1237 lines
59 KiB
HTML
1237 lines
59 KiB
HTML
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
<!-- PubChem template version 5.1 2012-05 -->
|
|
<!-- $Id: about.html 367034 2012-06-20 14:44:12Z jiazhang $ -->
|
|
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
<head xmlns:xi="http://www.w3.org/2001/XInclude">
|
|
<meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
|
|
<meta name="description" content="Help document for VAST Search, a tool that allows you to input the spatial coordinates of a 3D macromolecular structure in PDB format and retrieve similar 3D structures. Developed by the National Center for Biotechnology Information's Structure Group." />
|
|
<meta name="ncbi_db" content="pubchem" />
|
|
<meta name="keywords" content="Vector Alignment Search Tool (VAST), 3D macromolecular structures, three-dimensional structures, 3D, 3-D, structural alignments, similar structures, superpose, superpositions, superimpose, superimposition, proteins, chemicals, nucleotide sequences, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, nucleic acids, DNA, RNA, ligands, bound chemicals, drugs, medicine, Entrez Structure, Molecular Modeling Database (MMDB), VAST+, Conserved Domains Database (CDD), CDTree, CD Tree, PubChem, NCBI, National Center for Biotechnology Information" />
|
|
<meta name="robots" content="index,follow,noarchive" />
|
|
<title>VAST Search Help Document</title>
|
|
<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/Structure/script/loadbasics.min.js"></script>
|
|
<script type="text/javascript" src="https://www.ncbi.nlm.nih.gov/Structure/script/doc_tmp.min.js"></script>
|
|
<link rel="stylesheet" type="text/css" href="https://www.ncbi.nlm.nih.gov/Structure/stylesheets/struct_style_subset.css">
|
|
<!-- ========== BEGIN_GOVT_SHUTDOWN_NOTICE_added_20130927 =========== -->
|
|
|
|
<script type="text/javascript">
|
|
jQuery.getScript("/core/alerts/alerts.js", function () {
|
|
galert(['div#governmentshutdown', 'body > *:nth-child(1)'])
|
|
});
|
|
</script>
|
|
|
|
<!-- ========== END_GOVT_SHUTDOWN_NOTICE_added_20130927 =========== -->
|
|
</head>
|
|
|
|
<body>
|
|
<A NAME="Top"></A>
|
|
<A NAME="top"></A>
|
|
|
|
<!-- ======= BEGIN_GET_PUBCHEM_HEADER_AND_NCBILOCALNAV_PULLDOWN_MENUS ========= -->
|
|
<script type="text/javascript">doc_tmp.getDocHdr('structure');</script>
|
|
<!-- ======= END_GET_PUBCHEM_HEADER_AND_NCBILOCALNAV_PULLDOWN_MENUS ========= -->
|
|
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MiniText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ==================== END_VERTICAL SPACER ======================= -->
|
|
|
|
|
|
<!-- ##################### BEGIN_EDITABLE_CONTENT ##################### -->
|
|
<A NAME="3"></A>
|
|
|
|
<!-- ######### BEGIN_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT ######## -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCell">
|
|
|
|
<!-- ==================== TITLE_OF_DOCUMENT =================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
|
|
<TD class="DocTitleText" align="left"> <A HREF="../vast.shtml">VAST: <SPAN class="DocTitleTextSmall13">Vector Alignment Search Tool</SPAN></A></TD>
|
|
|
|
<!-- ===================== GREEN_BUTTONS ====================== -->
|
|
|
|
<TD width="350" bgcolor="#FFFFFF">
|
|
|
|
<TABLE width="350" border="0" style="border-collapse:separate;" cellspacing="1" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vast.shtml"> ABOUT </A></TD>
|
|
|
|
<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../MMDB/docs/mmdb_how_to.html#VAST"> HOW TO </A></TD -->
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vastsearch.html"> SEARCH </A></TD>
|
|
|
|
<TD class="NavResourceButtonActive" align="center" valign="center" style="white-space: nowrap;"><A href="vasthelp.html"> HELP </A></TD>
|
|
|
|
<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="vastsrchelp.html"> VAST SEARCH HELP </A></TD -->
|
|
|
|
<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../vastplus/docs/vastplus_help.html"> VAST+ HELP </A></TD -->
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="nrpdb.html"> nr-PDB </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="docs/vast_publications.html"> PUBLICATIONS </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A HREF="../MMDB/mmdb.shtml" title="Overview of macromolecular resources available from the NCBI Structure Group"> RESOURCES </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../MMDB/docs/mmdb_news.html" title="News about the macromolecular resources available from the NCBI Structure Group"> NEWS </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A HREF="../structure_discover.html" title="Discover associations among protein sequence, function, and structure"> DISCOVER </A></TD>
