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So finally the solution was easy access... Thanks to someone who suggest me to do that, I created a new user, to verify if coot was ok under that session, and it was fine. Then I went back on my session, I removed the files below: 0-coot-history.py 0-coot-history.scm 0-coot.state.py 0-coot.state.scm I restarted Coot, and loaded my files (.pdb, .mtz and .cif), Coot didn't crash and I am now able to do a real space refinement. It should be my first intention to remove Coot preferences. Regards. 2018-03-12 21:39 GMT+01:00 Paul Emsley <[log in to unmask]>: > > On 12/03/18 14:05, M T wrote: > > Dear all, > > > > I restart this topic because the problem was finally not solved... > > You give me an opportunity to comment, I had previously missed the boat > while traveling. > > > > > Summary: > > - I am working on a structure with an unnatural ligand and I want to > > refine this ligand using Coot. > > Sounds like a fine plan. > > > - Each time I try to import the .cif of my ligand produced by PRODRG > > web server or through CCP4/ProDrg, coot crashes with error message > > below (see quoted messages). > > The first thing to do, when Coot crashes is to check for a new revision. > There's a good chance that the problem has been fixed and is just > waiting for you to download it. > > > - I sent my files to someone else and they are working on his computer > > (both are Mac and are using CCP4/Coot on same SBGRID server, with same > > files, and macOS was different). > > - I saw that my macOS was outdated (Starting SBGRID saying "- MacOS X > > versions 10.10 (Yosemite) and earlier are no longer officially > > supported"). > > - I did an update of my macOS to High Sierra (10.13.3). > > - I retried with same files, Coot crashed. > > For the record, the crash log would be highly helpful. > > > - I went back to PRODRG server to generate a simple .cif > > (CH3-CH2-CH2-CH3). > > Fine as it was in its day, PRODRG is no longer what we use for ligands. > We use Acedrg. If you want to use SMILES, you can use it on the command > line (that's what I do). If you want to use it from a sketch, use the > Ligand Builder in Coot. You can also use pyrogen (I do). > > > - I started Coot, opened the .cif file using "Import CIF > > dictionary...", Coot crashed. > > > > It seems that opening any .cif file on my computer causes Coot crash. > > Edit -> Preferences -> File Selector -> Modern File Chooser > > For the record (again) this is the site that I use to download Coot mac > binaries: > > http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot > > > > > > > Anybody has an idea to solve the problem? > > It was discussed on the mailing list in January and fixed by the next day. > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1801&L=COOT&F=&S=&P=5852 > > Regards, > > Paul. > >