<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi John,<div class=""><br class=""></div><div class=""> Try using the "Ignore any cached data" in the Chimera menu File / Fetch... panel. I suspect Chimera cached a bad file when the fetch was broken. If you use this ignore cached data option it will fetch a new copy of the file.</div><div class=""><br class=""></div><div class=""> Unfortunately when RCSB disabled their legacy web fetch the last couple days they made it so when you tried to fetch it returned an html page saying "PDB has discontinued this fetch" with an http "success" code (200). Since Chimera got the success code it assumed that html text was actually the PDB file and it cached it in</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>~/Downloads/Chimera/PDB</div><div class=""><br class=""></div><div class="">Then when you try to open that same PDB file it is getting that cached html page instead of the cached PDB file. I asked RCSB to return an error code (404) on fetch so that does not happen, but they did even better and temporarily have reenabled the old fetch URLs to help Chimera users. They will still turn off the old fetch in a month or so.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div><div class=""><img apple-inline="yes" id="B3AA1034-A1E9-404D-A274-8AF7EAD74D1C" width="439" height="649" src="cid:ABD4F75C-DC74-4A8B-B445-B6E0E6FC10F6" class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 5, 2020, at 6:26 AM, John Rose <<a href="mailto:rose@bcl4.bmb.uga.edu" class="">rose@bcl4.bmb.uga.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">Downloaded the Chimera 1.15 build but the problem still persists.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class=""><br class=""></div><div class="">John Rose<br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div style="font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word;" class=""><div style="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px;" class=""><br class="Apple-interchange-newline"><br class=""></div><div style="margin: 0px;" class=""><font size="2" class="">John Rose Ph.D.</font></div><div style="margin: 0px;" class=""><font size="2" class="">Associate Professor</font></div><div style="margin: 0px;" class=""><font size="2" class="">SER-CAT Associate Director for Program</font></div><div style="margin: 0px;" class=""><font size="2" class="">Rm. B204B</font></div><div style="margin: 0px;" class=""><div style="margin: 0px;" class=""><font size="2" class="">Department of Biochemistry and Molecular Biology</font></div><div class=""><font size="2" class="">Davison Life Sciences Complex</font></div></div><div style="margin: 0px;" class=""><font size="2" class="">120 Green Street</font></div><div style="margin: 0px;" class=""><font size="2" class="">University of Georgia</font></div><div style="margin: 0px;" class=""><font size="2" class="">Athens, GA 30602-7229</font></div><div class=""><font size="2" class="">===============================</font></div><div style="margin: 0px;" class=""><font size="2" class="">Phone:<span class="Apple-tab-span" style="white-space: pre;"> </span>706-542-1750</font></div><div style="margin: 0px;" class=""><font size="2" class="">Fax: <span class="Apple-tab-span" style="white-space: pre;"> </span>706-542-3077</font></div><div style="font-family: Helvetica; font-size: 12px; font-weight: normal; font-style: normal; margin: 0px;" class=""> </div></div><br class="Apple-interchange-newline" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-variant-east-asian: normal; font-variant-position: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><br class="Apple-interchange-newline"></div>
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">On Nov 4, 2020, at 1:28 PM, Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error.<div class=""><br class=""></div><div class="">We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this.<div class=""><br class=""></div><div class="">What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. <a href="https://www.rcsb.org/pdb/files/1a0m.pdb" class="">https://www.rcsb.org/pdb/files/1a0m.pdb</a>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""></div></div></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></div></div></blockquote></div><br class=""></div></body></html>