:
pdb, sdf, mol2, or xyz.
If you don't specify a type, iCn3D will assume the file type is pdb (default).

The URL of the server should be encoded with encodeURIComponent in javascript (for example, use "%2F" to represent each forward slash in the URL of the server from which you would like to obtain the structure file).

For example:

http://foodzines.com/Structure/icn3d/full.html?
type=pdb&url=https%3A%2F%2Ffiles.rcsb.org%2Fview%2F1gpk.pdb


will open the for the Structure of Acetylcholinesterase Complex With (+)-huperzine a at 2.1a Resolution (1GPK) in the advanced version of iCn3D.

Note that the URL of the server that has the structure file is encoded with encodeURIComponent in javascript (using "%2F" to represent each forward slash in the URL of the server from which the structure file will be obtained). So the value of the url paramater is written as:
https%3A%2F%2Ffiles.rcsb.org%2Fview%2F1gpk.pdb
rather than as:
http://files.rcsb.org/view/1gpk.pdb

Structure records that contain specific protein and/or nucleotide molecules can be retrieved by specifying the unique identifier (GI number) of the protein or nucleotide sequence of interest:
gi=xxxx specifies the unique identifier of a protein or nucleotide sequence contained in a structure record in NCBI's Molecular Modeling Database (MMDB), and loads the default biological unit of the structure.

The UID should be entered as a GI number, which is an integer assigned by NCBI that uniquely identifies a protein or nucleotide sequence.

For example, the human oxyhemoglobin structure record (1HHO) contains two protein sequences that were provided by the author. Protein chain A has the GI number 229985 and protein chain B has the GI number 229986. Therefore, either one of the following URLs:

http://foodzines.com/Structure/icn3d/full.html?gi=229985   OR
http://foodzines.com/Structure/icn3d/full.html?gi=229986

will open the MMDB file for the structure (human oxyhemoglobin structure, 1HHO) that contains the protein you specified, in the advanced version of iCn3D.
The 3D structures of chemicals can be displayed in iCn3D:
cid=xxxx loads the 3D structure of the PubChem Compound, where xxxx is the compound's UID.

The UID should be entered as a PubChem compound identifier ().

For example:

http://foodzines.com/Structure/icn3d/full.html?cid=2244

will open the 3D structure of aspirin (CID 2244) from the PubChem Compound database, in the advanced version of iCn3D.

A separate section of this document provides an annotated illustration of the structure and its corresponding sequence data loaded into iCn3D as an PDB file. You can click on the illustration to open the live view in iCn3D.

Alignments of similar macromolecular structures can be viewed in iCn3D. To do this, you can use "align" as the input type, followed by the MMDB IDs, or the PDB IDs, of two structures that have been found to be similar by VAST or VAST+. iCn3D will then load the pre-computed alignment data from VAST and display their superposition.
align=xxxx,xxxx loads the 3D alignment of two macromolecular structures.

The UIDs can be entered as the PDB IDs, or the MMDB IDs, of two structures that have been found to be similar by VAST or VAST+.

For example, either:
http://foodzines.com/Structure/icn3d/full.html?align=1hho,4n7n   OR
http://foodzines.com/Structure/icn3d/full.html?align=1183,118837
will load the pre-computed alignment data of human oxyhemoglobin (1HHO) and human deoxyhemoglobin (4N7N) from VAST and display their superposition in the advanced version of iCn3D.

A separate section of this document provides an annotated illustrations of the alignment and the corresponding sequence data loaded into iCn3D. You can click on the illustrations to open the live view in iCn3D.


Note: An optional parameter of atype can be used to specify which type of alignment to display. Use a value of "0" to show the all matching molecules superposed (the initial alignment calculated by VAST+), or a value of "1" to show the invariant substructure superposed (the refined alignment calculated by VAST+). The default is "0".

The VAST+ help document provides additional details about the algorithm used to generate 3D alignments, describes the differences between the initial alignment (all matching molecules superposed) and the refined alignment (invariant substructure superposed), and links to examples of each.

Optional parameters The iCn3D API help document lists the complete set of controls to customize the display of a structure. Some of the controls include the following optional parameters, which can be included in a URL:
width Width of the structure image. It can be percentage such as '50%' (written as "50%25", where "%25" is the hexadecimal code for the percent symbol), or as a pixel values such as 400. The default is '100%'.

For example:
http://foodzines.com/Structure/icn3d/full.html?mmdbid=1hho&width=50%25
will display the human oxyhemoglobin structure (1HHO) as an image that is 50% of the width of your browser window.
height Height of the structure image. It can be percentage such as '50%' (written as "50%25", where "%25" is the hexadecimal code for the percent symbol), or as a pixel values such as 400. The default is '100%'.

