On 13/03/2018 07:36, M T wrote:
> 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 <http://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] <mailto:[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 - I saw that my macOS was outdated (Starting SBGRID saying "- MacOS X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
> <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
> <https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1801&L=COOT&F=&S=&P=5852>
>
> Regards,
>
> Paul.
>
>
In case it was not clear how Michel's answer was related to mine, the reason coot was fine when starting
from fresh is that the default option for the file selectors/choosers is "Modern" and Michel had changed
those to "Classic" - those options get stored in $HOME/.coot-preferences. You can additionally modify them
in your 0-coot.state.py and 0-coot.state.scm files (in the current directory).
Regards,
Paul.
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