Hi John, 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. 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 ~/Downloads/Chimera/PDB 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. Tom
On Nov 5, 2020, at 6:26 AM, John Rose <rose@bcl4.bmb.uga.edu> wrote:
Hi,
Downloaded the Chimera 1.15 build but the problem still persists.
Thanks,
John Rose
John Rose Ph.D. Associate Professor SER-CAT Associate Director for Program Rm. B204B Department of Biochemistry and Molecular Biology Davison Life Sciences Complex 120 Green Street University of Georgia Athens, GA 30602-7229 =============================== Phone: 706-542-1750 Fax: 706-542-3077
On Nov 4, 2020, at 1:28 PM, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Chimera PDB fetch is broken starting November 3 and a command like "open 1a0m" produces an empty model with no error.
We will be putting a new version (release candidate) of Chimera on the download page today or tomorrow that fixes this.
What happened is that the RCSB has shutdown the URL Chimera uses to fetch PDB files (e.g. https://www.rcsb.org/pdb/files/1a0m.pdb <https://www.rcsb.org/pdb/files/1a0m.pdb>). Although RCSB announced this long ago the Chimera development team missed that this URL was going away.
Tom
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