For example:
http://foodzines.com/Structure/icn3d/full.html?mmdbid=1hho&height=50%25
will display the human oxyhemoglobin structure (1HHO) as an image that is 50% of the height of your browser window.
resize Set "true" or "1" in order to resize the image when the container is resized. The default is "true".
rotate Set "right", "left", "up", or "down" to rotate the structure when it is displayed at the beginning. The default is "right".
showmenu Set "true" or "1" to show the menus and buttons at the top of the structure canvas. The default is "true".

This paramater is available only in the advanced version of iCn3D (that is, it can only be used in URLs that specify "full.html" as the iCn3D version).
show2d Set "true" or "1" to show the interactions schematic (2D view of the structure). The default is "false".

This paramater is available only when a structure is loaded into iCn3D in
MMDB file format because the interactions schematic is generated as part of MMDB data processing.

That is, the "show2D" paramater can be used only when the file type and unique identifier are specified as "mmdbid=xxxx", where xxxx can be either the numeric identifier that MMDB assigns to a structure record, or the alphanumeric PDB ID.)

A separate section of this document provides details about the interactions schematic and its features and functions.

showseq
(deprecated;
replaced by "showanno")
Set "true" or "1" to show the sequence window. The default is "false".

This paramater is available only in the advanced version of iCn3D (that is, it can only be used in URLs that specify "full.html" as the iCn3D version).

The "showseq" parameter has been deprecated because it has been replaced by the "showanno" parameter, as of iCn3D 2.0 (released April 17, 2018).
showanno Set "true" or "1" to show the "Sequence and Annotations" window. The default is "false".

This paramater is available only in the advanced version of iCn3D (that is, it can only be used in URLs that specify "full.html" as the iCn3D version).

The "showanno" parameter first became available in iCn3D 2.0 (released April 17, 2018) and replaces the previous "showseq" parameter.
showalignseq Set "true" or "1" to show the aligned sequence window. The default is "false".

Note:

This paramater is available only in the advanced version of iCn3D (that is, it can only be used in URLs that specify "full.html" as the iCn3D version), and only when the type of input file is "align."

The sequence alignment is based on the correlation of the 3D structures (i.e., the common spatial position of amino acids). Therefore, these views do not necessarily represent alignments of evolutionarily conserved sequence blocks. However, the 3D alignments often coincide with evolutionarily conserved sequence blocks. The VAST+ help document provides additional details about sequence alignments.
atype The "atype" parameter is used to specify the alignment type to display when you are viewing the 3D alignment of two similar structures. Use a value of "0" to show the initial alignment (all matching molecules superposed), or a value of "1" to show the refined alignment (invariant substructure superposed). The default is "0".

A separate section of this document provides additional details about viewing the alignment of two simlar structures. As an example, it includes an annotated illustration of the initial alignment, and an annotated illustration of the refined alignment, between 1HHO (human oxyhemoglobin) and 4N7N (human deoxyhemoglobin). You can click on either illustration to open the corresponding live view in iCn3D.

The VAST+ help document provides additional details about the algorithm used to generate 3D alignments, describes the differences between the initial alignment and refined alignment , along with links to examples of each.

This paramater is available only in the advanced version of iCn3D (that is, it can only be used in URLs that specify "full.html" as the iCn3D version), and only when the type of input file is "align."
command Commands that customize the display of the structure can also be included in the url by attaching the "command" parameter Several commands can be concatenated with the separator ";". (An alternative way to custimize the display of a structure is to use the command log in the advanced iCn3D display.)

This paramater is available only in the advanced version of iCn3D (that is, it can only be used in URLs that specify "full.html" as the iCn3D version).

For example:

http://foodzines.com/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


will generate a customized display of the crystal structure of human Abl2 in complex with Gleevec (3GVU).



Examples of properly formatted URLs back to top

Below are some examples of URLs that will open a structure of interest directly in the basic version or advanced version of iCn3D (if your web browser supports WebGL):

 
Log of Changes to iCn3D back to top
Below are some highlights of changes to iCn3D, such as the release of new versions. A more detailed change log is provided in the iCn3D Web API Help Document.
 
21 April 2020 iCn3D 2.15.0 was released on NCBI web servers and on GitHub (). To view the updated web application, retrieve any structure of interest from the Molecular Modeling Database (MMDB), open its structure summary page, and click the button for "full-featured 3D viewer" in the molecular graphic. For example, retrieve structures that contain the term "SARS-COV-2", click on any structure of interest to open its summary page, then follow the link for "full-featured 3D viewer." Alternatively, open iCn3D and use the "File" menu to retrieve a structure by its ID (for example, enter 2DD8 to load the crystal structure of Sars-Cov Spike Receptor-Binding Domain Complexed With Neutralizing Antibody) or to open a structure file on your local computer. A gallery with live examples demonstrates a variety of ways in which iCn3D can be used to view and analyze structures. The iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page.

