The superimposition of the wildtype and mutant structures using PyMol resulted in high RMSD values such as 22.694 ,23.491. But when checked through US-alignment the values were 3.31 and 2.41. why this happened and what does this very high RMSD value mean? kindly do let me know your answers. thank you
Which of the different alignment algorithms are you using? Are you aligning a single domain, a multi-domain protein, a multi-chain protein? A repeat protein containing internal sequence homology? A very high rmsd in a sequence dependent alignment can be due to a sub-optimal sequence alignment - check the sequence alignment and the number of atoms used for the alignment to troubleshoot the alignment. In general, a sequence-independent alignment is more robust. I've attached a pdf file discussing different methods available in PyMol.
Annemarie Honegger thank you so much for your response Ma'am.
well, it is a multi-domain protein. I have superimposed the wild type and mutant type protein with the help of "super" command in pyMol. And i had to check the RMSD value.
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