Dear Daniel, I was able to reproduce the same error, but also realised that I was 4-5 updates behind the latest version of CCP4 and using its Coot 0.8.9.1. With the latest update to 0.8.9.2 the problem went away. So it may have been a bug that was fixed within the latest CCP4.
Best, Tim On Sunday, January 19, 2020 7:54:47 PM CET Keedy, Daniel wrote: > I am indeed in a directory I own (~/Desktop in this case). I tried > downloading ccp4-7.0 instead of the older version I had (ccp4-6.5) and now > /Applications/ccp4-7.0/bin/coot works as expected. So, still not sure why > the package Coot didn’t work in this regard — but at least I have found a > workable solution. > Thanks all, > > ~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 7:13 PM, Yong Wang > <wang_yon...@lilly.com<mailto:wang_yon...@lilly.com>> wrote: > I believe the problem is with the networking protocol (access or security > related). I have had similar problems with my work computer (using > wincool) but on my home computer there is no problem. > Yong > > From: Mailing list for users of COOT Crystallographic Software > <COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK>> On Behalf Of Keedy, > Daniel Sent: Friday, January 17, 2020 4:45 PM > To: COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK> > Subject: [EXTERNAL] Re: error fetching coordinates from RCSB > > EXTERNAL EMAIL: Use caution before replying, clicking links, and opening > attachments. > 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<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_valid > ation.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 > > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
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