372 lines
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372 lines
24 KiB
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<!-- PubChem template version 5.1 2012-05 -->
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<meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
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<meta name="description" content="About iCn3D, a WebGL-based 3D structure viewing program for macromolecular structures, from the National Center for Biotechnology Information Structure Group." />
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<meta name="ncbi_db" content="pubchem" />
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<meta name="keywords" content="iCn3D structure viewing software for the World Wide Web, WebGL-based 3D viewer for macromolecular structures, Molecular Modeling Database, MMDB, 3D Domains, Vector Alignment Search Tool, VAST, VASTplus, VAST+, nrPDB, CBLAST, Entrez Protein related structure links, three-dimensional structures, 3D, 3-D, macromolecular structures, similar structures, neighbors, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, proteins, nucleic acids, DNA, RNA, ligands, bound chemicals, drugs, medicine, Conserved Domain Database (CDD), protein sequences, classification, families, superfamilies, superfamily, protein function, homologous, homologs, orthologs, multiple sequence alignment, protein sequence analysis and annotation, NCBI, National Center for Biotechnology Information" />
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<title>iCn3D Overview: web-based 3D structure viewer</title>
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<TR>
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<TD class="DocTitleText" align="left"> <A href="../icn3d.html">iCn3D</A>: web-based 3D structure viewer</TD>
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<!-- ===================== GREEN_BUTTONS ====================== -->
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<TD class="NavResourceButtonActive" align="center" valign="center" style="white-space: nowrap;"><A href="icn3d_about.html"> ABOUT </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="https://structure.ncbi.nlm.nih.gov/icn3d"> OPEN iCn3D </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="icn3d_help.html"> HELP </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="https://github.com/ncbi/icn3d"> GITHUB </A></TD>
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<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../MMDB/docs/mmdb_news.html"> NEWS </A></TD>
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<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../structure_discover.html"> DISCOVER </A></TD -->
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<TABLE width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
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<!-- ============== VERTICAL_SPACER ================ -->
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP" COLSPAN="3"> </TD>
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<!-- ============= END_VERTICAL_SPACER ============= -->
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<!-- ================== OVERVIEW ================== -->
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<TR>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"><A href="../icn3d.html"><B>iCn3D</B></A> ("<B>I see in 3D</B>") is a WebGL-based viewer for interactive viewing of three-dimensional <!-- A HREF="../../MMDB/docs/mmdb_help.html#WhatIs" --><A HREF="/structure/">macromolecular structures</A> and <A HREF="/pccompound/">chemicals</A> on the web, without the need to install a separate application. It can be accessed from the "<A HREF="../../MMDB/docs/mmdb_help.html#MolecularGraphic"><!-- A HREF="icn3d_help.html#MolecularGraphic" -->molecular graphic</A>" that appears on the structure summary page for any record in the <A HREF="/structure/">Molecular Modeling Database (MMDB)</A>.<br><br>
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As an <B>example</B>, open the <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1TUP">MMDB summary page for <B>1TUP</B></A>, then press the <!-- A HREF="../../MMDB/docs/mmdb_help.html#SpinIcon">spin icon <IMG SRC="../../MMDB/docs/images/mmdbsrv_molecular_graphic_icn3d_control_icon_spin_structure.png" width="14" height="14" border="0"></A --> <b>"3D view" button</b> in the lower left hand corner of the molecular graphic to load a basic version of iCn3D into the page. Alternatively, press the <!-- A HREF="../../MMDB/docs/mmdb_help.html#LaunchIcon">launch icon <IMG SRC="../../MMDB/docs/images/mmdbsrv_molecular_graphic_icn3d_control_icon_launch_full_feature_icn3d.png" WIDTH="14" HEIGHT="14" BORDER="0" ALT="icon that launches full feature iCn3D in another window"></A --> <b>"full-featured 3D viewer" button</b> in the lower right hand corner of the molecular graphic to open the advanced (full feature) version of iCn3D in a separate window. You can also access the advanced version directly at <A HREF="/Structure/icn3d/full.html">/Structure/icn3d/full.html</A>, where you can use the <A HREF="icn3d_help.html#MenuFile">"File" menu</A> to retrieve a structure by its ID or to open a structure file on your local computer.<BR><BR>
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<A HREF="../../icn3d/docs/icn3d_about.html"><B>iCn3D</B></A> <B>2.20.0 is now available</B> on NCBI web servers and from GitHub (<A HREF="https://github.com/ncbi/icn3d">https://github.com/ncbi/icn3d</A>). Users can now view the electrostatic potential map for any subset of 3D structures within 30,000 atoms. The potential is calculated using the DelPhi program by solving linear Poisson-Boltzmann equation. Users can show the potential on surface or show equipotential map. The potential map shows the effect of charges on molecular interactions qualitatively. This <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?XCxR6fSTmXHxR3o1A">example</a> shows the electrostatic potential for the binding of Gleevec to Abl2. The ligand shows the -25 mV (red) and +25 mV (blue) equipotential map with a grid size 65, salt concentration 0.15 M, and pH 7. The protein shows the surface potential with a gradient from -75 mV (red) to +75 mV (blue). This new feature can be accessed from the menu "Analysis > DelPhi Potential". Users can also download the PQR file format with assigned partial charges.