|
|
|
|
<TD class="WhiteCell" width="1"> </TD>
|
|
|
|
<TR>
|
|
</TABLE>
|
|
|
|
</TD>
|
|
|
|
<!-- =================== END_GREEN_BUTTONS ==================== -->
|
|
|
|
<TD class="MiniText" width="5"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- =========== COMMENT_ABOUT_HELP_DOC =========== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
|
|
<TD class="WhiteCellBlueEdgeAll ThumbText2" align="Left">
|
|
<SPAN class="MiniText"> <BR></SPAN>
|
|
<P class="indent20bottomspace">This <SPAN style="background-color: #FFFF00"><A HREF="vastsrchelp.html"><B>VAST Search help document</B></A></SPAN> describes how to use the <A HREF="vastsearch.html"><B>VAST Search page</B></A>, which allows you to enter a query structure as a <A HREF="#Submission"><B>PDB-formatted file</B></A>.
|
|
The search results will be returned in <A HREF="vasthelp.html#OriginalVAST"><B>original VAST output format</B></A>, which is described in the <SPAN style="background-color: #FFFF00"><A HREF="vasthelp.html"><B>VAST help document</B></A></SPAN>.<BR>
|
|
<I>(The new <A HREF="../vastplus/vastplus.cgi"><B>VAST+</B></A> output format is currently available only for structures that are publicly available in MMDB. The
|
|
<SPAN style="background-color: #FFFF00"><A HREF="../vastplus/docs/vastplus_help.html#IllustratedExamples"><B>VAST+ help document</B></A></SPAN> provides
|
|
<A HREF="../vastplus/docs/vastplus_help.html#IllustratedExamples"><B>illustrated examples</B> of VAST+ search results</A> and describes the <A HREF="../vastplus/docs/vastplus_help.html#Compare"><B>difference between VAST and VAST+</B></A>.)</I>
|
|
</P></TD>
|
|
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
<TD class="WhiteCell NormalText" align="center"> </TD>
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- =========== END_COMMENT_ABOUT_HELP_DOC =========== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MicroText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- the contents -->
|
|
|
|
<!-- #BeginEditable "content" -->
|
|
|
|
<!-- =================== BEGIN_EDITABLE_CONTENT_AREA ================ -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
|
|
<!-- ================= CONTENT_AREA_ROW_1 ================== -->
|
|
|
|
<TR>
|
|
|
|
<!-- ================= CONTENT_AREA_ROW_1_CELL_1 ================== -->
|
|
|
|
<TD class="WhiteCellWithPadding" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<!-- ======================== BOX1 =========================== -->
|
|
|
|
<A NAME="_____"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP"><B>VAST Search Help</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
<UL>
|
|
|
|
<LI><A HREF="#What">What is VAST Search?</A></LI><BR>
|
|
|
|
<LI><A HREF="#Submission">How to submit a file?</A></LI><BR>
|
|
|
|
<LI><A HREF="#DataSet">How to select a database search set?</A></LI><BR>
|
|
|
|
<LI><A HREF="#SumPage">Where to see the 3D structure of your query protein and how to launch a VAST Search job?</A></LI><BR>
|
|
|
|
<LI><A HREF="#RunTime">How long might it take to complete a VAST Search job?</A></LI><BR>
|
|
|
|
<!-- LI><A HREF="#TIME">How long do I have to wait for the launch page to appear after pressing the Submit Request button?</A></LI><BR><BR --><!-- from vastsearch_faq.html -->
|
|
|
|
<LI><A HREF="#ViewRes">How to view results of search?</A></LI><BR>
|
|
|
|
<LI><A HREF="#NbrPage">Where to see individual VAST structure neighbors?</A></LI><BR>
|
|
|
|
<LI><A HREF="#ALIGN">How can I save the alignments?</A></LI><BR><!-- from vastsearch_faq.html -->
|
|
|
|
<LI><A HREF="#Biostruc">What is a Biostruc and what does it mean when the error message "Missing Biostruc" appears?</A></LI><BR><!-- from vastsearch_faq.html -->
|
|
|
|
<LI><A HREF="#Cn3D">Do I need Cn3D to examine the list of structure neighbors?</A></LI><BR><!-- from vastsearch_faq.html -->
|
|
|
|
<LI><A HREF="#Privacy">What is the VAST Search privacy policy?</A></LI><BR>
|
|
|
|
<!-- LI><A HREF="#______">__________</A></LI><BR>
|
|
|
|
<LI><A HREF="#______">__________</A></LI -->
|
|
|
|
</UL>
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX1 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX2 =========================== -->
|
|
|
|
<A NAME="What"></A>
|
|
<A NAME="WhatIs"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>What is VAST Search?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
