Renaming ligands is a nightmare if you have a lot of structures or refinement runs to compare. For example, if you wanted to compare the results of a few different refinement strategies, and also look at the previous refinement run, you would have to rename the same ligand many times. I like the idea Paul suggested of specifying which molecule number to attach the cif to.
Kendall Nettles On Jan 24, 2012, at 2:59 PM, Miguel Ortiz Lombardia wrote: > 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
