I presume that you are talking about model-template RMSD. Depending on the quality of your alignment most of the models *will* have low RMSDs. That is the way MODELLER works.
One way you can choose a single model is by picking the one with the best objective function score. Alternately, you can assess the models with other programs that use potentials of mean force (statistical potentials; eg PROSAII) and choose one from the assessments they provide.
Eswar.
--- Eswar Narayanan, Ph.D Mission Bay Genentech Hall 600 16th Street, Suite N474Q University of California, San Francisco San Francisco, CA 94143-2240 (CA 94158 for courier) Tel +1 (415) 514-4233; Fax +1 (415) 514-4231 http://www.salilab.org/~eashwar
> -----Original Message----- > From: modeller_usage-bounces@salilab.org [mailto:modeller_usage- > bounces@salilab.org] On Behalf Of Binbin Liu > Sent: Sunday, March 28, 2004 4:10 AM > To: modeller_usage@salilab.org > Subject: [modeller_usage] The selection of models > > Dear Modellers, > > 100 models were generated based on one template. Their atomic RMSDs all > are > less than 0.4 Angstroms. Does any body know any other way I can find a > representative model from the 100 models. > > Many thanks. > > > Binbin > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage