Hi Tsjerk,<br><br>Thanks for all the clarifications about PCA you make on the mailing list! I have a question about the commandlines you wrote. Why do you use the .tpr file with the "-s" flag? Is it because you want to compare the mass-wheighted covariance matrices? I use to calculate the covariance matrices by giving to g_covar a .pdb file with the "-s" flag and then calculate the RMSIP without giving any structure file. I guess no masses are used in that covariance analysis, right? Do you recommend using atom masses for PCA in general?<br>
<br>Thanks in advance for any help.<br>Thomas <br><br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
- If you want to project the x-ray structures onto the eigenvectors<br>
from the MD simulations, you have to use<br>
<br>
g_anaeig -v eigenvec_from_md.trr -s reference.tpr -f xray_structures.pdb -proj<br>
<br>
- If you want to compare the similarity of the eigenvectors obtained<br>
from MD and from your crystal structures, you have to do PCA on both<br>
sets separately and then<br>
<br>
g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig<br>
eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr<br>
-inpr<br>
<br>
<br clear="all"></blockquote></div><br><br><br><br>-- <br>
<p style="margin-bottom:0cm" align="LEFT">======================================================================</p>
<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
<p style="margin-bottom:0cm" align="LEFT">Biomedical Research
Foundation, Academy of Athens</p>
<p style="margin-bottom:0cm" align="LEFT">4 Soranou Ephessiou , 115 27
Athens, Greece<br><br>email: <a href="mailto:tevang@bioacademy.gr" target="_blank">tevang@bioacademy.gr</a></p>
<p style="margin-bottom:0cm" align="LEFT"> <a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>website:
<a href="https://sites.google.com/site/thomasevangelidishomepage/" target="_blank">https://sites.google.com/site/thomasevangelidishomepage/</a></p>
<p style="margin-bottom:0cm" align="LEFT"><br>
</p>
<br>