[Chimera-users] Calculation of RMSD between 2 PDB structures automatically
u0601918 at nus.edu.sg
Wed Oct 21 04:46:16 PDT 2009
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. =]
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users