[Chimera-users] Calculation of RMSD between 2 PDB structures automatically

[Sumitro Harjanto]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20091021/cccce478/attachment.html>