Hi Tyler,<br><br>First, what question are you trying to answer? You're different peptides have completely different conformational spaces, simply because of the differences in degrees of freedom, so you can't compare the PCA results from one system with the other. That is, unless you pick a subset from each system, consisting of comparable particles, for which you can safely make the assumption that under equal circumstances should give the same eigenvectors and -values. From that assumption, you could try to make an assessment whether the behaviour between the systems is different.
<br><br>Also, since you're using only the first three residues for fitting, you generate a non-central covariance matrix. That would be useful if you would like to exaggerate certain motional features, right, but it makes the interpretation of PCA results difficult. If it's for the purpose of comparing things, I wouldn't go there if I were you. The non-centrality is also the reason that your standard deviations end up high. You're not subtracting the mean so your standard deviations is sqrt( sum(x^2)/N ) rather than sqrt( sum((x-average)^2))/N ). Is this really what you want to do? What are you expecting to get from this? I'd like to know the question your trying to answer and your assumptions on the nature of the data...
<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 4/7/06, <b class="gmail_sendername">Tyler Luchko</b> <<a href="mailto:tluchko@ualberta.ca">tluchko@ualberta.ca</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello,<br><br>Thank you for the previous responses. I still have some questions<br>about the eigenvalues however.<br><br>I should note that the frames of my trajectory have been fit to a<br>reference structure using the backbone atoms of the first three
<br>residues. This is because the peptide is a fragment of a much larger<br>protein.<br><br>1) If I wish to compare the eigenvalues of several peptides of<br>different lengths how would I normalize the eigenvalues? Do I simply
<br>divide by the number of atoms used in the calculation?<br><br>2) If the eigenvalue represents the sum of the variances for each<br>particle along the eigenvector then dividing the eigenvector by the<br>number of atoms used in the calculation should be the average
<br>variance. Likewise, the square root of this should be the average<br>standard deviation per atom. In my case, the first eigenvector is a<br>stretching in the length of the peptide. Shouldn't the average<br>standard deviation per atom along this stretching motion be smaller
<br>that the standard deviation in the length of the entire peptide, or<br>at least smaller than the extended length of the peptide?<br><br>Thank you,<br><br>Tyler<br><br>> Hi Tyler,<br>><br>> Note that the eigenvalue represents the sum of the variances for each
<br>> particle along the associated eigenvector. That seems quite<br>> reasonable to<br>> me.<br>><br>> Tsjerk<br>><br>> On 4/6/06, Tyler Luchko <<a href="mailto:tluchko@ualberta.ca">tluchko@ualberta.ca
</a>> wrote:<br>>><br>>> Hello,<br>>><br>>> I have performed PCA analysis, without mass weighting, on a peptide<br>>> using g_covar and g_anaeig. The first principal component generally<br>
>> corresponds to the stretching of the peptide. I understand that each<br>>> eigenvalue represents the variance in the motion along the associated<br>>> eigenvector. However, the square root of the variance for the first
<br>>> eigenvalue is ~20 nm while the maximum extended length of any peptide<br>>> is ~3 nm. I have tried normalizing the eigenvalues by the number of<br>>> atoms used for the analysis (73) but this gives the standard
<br>>> deviation of the motion to be ~2.2 nm, still much too large. I would<br>>> like to know how to normalize the eigenvalues to obtain reasonable<br>>> standard deviations from the eigenvalues.<br>>>
<br>>> Thank you,<br>>><br>>> Tyler<br>>><br>>><br>>> ________________________________________________________________<br>>> (_ Tyler Luchko Ph.D. Candidate _)
<br>>> _) Department of Physics University of Alberta (_<br>>> (_ Edmonton, Alberta, Canada _)<br>>> _) 780-492-1063 <a href="mailto:tluchko@ualberta.ca">
tluchko@ualberta.ca</a> (_<br>>> (________________________________________________________________)<br>>><br>>><br>>><br>>> _______________________________________________<br>>> gmx-users mailing list
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</a><br>>><br>><br>><br>><br>> --<br>><br>> Tsjerk A. Wassenaar, M.Sc.<br>> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>> Dept. of Biophysical Chemistry<br>> University of Groningen
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</div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
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