Hi Andrew,
On 28/04/15 10:35, Andrew Leslie wrote:
I am trying to get coordinates and maps into COOT for a PDB entry that is only
in mmcif format.
If I select any of the "Fetch PDB …" options in COOT, I get the following error
message:
DEBUG:: in get-url-str: "4wz7"
"http://www.ebi.ac.uk/pdbe-srv/view/files/4wz7.ent"; pdb
(handle-read-draw-molecule-with-recentre "coot-download/4wz7.pdb.ent" 0)
Reading coordinate file: coot-download/4wz7.pdb.ent
There was an error reading coot-download/4wz7.pdb.ent.
ERROR 20 READ: Attempt to read unknown-type file.
No Spacegroup found for this PDB file
There was a coordinates read error
PDB Accession Code: 4wz7
This indicates that Coot was trying to get the PDB file.
If I download the mmcif PDB file and read it into COOT using the "Open
coordinates" option then this works OK, so I can get the coordinates but I cannot
get the density map.
If I go direct to the EDS server (http://eds.bmc.uu.se/eds/) and put in the PDB code I
get the error message "Sorry, there is no structure factor entry for 4wz7".
Does anyone know an easy way around this to get the maps into COOT, or do I
just have to download the mmcif structure factor file and use a program (e.g.
refmac) to calculate the map coefficients ?
This is a pain, I agree. Perhaps Coot should try to get the mmcif/pdbx
file if the PDB file doesn't work.. Hmm.
Paul.
