[AMBER] Where can I find a tutorial/manual on the IED in VMD for visualizing PCA data from ABMER?

From: Catein Catherine <askamber23.hotmail.com>
Date: Fri, 23 Jul 2010 23:54:49 +0800

Dear Sir/Madam,


I am new to PCA analysis, I could like to read a tutorial or manual on the meaning of the data that I view in VMD+IED window. Could you pls kindly help?


I am using VMD+IED to visualize my PCA analysis of a trajectory. I classified the movement of the protein (represented by Ca) into 20 vectors.


I open the IED and found 20 eigenvectors, the 1st eigenvectors has a middle value of 20 (the value where the cursor stay when i click the eigenvector's box, but I can move the cusors from -20 to 30. While the other 19 eigenvectors has different values.


My questions is what does those values meant. How can I know if the first 3 vectors represent over 90% of the movement in the protein?


Did anyone come across a tutorial or manual on those values's meaning, it seems to me that they are not available in amber nor vmd nor IED webpages.


Best regards and pls kindly help,


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Received on Fri Jul 23 2010 - 09:00:05 PDT
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