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EDS - Uppsala Electron Density Server
<html> <head><script type="text/javascript" src="https://web-static.archive.org/_static/js/bundle-playback.js?v=7YQSqjSh" charset="utf-8"></script> <script type="text/javascript" src="https://web-static.archive.org/_static/js/wombat.js?v=txqj7nKC" charset="utf-8"></script> <script>window.RufflePlayer=window.RufflePlayer||{};window.RufflePlayer.config={"autoplay":"on","unmuteOverlay":"hidden"};</script> <script type="text/javascript" src="https://web-static.archive.org/_static/js/ruffle/ruffle.js"></script> <script type="text/javascript"> __wm.init("https://web.archive.org/web"); __wm.wombat("http://eds.bmc.uu.se/eds/index.html","20210321231009","https://web.archive.org/","web","https://web-static.archive.org/_static/", "1616368209"); </script> <link rel="stylesheet" type="text/css" href="https://web-static.archive.org/_static/css/banner-styles.css?v=p7PEIJWi" /> <link rel="stylesheet" type="text/css" href="https://web-static.archive.org/_static/css/iconochive.css?v=3PDvdIFv" /> <!-- End Wayback Rewrite JS Include --> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="robots" contet="index,nofollow"> <title>EDS - Uppsala Electron Density Server</title> </head> <body cellpadding="0" cellspacing="0" bgcolor="#FFFFFF"> <div align="left"> <table border="0" cellpadding="0" cellspacing="0" width="100%" bgcolor="#FFFFFF"> <tr> <td width="20%"><a href="https://web.archive.org/web/20210321231009/http://www.uu.se/"><img src="/web/20210321231009im_/http://eds.bmc.uu.se/eds/uulogo_120.gif" alt="Uppsala University" border="0" align="left" align="top"></a></td> <td align="center" width="60%"> <img src="/web/20210321231009im_/http://eds.bmc.uu.se/eds/eds_logo.gif" alt="EDS" align="middle" border="0"> </td> <td width="20%"> <img src="/web/20210321231009im_/http://eds.bmc.uu.se/eds/eu_logo.gif" alt="European Union" border="0" align="right" align="top"> </td> </tr> </table> </div> <p align="center"> <table border="10" cellpadding="10" padding="0" cellspacing="0" width="80%"><tr bgcolor="red" width="100%"> <td><center><b><font size="6" color="white">NOTICE: EDS will be retired during 2017!<br> Please use the LiteMol viewer at PDBe to view models and electron density.<br> For instance, the PDBe page for entry 1CBS is <a href="https://web.archive.org/web/20210321231009/http://pdbe.org/1cbs">http://pdbe.org/1cbs</a><br> For more information, please visit <a href="https://web.archive.org/web/20210321231009/http://www.ebi.ac.uk/pdbe/eds">http://www.ebi.ac.uk/pdbe/eds</a><br> </font></b></center></td></tr></table> </p> <p align="center"> <font size="+2"> <b> Welcome to the Electron Density Server at Uppsala University </b> </font> <p> <center> <table border="0" cellspacing="5" cellpadding="0" bgcolor="9999CC" width="600"> <tr> <td> <ul> <br> <form method="GET" action="/web/20210321231009/http://eds.bmc.uu.se/cgi-bin/eds/uusfs"> <b><i>Enter a PDB code (4 characters):</i></b><br> <input name="pdbCode" size="5" maxlength="4"> <input type="submit" value="Submit"> </form> </ul> </td> </tr> <tr> <td> <ul> <br> <form method="GET" action="/web/20210321231009/http://eds.bmc.uu.se/eds/edssearch.php"> <b><i>Or enter a search string:</i></b><br> <input name="findAnd" size="50"><br> <input type="submit" value="Search"> <input type="reset" value="Clear"> </form> </ul> </td> </tr> </table> </center> <p> <center> <a href="eds_help.html" target="EDS_OTHER">All about EDS</a> | <a href="https://web.archive.org/web/20210321231009/mailto:eds2@xray.bmc.uu.se">Contact us</a> | <a href="eds_holdings.txt" target="EDS_OTHER">Holdings</a> | <a href="eds_update.html" target="EDS_OTHER">Update statistics</a> | <a href="eds_news.html" target="EDS_OTHER">News</a> | <a href="https://web.archive.org/web/20210321231009/http://xray.bmc.uu.se/gerard/embo2001/modval/edso/ TARGET=" eds_other">EDS and O</a> <br><br> <a href="eds_sos.html" target="EDS_OTHER">Request for help from crystallographers</a> | <a href="/web/20210321231009/http://eds.bmc.uu.se/eds/ramachan.html" target="EDS_OTHER">Ramachandran server</a> | <a href="https://web.archive.org/web/20210321231009/http://xray.bmc.uu.se/gerard/supmat/eds/" target="EDS_OTHER">Supplementary information</a> <!