The gallery with live examples now includes COVID-19-related structures:
  • .
  • .
  • .
  • .
New features in this iCn3D release include the ability to:
  • Apply custom colors to individual residues by using the iCn3D menu option for "Color > Residue > Custom."
  • Add "Custom Color" for any chain in the "Sequences & Annotations" window.
  • Add multiple sequence alignments as tracks when clicking "Add Track" in the "Sequences & Annotations" window.
  • Show the same structure "Side by Side" in two views in the "View" menu. Each view has the same orientation, but can have an independent 3D display. One example is shown in the gallery, where each view shows one of the aligned structures.
  • 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.
    For example, some chains, such as 6ACK_C and 6M0J_E don't align well using dynamic alignment. Using the "Realign" function, you can select those two chains, which are then aligned based on their sequence data. The 3D coordinates of the residues in the sequence alignment are then used to generate a new structure alignment.
  • The Change Log section of the iCn3D Web API help document lists additional enhancements that have been made to iCn3D since its original release.
 
05 December 2019 iCn3D 2.10.0 was released on NCBI web servers and on GitHub (). To view the updated web application, retrieve any structure of interest from the Molecular Modeling Database (MMDB), open its structure summary page, and follow the link for "full-featured 3D viewer" in the molecular graphic. Alternatively, open iCn3D and use the "File" menu to retrieve a structure by its ID, or to open a structure file on your local computer. A gallery with live examples demonstrates a variety of ways in which iCn3D can be used to view and analyze structures. The iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page.

New features in this release include:
  • Show each hydrogen bond and contact in 3D using the menu "View > H-Bonds & Interactions".
  • Display membranes for transmembrane proteins using data from . The feature is at "File > Retrieve by ID > OPM PDB ID."
  • Display/output salt bridges; color helices and sheets with spectrum in the menu "Color > Secondary > Spectrum".
  • Enabled the mobile style menu with the URL parameter "mobilemenu=1".
  • Added "Label Scale" in the View menu to scale all labels.
  • Improved the display of binding sites with fog and slab.
  • Align any sequence to a hit structure by clicking "Align > Sequence to Structure" in the File menu.
  • The Change Log section of the iCn3D Web API help document lists additional enhancements that have been made to iCn3D since its original release.
31 January 2019 iCn3D 2.5.0 was released on NCBI web servers and on GitHub (). To view the updated web application, see the example structures below, or use iCn3D's "File" menu to retrieve a structure by its ID or to open a structure file on your local computer. The iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page.

New features in this release include:
  • Electron microscopy (EM) maps can now be displayed for any subset of a structure that was determined by EM (example: 6ENY), to supplement the electron density maps that became available in iCn3D 2.4.0 for structures determined by X-ray crystallography (example: 3GVU).
  • A new annotation, Disulfide Bonds, is now available in the Sequences and Annotations window.
  • Non-standard biopolymers, such as nucleotide or protein sequences that contain a large percentage of non-standard residues, are now displayed as parallelograms in iCn3D's 2D window (interactions schematic). As an example, open the structure for 4GLS in iCn3D. Click on any icon in the interactions schematic to highlight the corresponding molecule in the 3D window (molecular graphic) and to display only that molecule in the 1D window (sequences and annotations). Use Control+click to highlight multiple molecules in the 2D and 3D windows, and to show all of the selected molecues in the 1D view.
  • Additional enhancements are described in the change log section of the Web API help document.
17 APR 2018 iCn3D 2.0 was released on NCBI web servers and on GitHub (). As an example of the updated web application As an example of the updated web application, open the structure for 1TUP: Tumor Suppressor P53 Complexed With Dna on the web, or open a blank iCn3D window and use the "File" menu to retrieve a structure by its ID or to open a structure file on your local computer. An iCn3D Web APIs document describes how to use the iCn3D structure viewer in your own web page.