<A HREF="vastsearch.html">VAST Search</A> is a World Wide Web service for <B>"on the fly" searches</B> to compare the 3D structure of a query protein against the 3D structures of proteins in NCBI's <A HREF="https://www.ncbi.nlm.nih.gov/structure/">Molecular Modeling Database (MMDB)</A>. It finds <B>similar structures</B> (sometimes referred to as "<B>neighbors</B>") using the <A HREF="vast.shtml">Vector Alignment Search Tool (VAST)</A> algorithm.
|
|
<BR><BR>
|
|
|
|
The <A HREF="vastsearch.html">VAST Search</A> service allows you to <A HREF="#Submission">input</A> your data in <!-- a href="http://www.rcsb.org/pdb/" --><!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format"><B>PDB file format</B></A>. It <!-- converts the file into an <A HREF="../asn1.html">ASN1-formatted file</A --> identifies the <A HREF="../MMDB/docs/mmdb_help.html#DataProcessing3dDomains">3D domains</A> in each protein molecule of your query structure and finds other structures that are 3D similar to the individual protein molecules, and individual 3D domains, in your query.<!-- The VAST Search results display the alignment footprints of proteins that are 3D similar to proteins in your query structure, and enable you to view sequence alignments and 3D superpositions of your query and its neighbors. (The <A HREF="vasthelp.html">main VAST help document</A> provides an <A HREF="vasthelp.html#VASTGraph">illustrated example of alignment footprints</A>.) --><BR><BR>
|
|
|
|
This "on the fly" search service is typically used if your query structure is not yet publicly available (for example, if you have a newly resolved structure) and you want to identify other structures that might have a similar 3D shape.<!-- To do that, open the <A HREF="vastsearch.html">VAST Search</A> web page and input your data in <A HREF="http://www.wwpdb.org/documentation/file-format">PDB file format</A>. --> On the other hand, if your query structure is publicly available in <A HREF="https://www.ncbi.nlm.nih.gov/structure/">MMDB</A>, you can easily <A HREF="vast.shtml#RetrievePrecomputedResults">retrieve <B>pre-computed VAST results</B></A> by following the "Similar Structures" link near the upper right corner of an MMDB <A HREF="../MMDB/docs/mmdb_help.html#SummaryPage">structure summary page</A>.<BR><BR>
|
|
|
|
At this time, the "on the fly" <A HREF="vastsearch.html">VAST Search</A> service still returns results in the <A HREF="vasthelp.html#OriginalVASTDisplay">original-style VAST display</A>, which lists structures that have similarities to <B>individual protein molecules</B> and <A HREF="../MMDB/docs/mmdb_help.html#DataProcessing3dDomains"><B>3D domains</B></A> in your query structure, and allows you to view their sequence alignments and 3D superpositions. The <A HREF="vasthelp.html">VAST help document</A> provides <span style="color:#d70000"><I>illustrated examples</I></span> of the <A HREF="vasthelp.html#OriginalVASTDisplay">original VAST display</A>, <A HREF="vasthelp.html#VASTGraph">alignment footprints</A><!-- of proteins that are 3D similar to 1PTH (ovine Prostaglandin H2 Synthase), --> and a <A HREF="vasthelp.html#IllustrationLipocalins">3D superposition</A><!-- of lipocalins from bacteria, insect, and human -->.<BR><BR>
|
|
|
|
The new <A HREF="../vastplus/vastplus.cgi">VAST+</A> display, which ranks similar structures based on the 3D similarity of their <B>macromolecular complex</B> (<A HREF="../vastplus/docs/vastplus_help.html#OutputBiologicalUnit">biological unit</A>) to the query structure, and provides the ability to view sequence alignments and superpositions of the biological units, is currently available only for structures that are available in the public database.<!-- The original style VAST results does not rank results by biological unit similarity. --> If you <A HREF="vast.shtml#RetrievePrecomputedResults">retrieve pre-computed VAST results</A> for a record that's publicly available in MMDB, the VAST+ display will be shown by default. The <A HREF="../vastplus/docs/vastplus_help.html">VAST+ help document</A> provides <A HREF="../vastplus/docs/vastplus_help.html#IllustratedExamples"><span style="color:#d70000"><I>illustrated examples</I></span> of the new VAST+ results display</A> and describes the <A HREF="../vastplus/docs/vastplus_help.html#Compare">difference between VAST and VAST+</A>.<BR><BR>
|
|
|
|
<!-- ORIGINAL TEXT from vastsrchelp.html: VAST Search is a WWW service which allows you to compare the 3-dimensional structure of an input protein with other protein structures in NCBI's MMDB, using the <A HREF="/Structure/VAST/vast.shtml">VAST</A> algorithm.<BR><BR -->
