I understand that "X" labels the correspondent frames to the cluster
> members. I wrote a python script to translate "X" to frame number. But
> what I wanted to know was how to obtain or extract the frame numbers
> for the cluster representatives in "filename.rep.ci" files.
One "dumb" trick you may try is to use the representative structure as
reference and run rms fitting for the entire trajectory. The one with rmsd
of 0 should be the representative frame.
> Since ptraj already has "rms" command, rms fitting in clustering seems
> a bit redundant if "rms" command is explicitly required prior to
> running "cluster" command.
The rms command will fit to a specific structure. In clustering, the
structures in the trajectory will be aligned to different representative
structures of clusters to obtain reasonable centroids.
Good luck,
Jianyin
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun Jun 01 2008 - 06:08:00 PDT