New features in this release include:

  • A new "Sequences and Annotations" window is accessible from the iCn3D "Windows" menu, and has replaced the previous "Sequences" window.
    • A variety of biological annotations are now available, such as clinically significant sequence variations (ClinVar), single nucleotide polymorphisms (SNPs), 3D domains, conserved domains, functional sites, interaction interfaces, and more, and can be viewed on both the sequence data and the corresponding 3D structure.
    • As an example, open a view of the 1TUP: Tumor Suppressor P53 Complexed With DNA, customized to display ClinVar data and functional sites in the "Sequences and Annotations window."
    • The "Summary" tab in the "Sequences and Annotations" window shows a graphical summary of the annotations you choose to view. Click the name of an annotation track (e.g., ClinVar) to highlight all annotations from that track on the corresponding 3D structure.
    • The "Details" tab shows the annotations mapped onto the sequence data. Click on individual residues in the sequence to view their position in the 3D, and mouse over the annotations in the "Sequences and Annotations" window to read more about the individual annotations and/or link to related information in other databases.
  • 3D printing is now available in the "File" menu
    • This option exports both Stereolithography (STL) and Virtual Reality Modeling Language (VRML) files for 3D printing.
  • A "Search" button is located near the top-right corner of iCn3D, and enables you to enter one-letter for sequence residues, to find them within the sequence data and 3D structure.
    • As an example, open the structure for 1TUP: Tumor Suppressor P53 Complexed With DNA and:
      • Enter R in the "Search" box to find all arginine residues, or
      • Enter RLG to find all regions of sequence that contain an arginine, leucine, and glycine adjacent to each other.
      • The ambiguity code of X can be used to represent any amino acid, so a search for RXLG will find all regions of sequence that contain an arginine, followed by any amino acid, and then followed by leucine and glycine.
    • The sequence residues that you searched for will be highlighted in the 3D structure, 2D interaction schematic, and 1D sequence windows.
  • The "View Only Selection" option in the "View" menu refreshes all iCn3D windows (3D structure, 2D interactions schematic, and 1D sequences and annotations) to show only the objects you have selected.
    • As an example, open the structure for 1TUP: Tumor Suppressor P53 Complexed With DNA and:
      • Use CTRL+click to select proteins 1TUP_A and 1TUP_C from either the "Sequences and Annotations" (1D) window, or from the "Interactions" (2D) window.
      • Use the "View > View Only Selection" menu option to display only the selected proteins in all windows, including in the molecular graphic (3D) window.
      • Use the "View > Reset > All" menu option to revert back to the original view in the 3D window
      • Reload the iCn3D page to revert to the original view in all windows (3D, 2D, and 1D).
  • The "Defined Sets" option in the "Select" menu is a combined version of the previous "Advanced", "Structure", "Chain", "Custom" menus.
    • By default, the "Select Sets" window (that appears when you choose the "Select > Defined Sets" menu option) lists each protein and nucleotide molecule in the structure, allowing you to select one or more individual biomolecules. It also provides an option to select all "ions," "nucleotides," or "proteins" in the structure.
    • You can also add custom sets to the "Select Sets" window, if desired. To do this:
      • Open the "Details" tab in the "Sequences and Annotations" window, select items of interest (e.g., individual amino acids from a protein molecule)
      • Enter the name and description of the selected data set in the "Selection: Name" and "Description" text boxes.
      • Click the "Save" button
      • The name of the custom set will then appear in the "Select Sets" window.
      • The custom set can also be be used in conjunction with iCn3D options such as "View > View Selection Only," "Style," and "Color," allowing you to isolate the custom set in all iCn3D windows, and/or to render it in the desired style. It can also be saved for future use via the "File > Save Files > State File" menu option.
17 AUG 2016 iCn3D 1.2.0 was released on NCBI web servers (http://foodzines.com/Structure/icn3d/icn3d.html) and on GitHub ().

New features in this release include:
  • An interactions schematic (2D view) that is available when a structure is loaded as an MMDB file.
  • Calculation of secondary structures if the input PDB file does not define secondary structure information.
  • Previous files src/icn3d.js, src/full_ui.js, and src/simple_ui.js have been separated into small files.
28 APR 2016 First public release of iCn3D 1.0 on NCBI web servers: http://foodzines.com/Structure/icn3d/icn3d.html.
17 JAN 2016 First beta release of iCn3D (beta version icn3d-0.9.0-dev), on GitHub: . The on the GitHub server includes a change log section that lists subsequent beta releases.

 
References back to top


Citing iCn3D: back to top

To cite iCn3D, please reference:
Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A. iCn3D, a Web-based 3D Viewer for Sharing 1D/2D/3D Representations of Biomolecular Structures. Bioinformatics. 2019 June 20; pii: btz502. doi: 10.1093/bioinformatics/btz502. [Epub ahead of print] [PubMed PMID: 31218344] []  

Additional references: back to top

A separate page lists all publications about NCBI's 3D Macromolecular Structures Resources, including articles by the NCBI Structure group describing the results of computational biology research on the Molecular Modeling Database, such as 3D structure comparisons, and more.


Revised 27 April 2020