Dear Dr. Kelley,
I modeled one of the rice proteins in the intensive mode. I was very happy with the model because it looked like its Arabidopsis counter part, which has 80% I.D.. On close observation, I found that the server has chosen 6 other proteins which have only 32-41% I.D. but it has ignored the Arabidopsis model that has highest similarity. Is there any specific reason behind that? Is there a way that we can manually select the known models to consider?
Thanks in advance!