|
|
|
|
<!-- ORIGINAL TEXT from vastseach_faq.html: VAST Search is a World Wide Web service for an "on the fly" search for 3D structural neighbors of a query protein. A search is initiated by submitting files of the coordinates interactively to the VAST search World Wide Web site. If you have refined the structure of the query protein using the program X-PLOR, you are required to submit an X-PLOR PSF or protein structure file in addition to the coordinate file. -->
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX2 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX3 =========================== -->
|
|
|
|
<A NAME="Submission"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>How to submit a file to the <A HREF="vastsearch.html">VAST Search</A> service?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
The submitted file should be in <B>plain-text (ASCII)</B> in <SPAN style="background-color: #FFFF00"><!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format"><B>PDB file format</B></A></SPAN>. (<I>Important</I>: Word documents will not work!) The file only needs to contain ATOM records for chain(s), and HETATM records for any heterogens. It does not need any SEQRES records or others that do not contain atomic coordinates.
|
|
<!-- Click <A HREF="https://www.ncbi.nlm.nih.gov/Structure/pdb.submit.example">here</A> for an example input file. --><BR><BR>
|
|
|
|
To submit a data file to VAST Search:<BR>
|
|
|
|
<UL>
|
|
<LI>Open the <a href="vastsearch.html">VAST Search home page</a>.</LI>
|
|
<LI>The <A HREF="vastsearch.html#InputPDBFormatFile">first section of the page</A> allows you to "Input a PDB-formatted file directly into VAST Search."</LI>
|
|
<LI>Use the [Choose File] button to select the desired PDB-formatted data file from your computer.</LI>
|
|
<LI>Select the <a href="vasthelp.html#VASTNR">data set</a> (all or medium redundancy) against which you want to search.<BR>
|
|
The (default) "Medium-redundancy Subset of PDB" is about 1/10 the size of "All of PDB" and therefore the search will be much faster.</LI>
|
|
<LI>Click on the [Submit] button to begin the search. This step will convert the <!-- A HREF="http://www.wwpdb.org/docs.html" --><A HREF="http://www.wwpdb.org/documentation/file-format">PDB formatted file</A> into an <A HREF="../asn1.html">ASN1 formatted file</A>, which is used for the VAST Search.</LI>
|
|
<LI>A long, random numerical <A HREF="vsprivacy.html">request identifier</A> is assigned to each search. It can be used for one week to retrieve the search results without doing the search over.</LI>
|
|
</UL>
|
|
|
|
<!-- Use the [Choose File] button to select the desired PDB-formatted data file from your computer, and select the <a href="vasthelp.html#VASTNR">data set</a> (all or medium redundancy) against which you want to search. (The (default) "Medium-redundancy Subset of PDB" is about 1/10 the size of "All
|
|
of PDB" and therefore the search will be much faster.) Then click on the [Submit] button to begin. This step will convert the PDB-format file into the Asn1-format file that is used for the VAST Search. --
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"><img SRC="../IMG/spacer.gif" width="25" height="15" border="0" align="left"></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX3 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX4 =========================== -->
|
|
|
|
<A NAME="DataSet"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>How to select a database search set?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
<!-- ORIGINAL TEXT: You have the option of performing the search against a database consisting of a non-redundant subset of the PDB, or all of PDB. The non-redundant subset was selected by clustering the protein sequences at a BLAST P-value cutoff of 10e-40. The resulting set of representatives is about 1/10-th the size of the full database, and the search time should be proportionally faster.<BR><BR -->
|
|
|
|
You have the option of performing the search against a database consisting of a non-redundant subset of the PDB, or all of PDB. The non-redundant subset was selected by clustering the protein sequences at a BLAST P-value cutoff of 10e-40. The resulting set of representatives is about 1/10-th the size of the full database, and the search time should be proportionally faster. (Additional details about the <A HREF="vasthelp.html#VASTNR">non-redundant data sets</A> are provided in the VAST help document.)
