On 15/07/10 09:32, Huw Jenkins wrote:
I have noticed this too - I think it's because when you start coot with the command line argument '--pdb filename.pdb' the pdb is read*before* coot.py, coot-preferences.scm or ~/.coot so the bond preferences are only applied to the next pdb opened from within coot.
For the record, I think that it should read the pdb files after reading .coot.py - it is not trivial to fix.
Paul.
