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:
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.
2018-03-12 21:39 GMT+01:00 Paul Emsley <pems...@mrc-lmb.cam.ac.uk>:
> 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 - I saw that my macOS was outdated (Starting SBGRID saying "- MacOS X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
> > Anybody has an idea to solve the problem?
> It was discussed on the mailing list in January and fixed by the next day.