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<BLOCKQUOTE>
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<a href="/Structure/icn3d/icn3d.html"><b>Other recently introduced features </b></a>include:
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<UL>
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<LI>Visualization of <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?X3whJjau5t91j6i98">observed sequence variation for selected SARS-CoV-2 structures</a></LI>
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<LI>Availability of iCn3D in the Jupyter Notebook with the widget "icn3dpy"<a href="https://pypi.org/project/icn3dpy/">(pypi.org/project/icn3dpy)</a></LI>
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<LI>Visualization of a <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?JR5B">binding site</a> or an <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?CuXYgGLCukDeUKnJ6">interaction interface</a></LI>
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<LI>Ability to export models for <a href="/Structure/icn3d/full.html?mmdbid=1tup&command=export+stl+stabilizer+file">3D printing</a></LI>
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<LI>Displaying <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?TuSd">transmembrane proteins</a></LI>
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<LI>Showing the <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?aYAjP4S3NbrBJX3x6">surface map, </a><a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?L4C4WYE85tYRiFeK7">EM map, </a>or<a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?QpqNZ3k65ToYFvUB6"> electron density map</a></LI>
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<LI>Viewing 1D sequences and 2D interactions</LI>
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<LI>Aligning <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?wPoW56e8QnzVfuZw6">two structures, <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?ijnf"> two chains, or <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?Mmm82craCwGMAxru9"> a protein sequence to a structure</a> and <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?tu166KaK8jQYUAVf7">realigning </a>these alignments .</LI>
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<LI>Addition of <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?pUzP">custom tracks</a> in various formats (FASTA, bed file, etc.)</LI>
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<LI>Showing a <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?rshvjTFXpAFu8GDa9">force-directed graph for interactions</a></LI>
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<LI>Calculating and displaying <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?xKSyfd1umbKstGh29">solvent accessible surface area (SASA) </a></LI>
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<LI>Showing <a href="https://structure.ncbi.nlm.nih.gov/icn3d/share.html?bGH1BfLsiGFhhTDn8">symmetry</a> when available</LI>
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</BLOCKQUOTE>
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<BLOCKQUOTE>
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More features are listed and described at <a href="/Structure/icn3d/icn3d.html">/Structure/icn3d/icn3d.html</a>
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</BLOCKQUOTE>
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<!-- iCn3D can be accessed from the "<A HREF="../../MMDB/docs/mmdb_help.html#MolecularGraphic"><A HREF="icn3d_help.html#MolecularGraphic">molecular graphic</A>" that appears on the <A HREF="../../MMDB/docs/mmdb_help.html#SummaryPage">structure summary page</A> for any record in the <A HREF="/structure/">Molecular Modeling Database (MMDB)</A>. The iCn3D tool can also be opened directly by entering a <A HREF="icn3d_help.html#AccessURLFormat">formatted URL</A> that includes the unique identifier of the macromolecular structure (in the format of <A HREF="../../MMDB/docs/mmdb_help.html#MMDBID">MMDB ID</A> or <A HREF="../../MMDB/docs/mmdb_help.html#PDBID">PDB ID</A>) or the chemical (in the format of <A HREF="/pccompound/">PubChem Compound</A> identifier, <A HREF="https://pubchem.ncbi.nlm.nih.gov/docs/subcmpd_summary_page_help.html#MoleculeCID">CID</A>) to be displayed. iCn3D can also easily be <A HREF="icn3d_help.html#AccessWebAPI">embedded</A> in your web pages, as either a <A HREF="icn3d_help.html#AccessWebAPIBasic">basic version</A> or <A HREF="icn3d_help.html#AccessWebAPIFull">full feature version</A>. (As an example, the basic version is featured below.) -->
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<!-- The source code is available from GitHub <A HREF="https://github.com/ncbi/icn3d">https://github.com/ncbi/icn3d</A>. Developers who are interested in <A HREF="/Structure/icn3d/icn3d.html#APIs">customizing</A> and/or contributing code can use the "Download ZIP" button in the upper right corner of the GitHub page to download the source code written at NCBI. Users who would like to install iCn3D on their local computer can obtain it from <A HREF="/Structure/icn3d/icn3d-0.9.6-dev.zip">/Structure/icn3d/icn3d-0.9.6-dev.zip</A>. That is the complete distribution copy of iCn3D, which includes the code written by NCBI as well as the corresponding third party JavaScript libraries such as jQuery and Three.js. -->
