Hi Phil, The only output in the terminal for me when I try the File -> Fetch command is this:
PDB Accession Code: 1sug BL WARNING:: retrieve of url http://www.ebi.ac.uk/pdbe-srv/view/files/1sug.ent failed handle_read_draw_molecule_with_recentre ("coot-download/1sug.pdb.ent", 1) WARNING:: Error reading coot-download/1sug.pdb.ent Here is my output for the command you mentioned: ❯ pwd /Users/dkeedy ❯ env | grep -i coot ❯ which coot /usr/local/bin/coot ❯ ls /Applications/ccp4-6.5/bin/coot /Applications/ccp4-6.5/bin/coot BTW, when I run “/Applications/ccp4-6.5/bin/coot” directly, my windows pop up in the expected places (suggesting ~/.coot has been read), but fetch still fails as follows (the error message is slightly different which may be just due to a different Coot version, 0.8.1 instead of 0.8.9.2): PDB Accession Code: 1sug (get-ebi-pdb "1sug") DEBUG:: in get-url-str: "1sug" "http://www.ebi.ac.uk/pdbe-srv/view/files/1sug.ent"; pdb (handle-read-draw-molecule-with-recentre "coot-download/1sug.pdb.ent" 0) Reading coordinate file: coot-download/1sug.pdb.ent There was an error reading coot-download/1sug.pdb.ent. ERROR 44 READ: Non-existent or empty file. No Spacegroup found for this PDB file There was a coordinates read error Any other ideas? ~Daniel — Daniel A. Keedy, PhD Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry PhD Programs, CUNY Graduate Center dke...@gc.cuny.edu<mailto:dke...@gc.cuny.edu> (NOT @asrc) | https://keedylab.org | 212-413-3246 On Jan 17, 2020, at 4:33 PM, Phil Jeffrey <pjeff...@princeton.edu<mailto:pjeff...@princeton.edu>> wrote: 0.8.9.2 via CCP4 installation gives me: PDB Accession Code: 1sug (get-ebi-pdb "1sug") DEBUG:: in get-url-str: "1sug" "https://www.ebi.ac.uk/pdbe-srv/view/files/1sug.ent"; pdb INFO:: Creating directory coot-download ------------- no veryifypeer https://www.ebi.ac.uk/pdbe-srv/view/files/1sug.ent coot-download/1sug.pdb.ent (handle-read-draw-molecule-with-recentre "coot-download/1sug.pdb.ent" 0) INFO:: Reading coordinate file: coot-download/1sug.pdb.ent PDB file coot-download/1sug.pdb.ent has been read. Spacegroup: P 31 2 1 INFO:: Found 1 models Model 1 had 0 links in add_molecular_symmetry_matrices() made 1 biomt matrices Molecule 0 read successfully DEBUG:: there were 1 types with no dictionary WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() WARNING:: missing atoms bad atom indexing in atom_index_quad::torsion() --------- run this python-string: "pdb_validate(\"1sug\",0)" ------------- no veryifypeer http://ftp.ebi.ac.uk/pub/databases/pdb/validation_reports/su/1sug/1sug_validation.xml.gz pdb-validation-1sug.xml.gz and successfully loads the file I would guess your installations might be a little mangled from having multiple versions - do [mol-xray2:~/Desktop/test] phil% env | grep -i coot [mol-xray2:~/Desktop/test] phil% which coot /Applications/ccp4-7.0/bin/coot (but I don't rely on a ~/.coot file) Phil On 1/17/20 3:58 PM, Keedy, Daniel wrote: Hello, I have Coot installed on macOS 10.14.6, using the Bill Scott binary method. It has worked well for me for awhile. However, recently it stopped being able to fetch PDB files using several approaches I commonly use. For File -> Fetch PDB using accession code, it gives an error: “Failed to read coordinates file 1sug.pdb.ent” and does nothing else. The coot-download folder is empty. For File -> Fetch PDB & map using EDS, it gives a similar but slightly different error: “Failed to read coordinates file pdb1sug.ent” and does nothing else. The coot-download folder is empty. However, for File -> Fetch PDB & map using PDB-REDO, it works. The coot-download folder is still empty — but the model and map appear in the graphics window. I was previously using an older version of Coot from perhaps 2018ish. I then removed it entirely from /usr/local/bin/coot and /opt/coot and ~/Library/Coot, and re-installed using the Bill Scott binary method. Now I have 0.8.9.2-pre EL (revision count 7607) — though the splash screen actually says 0.8.9.1. The problem persists. (Moreover, it doesn’t seem to have loaded my ~/.coot file anymore, since I had specified pre-set window positions in that file which previously were reflected when the program started, but now are not.) Can anyone provide any help please? Thanks in advance, ~Daniel — Daniel A. Keedy, PhD Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry PhD Programs, CUNY Graduate Center *dke...@gc.cuny.edu<mailto:dke...@gc.cuny.edu> <mailto:dke...@gc.cuny.edu> (NOT @asrc)* | https://keedylab.org<https://keedylab.org/> | 212-413-3246 ------------------------------------------------------------------------ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
