Greetings to all,
I am working on two homologous proteins from two different species (one from humans and the other one is from plasmodium falciparum. I was trying to do structure alignment of the respective modelled structures using Matchmaker of UCSF chimera to analyze the structural difference in terms of RMSD. I am getting two types of RMSD which I am not able to understand. I am attaching the Reply Log file for reference.
Kindly help me with the same.
Thank you
Regards
Juhi
Hi,
One of them is sequence dependent RMSD and the other is sequence independent RMSD value. Basically, in sequence dependent, you perform an alignment on structures and calculate the RMSD over conserved residues. The other is using the unit vectors of all CA atoms to calculate RMSD.
Cheers,
Ali
In MatchMaker, it first generates pairwise-sequence alignment of your input structures and then try to fit them by superimposing. So 8.43 is the overall RMSD here. Then it runs some iterative pruning process to remove residue pairs (which are far apart from each other structurally/conformationally) using a default cut-off value 2 Angst. So 0.594 is the RMSD between the only structurally (most) similar regions.
Thank you so much Kazi Amirul Hossain Ali Osman Acar for your time and help.
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