PCA/NMA differences
Issue #817
new
Hello Bio3D community, I am currently working on PCA and NMA ~100 protein structures. Will removing a single protein structure alter my PCA/NMA results by a lot? For example, when I run PCA/NMA with a certain protein structure, I get significantly different results from when I remove that certain protein structure. It seems as there is a huge differences within the results, please let me know if this is normal.
Comments (2)
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The first figure shows the pc1 and pc2 axes with the 3rag protein. On the other hand, the 2nd figure shows the pc1 and pc2 axes without the 3rag protein. - Log in to comment
For the PCA, yes, removing one structure may affect the result. But for NMA, it should have no big effect because each NMA is calculated separately for each structure.
It would be helpful if you can provide more detail, for example, post some of the results you worried about, along with example data for us to reproduce the results/problems.