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the failure seems to be due to outdated or incorrect PDBe links, rather than a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
<[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
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