For additional informations when launching Coot from the terminal I get these messages at startup. Wonder if the presence of 2 data is OK ?
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON: /Applications/ccp4-8.0/coot_py2/lib/data/monomers/ There are 244 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/list/mon_lib_list.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ALA.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ASP.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ASN.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/CYS.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLN.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLY.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GLU.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PHE.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/h/HIS.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/i/ILE.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/l/LYS.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/l/LEU.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/m/MET.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/m/MSE.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PRO.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/ARG.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/s/SER.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/THR.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/v/VAL.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/TRP.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/t/TYR.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/p/PO4.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/s/SO4.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/GOL.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/CIT.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/e/EDO.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/a/A.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/c/C.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/g/G.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/u/U.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DA.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DC.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DG.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/d/DT.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/h/HOH.cif There are 2 data in /Applications/ccp4-8.0/coot_py2/lib/data/monomers/n/NA.cif Spacegroup: P 1 (filter-fileselection-filenames-state) (get-active-map-drag-flag) (use-graphics-interface-state) INFO:: coot.py imported ... > Le 28 avr. 2022 à 19:35, Georg Mlynek <[email protected]> a écrit : > > Dear Xavier, for the nomenclature error there is this fix. > > add this to your startup-script > > set_nomenclature_errors_on_read("ignore") > > > I would be also interested to answer the first issue. > > Br, Georg. > > > > Am 28.04.2022 um 19:22 schrieb Xavier Brazzolotto: >> Dear Phenix and Coot users and developers >> >> I've recently observed a kind of conflict between Phenix and Coot. >> >> I am using Phenix v1.20.1-4487 and Coot 0.9.8.1 from thee CCP4 8.0 suite >> under macOS Monterey (v12.3.1). >> >> If I launch Coot through Phenix via the « Open in Coot » tab (the path to >> Coot has been defined in Phenix preferences), Coot opens correctly and >> displays the structure with the « Connected to Phenix tab". However if I >> wand to do some RSR then, I get this error message. >> >> <Capture d’écran 2022-04-28 à 18.48.33.png> >> >> In parallel if I use Coot by itself (launched through the terminal), RSR >> works well… but upon opening Coot states that there is some "Nomenclature >> errors ». >> >> <Capture d’écran 2022-04-28 à 19.19.29.png> >> >> I wonder if there would be some conflict between residue libraries between >> Phenix and Coot ? >> >> Just to leet you know I’ve also recently tried to install/comlplie the Coot >> v1 pre-version to have a loot at it and I do also have libccp4 installed in >> my Homebrew. Maybe everything comes from that ? >> >> Xavier >> >> >> >> To unsubscribe from the COOT list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 >> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
