Re: [AMBER] Amber calculated structure(PDB) visualization in pymol vs chimera

From: Carlos Simmerling <>
Date: Wed, 2 Dec 2015 14:56:23 -0500

this might be better to post on the VMD support list and see if VMD
supports secondary structure calculation for non-standard amino acids.

On Wed, Dec 2, 2015 at 2:38 PM, V. Kumar <> wrote:

> Dear AMBER
> I have calculated NMR structure of a peptide with non standard residues.
> I m surprised, if I load same pdb in to pymol and chimera, both software's
> are showing different behaviours particularly in cartoon representation
> (helix & b-sheet). Pymol shows b-sheet properly but chimera detects same
> b-sheet region as random coil. With "sticks" of backbone representation is
> identical in both pymol and chimera.
> So, to visualise AMBER calculated structure in 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
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Received on Wed Dec 02 2015 - 12:00:04 PST
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