That didn't come out right. What I meant to say was that he are often comparing structures from a series of closely related compounds.
Kendall On Jan 24, 2012, at 3:19 PM, "Kendall Nettles" <[email protected]> wrote: > 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
