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

From: Daniel Roe <>
Date: Wed, 2 Dec 2015 13:06:07 -0700


I suspect this is because pymol and chimera use different methods of
secondary structure assignment. For pymol

"It is recommended that you read in PDB files which already have
correct secondary structure assignments from a program like DSSP.
However, PyMOL does have a reasonably fast secondary structure
alignment algorithm called "dss". Please be aware that due to the
subjective nature of secondary structure assignment in borderline
cases, dss results will differ somewhat from DSSP."

For chimera (

"If the input protein PDB file has HELIX and SHEET information, that
information is used. If the input file does not have secondary
structure information, the "ksdssp" function is automatically used to
assign it."

So the different behavior you observe likely stems from differences
between "dss" and "ksdssp".


PS - This info was pretty easy to find via typing 'pymol secondary
structure' and 'chimera secondary structure' into Google.

On Wed, Dec 2, 2015 at 12:38 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
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Dec 02 2015 - 12:30:03 PST
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