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[EMAIL PROTECTED] wrote on 06/08/2006 11:43:43 AM: > *** 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 > Hi Huangwei - Most (all?) NMR ensembles from the PDB have a minimized, averaged structure associated with them - look for other submissions from the same authors. Unless the authors have done something rather odd, the averaged structure and the ensemble should be in the same position and orientation; thus, you can apply the same rotations and translations to the averaged structure as Amore applied to the ensemble and get the equivalent result. (Note that you also need to apply the initial translation to the origin and reorientation that Amore does.) Probably just as effective would be to least-squares superimpose the averaged structure on your Amore-output ensemble. LSQMAN will do this, I believe. For further refinement, don't forget to trim off the floppy bits - N and C termini and disordered loops that have very high rmsd's in the ensemble but show up in the averaged structure anyway. - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
