Hi all, When opening Coot from ccp4 8 in Phenix, there may be an issue with the restraints since some environment variables may not be set. The terminal should show something like
/Applications/ccp4-8.0/coot_py2/bin/coot: line 81: /Applications/ccp4-8.0/coot_py2/bin/ccp4.setup-sh: No such file or directory WARNING:: Coot REFMAC dictionary override COOT_REFMAC_LIB_DIRfailed to find a dictionary /Applications/ccp4-8.0/coot_py2/share/coot/lib WARNING:: COOT_PREFIX set, but no dictionary lib found WARNING: Failed to read restraints dictionary. WARNING: in init_refmac_mon_lib, file "/data/monomers/list/mon_lib_list.cif" not found. WARNING: file /data/monomers/a/ALA.cif is not a regular file ... One workaround that should work is to make a symbolic link of the ccp4-8.0/bin/ccp4.setup-sh file in ccp4-8.0/bin/ccp4/coot_py2/bin. You should then see that Coot loads restraints INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /Applications/ccp4-8.0/lib/data/monomers/ There are 223 data in /Applications/ccp4-8.0/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Applications/ccp4-8.0/lib/data/monomers/a/ALA.cif ... Alternatively, you can also source the ccp4-8.0/bin/ccp4.setup-sh file before starting Phenix, or manually set CLIBD_MON. Then, the necessary environment variable is set. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Tue, Jul 26, 2022 at 7:17 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On 27/07/2022 01:44, Dale C wrote: > > Hi all, > > > > I recently updated my ccp4 package to Program suite v8.0.002 and i have > now run into a few issues with other programs. The issues are highlighted > below... > > > > - When i click 'Open in Coot' on any output through Phenix (so far only > tested phenix.refine and phenix.phaser), i no longer see anything open. Nor > do i see the "Connected to Phenix" button in the toolbar on Coot. > There is probably useful information written to the terminal. AFAIR, you > are not the first person to experience this, I forget what the problem > and solution was but I think that it was trivial. > > > > - Coot also seems to have an issue with not loading the amino acid > restraints so when i click real-space refine, i get the error 'unable to > find restraints for residue x,y,z'. > > > When you start Coot, what does it say as it tries to load the > dictionaries for the standard residues? > > Paul. > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
