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 - I saw that my macOS was outdated (Starting SBGRID saying "- MacOS X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.