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</TD>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<!-- =============== END_OVERVIEW ================== -->
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<!-- ============== VERTICAL_SPACER ================ -->
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<TR>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP" COLSPAN="3"> </TD>
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</TR>
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<!-- ============= END_VERTICAL_SPACER ============= -->
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<!-- ========== iCn3D_EXAMPLE_DEMO_BASIC_VERSION ========= -->
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<TR>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD CLASS="WhiteCell NormalText">
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<div id="icn3dwrap"></div>
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<script type="text/javascript">
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var cfg = {
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divid: 'icn3dwrap',
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width: 500,
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height: 500,
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resize: false,
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rotate: 'right',
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mobilemenu: 1,
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showcommand: 0,
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mmdbid: '3gvu',
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usepdbnum: 0,
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command: 'set chemicalbinding show; select :water; color grey; select .STI:1; zoom selection; set background white; set delphi map | contour 1 | gsize 65 | salt 0.15; select chain !A; color charge; set delphi surface | contour 3 | gsize 65 | salt 0.15 | surface 22 | opacity 1.0 | wireframe no|||{"factor":"1.026","mouseChange":{"x":"0.000","y":"0.000"},"quaternion":{"_x":"0.2750","_y":"0.7154","_z":"0.5163","_w":"0.3821"}}'
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};
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var icn3dui = new icn3d.iCn3DUI(cfg);
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icn3dui.show3DStructure();
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</script>
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</TD>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<!-- ======= END_iCn3D_EXAMPLE_DEMO_BASIC_VERSION ======= -->
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<!-- ====== LINKS_TO_1TUP_in_MMDBSRV_BASICiCn3D_FULLiCn3D ====== -->
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<!-- TR>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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If desired, use the following links to open <A HREF="/Structure/icn3d/index.html?mmdbid=1tup">1TUP in the basic version of iCn3D</A> (same view as above, but in its own tab), <A HREF="/Structure/icn3d/full.html?mmdbid=1tup">1TUP in the advanced (full feature) version of iCn3D</A>, or <A HREF="/Structure/mmdb/mmdbsrv.cgi?uid=1TUP">1TUP in the MMDB structure summary page</A>.
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</TD>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR -->
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<!-- ====== END_LINKS_TO_1TUP_in_MMDBSRV_BASICiCn3D_FULLiCn3D ====== -->
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<!-- ============== VERTICAL_SPACER ================ -->
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<TR>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP" COLSPAN="3"> </TD>
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</TR>
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<!-- ============= END_VERTICAL_SPACER ============= -->
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<!-- ====== NEED_WEB_BROWSER_THAT_SUPPORTS_WebGL ====== -->
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<TR>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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<A NAME="WebGL"></A>
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There is no need to install a separate application in order to use iCn3D; you just need to use a <B><I>web browser that supports <A HREF="https://get.webgl.org/">WebGL</A></I></B>. 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 <a href="https://get.webgl.org/">WebGL</a> site for more information about compatibility with various web browsers.)
