Hi, By using modeller, I have generated 100 models. My next task is to cluster these models based on RMSD. Is there any option in the modeller to cluster models based on RMSD? Please let me know.
Thanks in advance
Regards Chandu
-------------------------------------------------- C.CHANDRA SEKHAR REDDY(Research Scholar) Dr.SOWDHAMINI'S LAB NATIONAL CENTRE FOR BIOLOGICAL SCIENCES TATA INSTITUTE OF FUNDAMENTAL RESEARCH UAS-GKVK CAMPUS BELLARY ROAD BANGALORE-560065 INDIA PHONE NO.#+91-(0)80- 2366 6251 E.MAIL# csreddy@ncbs.res.in chandubio@yahoo.co.in URL# http://www.ncbs.res.in/ --------------------------------------------------
csreddy@ncbs.res.in wrote: > By using modeller, I have generated 100 models. My next task is to cluster > these models based on RMSD. Is there any option in the modeller to cluster > models based on RMSD? Please let me know.
Sure, you can do simple RMSD-based clustering. See the cluster_cut argument to transfer_xyz: http://salilab.org/modeller/9v2/manual/node181.html
This is also used by automodel.cluster(): http://salilab.org/modeller/9v2/manual/node65.html
Ben Webb, Modeller Caretaker
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csreddy＠ncbs.res.in -
Modeller Caretaker