Extracting f, v , u vectors

[arianabrenner]

How do I extract the f, v, and u vectors (as defined in the 1CPN publication) for each bead? Specifically, I am most interested in the orthonormal (or f) vector of each nucleosome. Are these the c_q[x] values in the traj.dump file (where 1<=x<=4)? If so, is there a script to extract these values in a format similar to the traj_1cpn.xyz format? Thanks!

[lequieu]

c_q[x] in traj.dump is the quaternion that rotates f0,v0,u0 vectors into the instantaneous f,v,u vectors of a given site. There's a trajectory parsing tool located in src/include/trajectory_iterator.h where this calculation is performed. Take a look at the many scripts in src/analysis/ for how to use it. Its been a while since I've used these tools myself but src/analysis/calc_fvu_angle.cpp looks like a reasonable place to start.