El 24/01/12 18:53, Paul Emsley escribió: > Now that Coot uses the restraints dictionary to render ligands it has > become apparent that the method of doing so is problematic for typical > working situations. > > Say for example your read in > complex-XYZ00123456.pdb in which the ligand is called LIG > You read in the dictionary for XYZ00123456 and the ligand looks fine. > > Now read in > complex-XYZ00123457.pdb in which the ligand is called LIG > Different compound, same name, so same dictionary is used to render > XYZ00123457. > Result: tangled mess > > Read in dictionary for XYZ00123457 and now complex-XYZ00123457 looks > fine but XYZ00123456 is a tangled mess because the restraints for LIG > have been overwritten. > > So I am considering adding in a hack to Coot to make this situation less > problematic. > > A potential hack is to specify that it is to be used for molecule number > N (or a set of Ns) only. > > Doing this would make Coot internals messy so I have make this request > for comments before I spend time reworking things and producing a > solution that no-one will use. > > Thanks, > > Paul. >
I would prefer to give unique residue names to ligands rather than messing around with Coot internals: they could get infected with bugs. And really, is it so hard to give a unique identifier to each ligand? Make the messy people pay for their mess, not Coot. Please. -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
