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Clustering is the process of gathering objects into groups based on their feature's similarity. In this paper, we concentrate on Weighted Kernel K-Means method for its capability to manage nonlinear separability and high dimensionality in the data. A new slight modification of WKM algorithm has been proposed and tested on real Rice data. The results show that the accuracy of proposed algorithm is higher than other famous clustering algorithm and ensures that the WKM is a good solution for real world problems.