PCA (contribution of each residue to PCA)

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Rezvan Chitsazi

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Aug 9, 2022, 4:47:13 PMAug 9
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Hello all,

How we can show/plot the contribution of each residue vs. PCA components (e.g. residue position vs. PC(1))? 
& how we can just show (color-code) those residues that contributed most (e.g. PC1, PC2) on the structure?

any suggestions/comments would be appreciated.

Thank you!!
Leila

Kabir Biswas

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Sep 25, 2022, 7:05:40 AM (2 days ago) Sep 25
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It would be nice to see a script to get individual residue contributions to PC1 and PC2.
Thanks,
Kabir

Oliver Beckstein

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Sep 26, 2022, 12:53:44 PM (20 hours ago) Sep 26
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Hi Kabir and Leila,

If you provide the equations that are needed to calculate the desired quantities then members of the list can help with how to implement them using MDAnalysis.

In general, if you're looking for a new feature or want help with a question then it's best to provide as much information as possible. For instance, find papers that already describe the methods (and cite them together with a link to the paper itself so that anyone interested could easily look at it). Include equations in your email. Say clearly what the input is and what you expect as output. The more of the work you already do, the more likely it is that you get a useful answer.

(Just speaking for me: I have plenty of other things to do in my normal jobs and I don't get paid for working on MDAnalysis (and this is true for almost everyone on the list). I might have a maximum of 5 mins time to spare to answer a mailing list question. If I can see that a response requires longer that this time then I'll typically don't send a response at all.)

Best wishes,
Oliver
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