Hi,

I have about 150 peptide structures in PDB format. I would like to compare each of them with a Template Structure (also in PDB format) and obtain an RMSD measurement for each comparison.

These peptides are similar in structures to the template but may have very low sequence similarity/conservation.

So my question is:

1. what is the command I should use given this scenario..? I was quite confused with the many different commands such as: rmsd, match, ensemblematch, matchmaker,… can anyone enlighten me on the differences among them. I would like to find one which can align/superimpose 2 peptides and calculate RMSD (Ca or backbone)

2. Is there a way to automate the process through scripting..?

I’m still young with CHIMERA so please pardon my ignorance. =]

Cheers,

Sum