VMD-L Mailing List

From: V. Kumar (vin.vasanth_at_gmail.com)
Date: Wed Dec 02 2015 - 17:16:46 CST

Dear VMD experts

I have calculated NMR structure of a peptide with non standard residues.
I m surprised, if I load same pdb in to pymol and vmd, both software's are
showing different behaviours particularly in cartoon representation (helix
& b-sheet). Pymol shows b-sheet properly but vmd & chimera detects same
b-sheet region as random coil. The backbone representation as sticks looks
identical in both pymol and vmd & chimera.

So, to visualise AMBER calculated structure in vmd & chimera do I have to
convert my pdb format? Does any one faced same problem.?

Thanks in advance..

Have a good day..
with best regards
Vince