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The resolution is 2.5 A. Indeed, there should be no constraint to tie the ligands together, but why do the 2 compounds overlap exactly (in the identical part) if I refine only one of them at a time in REFMAC and superimpose the structures afterwards ?? Why do they overlap exactly when I use CNX istead? Biochemically, I expect them to bind in a similar way, but for sure there is no guarantee that they will bind exactly the same way (for the identical part). Regards Christian Dr. Christian Engel Research Scientist Structural Biology Sanofi-Aventis Tel.: +49 (0)69 305 12946 Fax: +49 (0)69 305 80169 Sanofi-Aventis Industriepark Höchst Building G865A 65926 Frankfurt am Main Germany -----Ursprüngliche Nachricht----- Von: Eleanor Dodson [mailto:[EMAIL PROTECTED] Gesendet: Donnerstag, 1. Juni 2006 12:21 An: Engel, Christian PH/DE Cc: [EMAIL PROTECTED]; [email protected] Betreff: Re: AW: [ccp4bb]: multiple occupancy/different ligands You dont say what the resolution for your data. However there is no constraint to tie the ligands together, so I am not too surprised that they dont exactly overlap after refinement. Would you even expect this to happen biochemically? I would half expect the peripheral differences to push them a little apart.. Eleanor [EMAIL PROTECTED] wrote: >I am not 100% sure that REFMAC is sorting that out correctly, though. > >I had a case recently where I tried to refine two very similar ligands binding >to the same binding site. I tried the way Eleanor suggested and I also tried >defining them as Alig and Blig. REFMAC doesn't complain and refines the two >ligands, but in the part where the two ligands are identical they don't >superimpose exactly anymore. If I refine them separately and superimpose them >afterwards they are superimposing exactly in the parts that are identical! > >To me it looks as if the two ligands in the same site still repel each other >but that they are kept together by the x-ray term. Is there a well documented >example, where somebody successfully managed to refine two ligands in the same >binding site and how (s)he defined the two ligands and created the >dictionaries exactly? > >If I try the same refinement in CNX with some patching, the two ligands >superimpose exactly in the identical parts. > >Regards >Christian > >Dr. Christian Engel >Research Scientist >Structural Biology >Sanofi-Aventis >Tel.: +49 (0)69 305 12946 >Fax: +49 (0)69 305 80169 > >Sanofi-Aventis >Industriepark Höchst >Building G865A >65926 Frankfurt am Main >Germany > > > >-----Ursprüngliche Nachricht----- >Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Auftrag von >Eleanor Dodson >Gesendet: Donnerstag, 1. Juni 2006 10:50 >An: Elena Kovaleva >Cc: [email protected] >Betreff: Re: [ccp4bb]: multiple occupancy/different ligands > > >Just put them both in, each with partial occupancy, and 2 dictionary >entries. REFMAC should sort it out.. > Eleanor > >Elena Kovaleva wrote: > > > >>*** For details on how to be removed from this list visit the *** >>*** CCP4 home page http://www.ccp4.ac.uk *** >> >> >>Hi, >>I wonder if there is someone out there who knows a way to trick Refmac >>into doing simultaneous refinement of somewhat superimposable but >>structurally different ligands (both of which partially occupy the >>same site). For example if a substrate and an intermediate are present >>or an intermediate and a product. Would making a library file for a >>"macro"-ligand consisting of 2 separate parts (separate connectivity, >>partial occupancy, etc) be a reasonable approach or is there an >>easier/proper way to refine partially present ligands? >>Will be grateful for any suggestions. >>Thanks, >>Lena >> >>Elena G. Kovaleva, Ph.D. >>Department of Biochemistry, University of Minnesota >>5-202 BS&BE, 312 Church St, Minneapolis, MN 55455 >>Ph (612) 625-3688, Fax (612) 625-2163 >> >> >> >> > > > > > >
