leila karami wrote:
Hi
I used command : [g_confrms -f1 initial.gro -f2 final.gro -n1 1.ndx -n2
2.ndx -o fit.pdb] to obtain superimposed structure of initial and
final structures. I saw fit.pdb file by vmd but fit.pdb obtained was
very mixed,busy and unclear.
This is what VMD representations are for. If you don't want atomistic
detail, then choose tube, or ribbon or something.
Mark
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