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</TD>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<!-- ====== END_NEED_WEB_BROWSER_THAT_SUPPORTS_WebGL ====== -->
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<!-- ============== VERTICAL_SPACER ================ -->
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<TR>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP" COLSPAN="3"> </TD>
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</TR>
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<!-- ============= END_VERTICAL_SPACER ============= -->
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<!-- ====== GITHUB_WEBSITE_FOR_DOWNLOADING_SOURCE_CODE ====== -->
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<TR>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
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The <B>source code</B> for iCn3D is available from GitHub <A HREF="https://github.com/ncbi/icn3d">https://github.com/ncbi/icn3d</A> for those who would like to run the program locally, and for those who would like to customize iCn3D and/or contribute code:
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<UL>
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<LI>The <B>complete distribution copy</B> of iCn3D can be obtained for use on your local computer from:
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<A HREF="/Structure/icn3d/icn3d-2.24.5.zip">/Structure/icn3d/icn3d-2.24.5.zip</A>.
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That file includes the code written by NCBI as well as the corresponding third party JavaScript libraries such as jQuery and Three.js.</LI><BR>
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<LI>The <B>development version</B> of iCn3D is available for developers who want to customize and/or contribute code to the iCn3D program. Click on the <B>"Download ZIP" button</B> in the <B>upper right corner</B> of the <A HREF="https://github.com/ncbi/icn3d">GitHub</A> 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.</LI>
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</UL>
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</TD>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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<!-- ====== END_GITHUB_WEBSITE_FOR_DOWNLOADING_SOURCE_CODE ====== -->
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<!-- ============== VERTICAL_SPACER ================ -->
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<TR>
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<TD CLASS="WhiteCell MiniText" ALIGN="LEFT" VALIGN="TOP" COLSPAN="3"> </TD>
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</TR>
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<!-- ============= END_VERTICAL_SPACER ============= -->
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<!-- ========== LINKS_TO_ADDITIONAL_INFORMATION ============= -->
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<TR>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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<TD CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">Additional information about iCn3D is available on the following pages:
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<UL>
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<LI><A HREF="/pubmed/31218344">iCn3D publication: Wang J, et al., 2020 (PubMed ID 31218344)</A></LI>
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<LI><A HREF="icn3d_help.html">iCn3D Help Document</A></LI>
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<LI><A HREF="../icn3d.html">iCn3D Web API Help Document</A></LI>
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<LI>GitHub: <A HREF="https://github.com/ncbi/icn3d">https://github.com/ncbi/icn3d</A><!-- A HREF="/Structure/icn3d/README.md"><A HREF="https://github.com/ncbi/icn3d/blob/master/README.md">iCn3D Readme file</A --></LI>
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<LI><A HREF="../LICENSE">iCn3D Public Domain Notice</A></LI>
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</UL>
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</TD>
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<TD WIDTH="20" CLASS="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP"> </TD>
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</TR>
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</TR>
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</TABLE>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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<TR>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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<TD class="WhiteCell NormalText" align="center"> </TD>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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</TR>
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</TABLE -->
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<!-- =========== BOX_WITH_iCn3D_EXAMPLE_DEMO =========== -->
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<TR>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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<TD class="WhiteCellBlueEdgeAll NormalText" align="left">
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<SPAN class="MiniText"> <BR></SPAN>
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Place a demo version of iCn3D here, showing 1tup
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</TD>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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<TD class="WhiteCell NormalText" align="center"> </TD>
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<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
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</TR>
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</TABLE -->
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<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
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<TR>
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 21 October 2020</SPAN></TD>
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<TD width="25"><IMG SRC="/coreweb/template1/pix/pixel.gif" width="1" height="1" alt="" border=0></TD>
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</TR>
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<!-- ##################### END_EDITABLE_CONTENT ##################### -->
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<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="/research/">Computational Biology Branch</A> > <A HREF="/Structure/index.shtml">Structure Group</A> > <A HREF="/Structure/MMDB/mmdb.shtml">Macromolecular Structures</A> > <A HREF="/Structure/icn3d/icn3d.html">iCn3D</A> > About','other');</script>
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<!-- script type="text/javascript">doc_tmp.getDocFtr(' > <A HREF="______">__________</A> > <A HREF="______">__________</A> > <A HREF="______">__________</A> > ___currentpage_____', 'other');</script -->
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</body>
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