VMD-L Mailing List

From: L. Signorile (l.signorile_at_erasmusmc.nl)
Date: Thu Oct 13 2016 - 06:32:24 CDT

Hi,
 I am trying to compare three structures of the same protein (i.e., wild-type and two mutants) after performing EDA with ProDy. When I load the .nmd files the structures and modes are displayed, but are not aligned, since in the original .pdb files the coordinates were quite different.
How can I align the alpha carbon traces (and modes) for the three structures AFTER I have obtained the .nmd files? I would rather avoid first aligning the structures and then re-write the pdb files with the new transformed coordinates (and then re-perform EDA).
Any suggestions?
Thanks

Luca Signorile
PhD candidate, Cell Biology dept.
Erasmus MC
Rotterdam, NL