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX4 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX5 =========================== -->
|
|
|
|
<A NAME="SumPage"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>Where to see the 3D structure of your query protein and how to launch a VAST Search job?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
After the input file is processed you will be taken to the structure summary page and informed "Data Parsing Done". Your <A HREF="vsprivacy.html">request identifier</A> is displayed; copy and save it, you will need it to see the final results!<BR><BR>
|
|
|
|
The structure summary of your query is displayed in a table and in graphics as well. The graphic "rulers" corresponding to the chains in your input file. If there are protein chains and 3D domains are present, then these domains will also be displayed with graphics, where you can see the locations and boundaries of each 3D domain on the protein chain.<BR><BR>
|
|
|
|
You can also use the [View 3D Structure] button to verify that your file has been input correctly. The option "Display" will display the structure using the Cn3D graphics viewer. The options "See File" or "Save File" allow you to directly view the ASN1-format file, or to save it to your local disk. If you are satisfied that your file has been converted correctly, then click on the [Start] button to begin the actual VAST Search. This will take you to the status monitoring page, tell you that the "Search [is] in Progress" and inform you of the results of your search job time.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX5 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX6 =========================== -->
|
|
|
|
<A NAME="RunTime"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>How long might it take to complete a VAST Search job?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
There are 3 main factors that will influence the running time of VAST Search. First, if you choose to search the non-redundant subset (which is recommended), then the search will run about 10 times faster than for searching the entire database. Second, if you have multiple protein chains in your file, or large chains that split into many domains, then this will also lengthen the time to complete the search. Third, the type of the fold will also have an influence. A VAST Search with a structure such as a TIM barrel, for which there are very many other TIM barrels in the database (even the non-redundant one), will take much longer than a search with a fold that is less populated in the database.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX6 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX7 =========================== -->
|
|
|
|
<!-- from vastsearch_faq.html -->
|
|
<A NAME="TIME"></A>
|
|
<!-- TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll" -->
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<!-- TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>How long do I have to wait for the launch page to appear after pressing the Submit Request button?</B></TD>
|
|
</TR -->
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
The amount of time needed for the server program to send back the launch page depends on the size of the query protein, the number of chains the protein, and the CPU load during the submission process. A protein composed of a single chain and about 100 amino acids will almost always take less than a minute. An immunoglobulin with two chains will take somewhere between minute and a half to two minutes. Since VAST search calculates structure neighbors of each individual chain, we strongly recommend that you submit a separate job for each chain.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE -->
|
|
|
|
<!-- ======================== END_BOX7 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE -->
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX8 =========================== -->
|
|
|
|
<A NAME="ViewRes"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>How to view results of VAST search?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
The status monitoring page will take you to the result summary page automatically after a search job has completed. Or on the VAST Search <a href="vastsearch.html">home page</a> enter your Request Id in the box adjacent to the [Show] button. Then click on [Show]. If the VAST Search job has not yet completed, then you will be informed of the status; if it has, then you will see the result summary page which tell you that "Search Job Completed".<BR><BR>
|
|
|
|
