VMD-L Mailing List

From: Karne, Sai Harish Babu (saikarne_at_iupui.edu)
Date: Mon Apr 20 2009 - 17:09:51 CDT

Hi All,

I am new to VMD, I am using the multiseq to plot the per residue RMSD
plot for a bunch of proteins (same proteins but different pdb_id's).
After I align the structures using the STAMP from tools option in
Multiseq, I notice some gaps (represented by dashes in the multiseq
window). Can anyone tell me what this gaps or dashes signify. I looked
in the aquaporin and evolutionary tutorials but not much information
about the gaps.

Thanks in advance
Harish.