Kendall, not sure if COOT is the right tool for this purpose. The main focus of the program is for easy and excellent model building one structure at a time, which it does very well. What you are describing is really more in the realm of 'density aware' professional modeling tools, like MOE or MAESTRO, which are really more geared towards that purpose.
Carsten -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[email protected]] On Behalf Of Kendall Nettles Sent: Tuesday, January 24, 2012 3:26 PM To: [email protected] Subject: Re: [COOT] New restraints, same name 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