The summary information will be detailed in a summary table. Besides the structure summary about the query chains/domain, the table describes how many structures in the database search set you chose when you sumbmitted your file are significantly similar to the query chain/domain, as found by VAST. Follow the links in the table, you will see the detailed footprints of alignments between each query chain/domain and their neighbors. <I>Important:</I> Since VAST returns neighbors that are deemed significant according to it's E-value, and this E-value is related to the size of the structure, it is not unusual for the neighbor lists for the entire chain and the domains to be different.<BR><BR>
|
|
|
|
If you forget what your protein looks like and want to view its 3D structure,
|
|
you may click on the [View] button of "View the Summary (graphical)" on the
|
|
summary page. Besides viewing the structure in the graphics, you may click on
|
|
the ruler for an entire chain to see the VAST structure neighbors for that
|
|
entire chain; click on the bars for the domains to see the VAST structure neighbors for those domains.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX8 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX9 =========================== -->
|
|
|
|
<A NAME="NbrPage"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>Where to see individual VAST structure neighbors?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
The VAST structure neighbors are introduced to you by clicking links in the VAST Search result summary page. All neighbors are given their names and alignment footprints in the graphics on the neighboring page. Besides, the page has several options available for viewing the alignments, selecting a subset to display, sorting neighbors based on various measures and looking for possible structure similar candidates:
|
|
|
|
<UL>
|
|
<LI><B>[View 3D Structure]</b>: This button can be used to view structural superpositions in Cn3D, or to output the superpositions into a file. Select the neighbors you wish to view by clicking the checkboxes to the left of the PDB codes in the neighbor list. Up to 10 neighbors may be selected. If you wish to See or Save the file, see the options under "Display".</LI>
|
|
<LI><b>[View Alignment]</b>: This may be used to obtain a text version of the sequence alignments corresponding to the structural superposition of selected (check-boxed) neighbors.</LI>
|
|
<LI><b>[List]</b>: for selecting subsets, sorting by alignment quantities such as alignment length, root mean square deviation, percent identical residues, etc.</LI>
|
|
<LI><b>[Find]</b>: for selecting or looking for neighbors by PDB/MMDB/or domain identifiers.</LI>
|
|
</UL>
|
|
|
|
The VAST Help document provides additional information and illustrated examples of the <A HREF="vasthelp.html#VASTMoleculeList">initial VAST results page</A> and the <A HREF="vasthelp_v07.html#VASTGraph">graphic display of alignment footprints</A>.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX9 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX10 =========================== -->
|
|
|
|
<A NAME="ALIGN"></A> <!-- from vastsearch_faq.html -->
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>How can I save the alignments?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
Search results will remain on the server for a week to allow you
|
|
time to save the hit lists and the alignments. The HTML page containing
|
|
the list of neighbors can be saved locally and reloaded into your browser.
|
|
Alignments can be saved in either binary or text ASN.1 format to be viewed
|
|
locally with Cn3D. For any hit list of five or more neighbors, a maximum
|
|
of five neighbors can be viewed with Cn3D and saved in ASN.1. Alternatively,
|
|
you can save the alignments of the query protein and a single hit as a
|
|
kinemage file to read with the program MAGE or save the rotated PDB file
|
|
of each neighbor, which should allow you to view the alignments with a program that reads PDB files.<BR><BR>
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX10 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX11 =========================== -->
|
|
|
|
<A NAME="Biostruc"></A> <!-- from vastsearch_faq.html -->
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>What is a Biostruc and what does it mean when the error message "Missing Biostruc" appears?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
Biostruc is a file format specificed in data description
|
|
language called ASN.1. It includes a complete chemical description
|
|
of a molecules, which is not present in PDB formatted files.
