To give some context, I have a set of decoys that I've run cluster analysis on and now I'm trying to look at analyzing the clusters to see what similarities there are within the cluster. The long term goal is to analyze the 0th cluster, which contains the most structures, which is hypothesized to be the most likely place for where the true structure will be. That being all fine and dandy, I've isolated the poses that I need and was trying to determine the rms of each pose against the middle pose of the cluster. This was supposed to be a 15 minute exercise in double checking assumptions, but it became more complicated.
I used the 'score.linux.gccrelease' script with the following flags:
I've removed a lot of the directory pointing and renamed from what my file names are, but that's the gist of it. At that point everything seemed to be working fine. In the output I had a slew of information, including columns for rms and allatom_rms. In hopes of lining up the poses with the corresponding values, I discovered that I had more values than I had poses. I then tried getting a smaller cluster and retrying the whole process. With a 24 pose cluster I received 35 pairs of values(rms, fullatom_rms), two of which had rms and fullatom_rms equal to zero.
If there is anything else that would be helpful in solving the problem, let me know.