-- | <A HREF="http://md.chem.rug.nl/~berends/IUBG-FinalReport.html" TARGET="EDS_OTHER">IUBG report</A> --> <br><br> <table border="0" cellspacing="5" cellpadding="0" bgcolor="ffffff" width="90%"><tr><td><center> <font size="-1" color="green"> If you use this server, please cite: GJ Kleywegt, MR Harris, JY Zou, TC Taylor, A Wählby & TA Jones (2004), "<i>The Uppsala Electron-Density Server</i>", Acta Cryst. D60, 2240-2249 (<a href="https://web.archive.org/web/20210321231009/http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15572777" target="EDS_OTHER">PubMed</a>). Please, also cite the primary literature sources for any structure whose information you retrieve from EDS. </font> <br><br> <font size="-1" color="green"> Interested in data-mining using EDS data ? <a href="https://web.archive.org/web/20210321231009/mailto:eds2@xray.bmc.uu.se">Contact us</a> to see if we can help or collaborate with you. Please do <i>not</i> download large chunks of EDS data without our prior consent. Please note that it is <i>illegal</i> under Swedish law to download information that is not explicitly linked to. </font> <br><br> <font size="-1" color="green"> EDS is currently indexed by <a href="https://web.archive.org/web/20210321231009/http://www.rcsb.org/pdb/" target="EDS_OTHER">RCSB-PDB</a>, <a href="https://web.archive.org/web/20210321231009/http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/" target="EDS_OTHER">PDBsum</a>, <a href="https://web.archive.org/web/20210321231009/http://www.fli-leibniz.de/IMAGE.html" target="EDS_OTHER">Jena Library of Biological Macromolecules</a>, and <a href="https://web.archive.org/web/20210321231009/http://bip.weizmann.ac.il/oca-bin/ocamain" target="EDS_OTHER">OCA</a><a href="https://web.archive.org/web/20210321231009/http://frozentime.se/">.</a> In the future it will also be indexed by <a href="https://web.archive.org/web/20210321231009/http://www.ebi.ac.uk/msd/Services.html" target="EDS_OTHER">MSD</a>. (More information about linking to EDS can be found <a href="eds_help.html#LINK" target="EDS_OTHER">here</a>.) </font> <br><br> <font size="-1" color="green"><i> Previously supported by EU grant QLRT-2001-00015. </i></font> </center></td></tr></table> </center> <!-- <?PHP> // Include contents of update file $updateFile = "/pub/db/eds/update.dat"; $uf = @fopen($updateFile,"r");// Open the update data file if ($uf) { while ($line = @fgets($uf,1024)) { // Loop through the file echo "$line\n"; } } <?> --> <!-- <P> <B>This server is a prototype version.</B> <BR> The information on this server is based on the deposited coordinates and structure factors on <a href="http://www.rcsb.org/pdb/" target="extern">Protein Data Bank.</a> The electron density maps are generated with an automatic script using the <A HREF="http://www.ccp4.ac.uk/" target="extern">CCP4</A> package. <BR> To view the electron density you can either use our Java-based density viewer by simply clicking the residue you are interested in the various plots (Real Space Fit, Significant Regions, Z-scores), or use other external programs, such as <A HREF="http://xray.bmc.uu.se/alwyn" target="extern">O</A> or <A HREF="http://www.expasy.ch/spdbv/" target="extern">Swiss-Pdb Viewer</A>. If you use O, you can also download an O macro for each entry, which, if you download the map and the pdb file, will make a nice picture of the molecule and set up the map for drawing. The electron density maps are in O (<i>a.k.a.</i> DSN6) format.<BR> <B>Note:</B> Because the EDS viewer uses the Swing 1.2 API, it requires Java Plug-in 1.2 or later. It won't work with Java Plug-in 1.1.1 or uncustomized 1.1 browsers. You may download the plugin at the <a target="sun" href="http://java.sun.com/products/plugin">Java Home Page</a>. <BR><BR> <B>Beware</B> of maps for which the calculated R factor is high. This may indicate a problem during the parsing of the structure factor or coordinate files. <BR><BR> <BR> <IMG SRC="http://xray.bmc.uu.se/cgi-bin/nph-count?width=5&link=http://portray.bmc.uu.se/eds"> --> </body> </html> <!-- FILE ARCHIVED ON 23:10:09 Mar 21, 2021 AND RETRIEVED FROM THE INTERNET ARCHIVE ON 12:34:07 Feb 26, 2025. 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