[Chimera-users] RMSD for two ligands

Pavithra meetpavithramsc at gmail.com
Wed Aug 21 01:05:48 PDT 2013

Dear Users,

I want to calculate the RMSD of two ligand molecules of different atom
counts but have a common scaffold.
I tried rmsd #0 #1
but I'm getting the error: unusual numbers of atoms chosen for evaluation.

rmsd #0:15-17 #1:15-17
atleast one atom must be selected.

could somebody help me to find the RMSD between two ligands of different
atom counts.

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