Re: [ccp4bb]: how to convert an ensemble model into a single model

[Jeroen Mesters]

The reason(s) for obtaining (calculating) an ensemble of structures are 1) true flexibility and of course 2) lack of data! This holds true for both NMR and Xtallography. Each single model is in agreement with the data (i.e. was refined against the data) and an average model is probably the worst one of all to take. Better to use one of the models and remove the parts that differ most among all the models. J. [EMAIL PROTECTED] wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** An easy alternative is to calculate the average structure and choose the individual model with lowest rms deviation from the average as representative of the ensemble. Since this is a typical task in the NMR field, this option is mostly found in NMR software, e.g. MOLMOL. Of course, conclusions drawn using these two methods may differ, particularly if the individual models deviate a lot in certain parts of the structure. In this case, an energy-minimized average structure would probably be more "representative". CNS provides such a model_minimize input (for use without experimental data). Oliver --------------------- Dr. Oliver H. Weiergraeber IBI-2 (Structural Biology) Research Centre Juelich D-52425 Juelich Germany Phone: +49-2461-612028 Fax: +49-2461-612020 --------------------- ----- Original Message ----- From: huangwei <[EMAIL PROTECTED]> Date: Thursday, June 8, 2006 5:43 pm Subject: [ccp4bb]: how to convert an ensemble model into a single model *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Hi guys, I have tried AmoRe using a NMR ensemble, thus get an solution in the form of ensemble.I was informed that "a single macromolecular model derived from an ensemble of NMR models by averaging atom positions and minimizing the energy".Could you please tell me some software about this? Or any better way to convert an ensemble model into a single model? Best regards! ????????huangwei [EMAIL PROTECTED] ??????????2006-06-08 -- Jeroen Raymundus Mesters, Ph.D. Institut fuer Biochemie, Universitaet zu Luebeck Ratzeburger Allee 160, D-23538 Luebeck Tel: +49-451-5004070, Fax: +49-451-5004068 E-mail: [EMAIL PROTECTED] Http://www.biochem.uni-luebeck.de -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --