Indeed, newer versions should have the download location fixed (*). If needed, you can always rely on PDB-REDO since the location doesn’t change (x).
HTH, B (*) note to self: maybe this could be configurable so that it doesn’t break when ebi changes path.... (x) well it hasn’t so far... *************************************************** Dr. Bernhard Lohkamp | Associate Professor/Lektor/Docent Teaching Unit/Biomedicum D9 Dept. of Medical Biochemistry and Biophysics (MBB) | Karolinska Institutet SE-171 77 Stockholm Sweden +46 8 52487055 [email protected] | ki.se > -----Original Message----- > From: Mailing list for users of COOT Crystallographic Software > <[email protected]> On Behalf Of Andrea Smith > Sent: 12 September 2025 09:20 > To: [email protected] > Subject: Re: WinCoot cannot load model and map > > You don't often get email from 00010d84b4ba0dbf-dmarc- > [email protected]. Learn why this is important > <https://aka.ms/LearnAboutSenderIdentification> > > > It looks like the issue for me is not with opening maps or models in WinCoot1 > (that works fine, e.g. with PDB-Redo fetch). The problem seems to only > happen when WinCoot tries to fetch data directly from PDBe — the URLs it > calls (e.g. https://www.ebi.ac.uk/pdbe/entry-files/download/2psf.ent) fail to > download. So the failure seems to be due to outdated or incorrect PDBe > links, rather than a problem with my local installation. Since I am using > WinCoot 1.1.07 (from CCP4-9), this may already be corrected in newer > standalone versions. > > For me: > > * fetch from PDB redo works. I get both map and model. > * fetch PDB using accession code gives: > PDB Accession Code: 2psf > frame: 0x1974be52310 > DEBUG:: extracted accession code handle mode n 10 > debug:: safe_python_command() PyRun_SimpleString() import > get_ebi ; get_ebi.get_ebi_pdb("2psf") > INFO:: Creating directory coot-download > WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe/entry- > files/download/2psf.ent failed > WARNING:: Error reading coot-download/2psf.pdb.ent > WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe/entry- > files/download/2psf.cif failed > WARNING:: Error reading coot-download/2psf.cif > * fetch PDB and map using EDS gives: > PDB Accession Code: 2psf > frame: 0x1974be52310 > DEBUG:: extracted accession code handle mode n 12 > debug:: safe_python_command() PyRun_SimpleString() import > get_ebi ; get_ebi.get_eds_pdb_and_mtz("2psf") > ::::::::: pdb_file_name: coot-download\pdb2psf.ent > ::::::::: mtz_file_name: coot-download\2psf_map.mtz > model_url: https://www.ebi.ac.uk/pdbe/entry- > files/download/pdb2psf.ent > mtz_url: https://www.ebi.ac.uk/pdbe/entry- > files/download/2psf_map.mtz > WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe/entry- > files/download/pdb2psf.ent failed > WARNING:: retrieve of url https://www.ebi.ac.uk/pdbe/entry- > files/download/2psf_map.mtz failed > INFO:: read pdb model status: False > INFO:: read mtz data status: False > > > > > Čtvrtek, Září 11, 2025 20:17 CEST, Leticia Leon <00012f02353b1731-dmarc- > [email protected]> napsal: > > > > In my case, I can upload the .pdb or .cif, for the model, the electron > density map I cannot upload and in the case of Fetch a PDB and Map, I have > this error: > > (MacCoot:26462): GLib-GIO-CRITICAL **: 12:16:02.789: > g_simple_action_activate: assertion 'simple->parameter_type == NULL ? > parameter == NULL : (parameter != NULL && g_variant_is_of_type > (parameter, simple->parameter_type))' failed > > ######################################################### > ############### > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > > > ________________________________ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww > .jiscmail.ac.uk%2Fcgi-bin%2FWA- > JISC.exe%3FSUBED1%3DCOOT%26A%3D1&data=05%7C02%7CBernhard.Lohk > amp%40KI.SE%7Cb978f59651274bba0fa008ddf1ccc24a%7Cbff7eef1cf4b4f32 > be3da1dda043c05d%7C0%7C0%7C638932584105515123%7CUnknown%7CT > WFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXa > W4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=1701 > GYOEVhV5hxmcW8PabecKFk5rzSM9YDH4wKY6Xbs%3D&reserved=0> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. 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