Subject: RE: [modeller_usage] The selection of models
From: "Eswar Narayanan" <>
Date: Sun, 28 Mar 2004 20:37:18 -0800
Cc:
Organization: University of California - San Francisco
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: [mailto:modeller_usage-
> ] On Behalf Of Binbin Liu
> Sent: Sunday, March 28, 2004 4:10 AM
> To:
> 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
>
> http://salilab.org/mailman/listinfo/modeller_usage