THESEUS can do it, and it comes bundled with ccp4 so definitely on-topic.
If you want RMSD of “equivalent” amino acids, you must tell THESEUS which residues are equivalent with a sequence alignment. Then use the -I option to get the RMSD (and other stats) of the pdb files in their current orientation. E.g.,
theseus -A cytc.aln -I d1cih__.pdb d1crj__.pdb
> On Jun 26, 2015, at 3:52 AM, Kaushik Hatti <[log in to unmask]> wrote:
> Is there a tool which can calculate C-beta RMSD for equivalent amino acids of homologous structures, post C-alpha superposition?
> Sorry if its off topic,
> Stupidity is everyone’s birthright. However, only the learned exercise it!
> --Kaushik (28Oct2014)
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