|
|
Biostruc format allows the submitter to view the structure of the query
|
|
protein and alignment superpositions with it's neighbors in Cn3D and is
|
|
needed to browse the list of neighbors. When the error message "Missing
|
|
Biostruc" is returned, the means that this file was not created and the search for neighbors cannot begin.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX11 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX12 =========================== -->
|
|
|
|
<A NAME="Cn3D"></A> <!-- from vastsearch_faq.html -->
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>Do I need Cn3D to examine the list of structure neighbors?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
No. You have the option to view the alignments with any graphics
|
|
program of your choice, but we recommend you view the structural alignments with Cn3D, which we distribute for free with VAST Search.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX12 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOX13 =========================== -->
|
|
|
|
<A NAME="Privacy"></A> <!-- from /Structure/VAST/vsprivacy.html -->
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>What is the VAST Search privacy policy?</B></TD>
|
|
</TR>
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
When you submit a data file to <!-- A HREF="vast.shtml"><B>VAST</B>, short for <B>V</B>ector <B>A</B>lignment <B>S</B>earch <B>T</B>ool</A --><A HREF="vastsearch.html"><B>VAST Search</B></A>, a long, random numerical request identifier is assigned to each search. The request identifier is presented to you when the VAST Search is initiated. The structures of the query protein and results of the search can be viewed only if the request identifier is specified, either by bookmarking the "Data Parsing Done" or "Search In Progress" page, or recording the identifier. This ensures that the original data and the search results are confidential. Note that results are maintained on the server for one week only. After that time please submit a new request.
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR -->
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ======================== END_BOX13 =========================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE -->
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ======================== BOXN =========================== -->
|
|
|
|
<A NAME="_____"></A>
|
|
<!-- TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCellBlueEdgeAll" -->
|
|
|
|
<!-- ########## BLUE_HEADER ########## -->
|
|
<!-- TR>
|
|
<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">
|
|
<A HREF="#Top"><img SRC="../IMG/arrowup_blue.gif" width="12" height="12" border="0" align="right" alt="back to top"></A>
|
|
<B>_____________</B></TD>
|
|
</TR -->
|
|
<!-- ########## END_BLUE_HEADER ########## -->
|
|
|
|
<!-- TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell NormalText">
|
|
|
|
<TR>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
<TD class="WhiteCell NormalText" ALIGN="Left" VALIGN="TOP">
|
|
|
|
Text text text text...<BR><BR>
|
|
|
|
Text text text text...<BR><BR>
|
|
|
|
</TD>
|
|
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP">
|
|
<img src="________.png" width="500" height="100"><BR><BR>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="15" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" ALIGN="Center" VALIGN="TOP"> 
|
|
<BR> <BR></TD>
|
|
</TR>
|
|
|
|
</TABLE -->
|
|
|
|
<!-- ======================== END_BOXN =========================== -->
|
|
|
|
</TD>
|
|
|
|
<!-- ============== END_CONTENT_AREA_ROW_1_CELL_1 ================= -->
|
|
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ============== END_CONTENT_AREA_ROW_1 ================= -->
|
|
|
|
<!-- ===== VERTICAL_SPACER_SEPARATING_ROW_1_and_ROW_2 ===== -->
|
|
|
|
<!-- TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MiniText"> </TD>
|
|
</TR>
|
|
</TABLE -->
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- end of content -->
|
|
|
|
<!-- =========== PAGE_MARGIN_TO_RIGHT_OF_CONTENT_AREA =============== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT ######## -->
|
|
|
|
<!-- =================== PAGE_FOOTER_AND_DATE_REVISED ================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 26 September 2016</SPAN></TD>
|
|
<TD width="25"><IMG SRC="https://www.ncbi.nlm.nih.gov/coreweb/template1/pix/pixel.gif" width="1" height="1" alt="" border=0></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- =================== END_PAGE_FOOTER_AND_DATE_REVISED ================== -->
|
|
|
|
|
|
<!-- ##################### END_EDITABLE_CONTENT ##################### -->
|
|
|
|
<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="https://www.ncbi.nlm.nih.gov/research/">Computational Biology Branch</A> > <A HREF="https://www.ncbi.nlm.nih.gov/Structure/index.shtml">Structure Group</A> > <A HREF="https://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml">Macromolecular Structures</A> > <A HREF="https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml">VAST</A> <A HREF="https://www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html">VAST Search</A> > Help','other');</script>
|
|
|
|
<!-- script type="text/javascript">doc_tmp.getDocFtr(' > <A HREF="______">__________</A> > <A HREF="______">__________</A> > <A HREF="______">__________</A> > ___currentpage_____', 'other');</script -->
|
|
|
|
</body>
|
|
</html>
|