Dear Daniel
I have used ksdssp -s strand_min 63-65 -v atom-spec || it doesn't works
but ksdssp -s 63-65 it works and puts beta-sheet, for the helix where all
are
non standard residues he is giving error and not changing the
representation.
May be wrong is in the command, I will play a bit.
thank you so much my half problem is solved
best wishes
Vince
On 2 December 2015 at 21:06, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> I suspect this is because pymol and chimera use different methods of
> secondary structure assignment. For pymol
> (http://pymol.sourceforge.net/newman/user/S0260cartoons.html):
>
> "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 (
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-January/001180.html):
>
> "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".
>
> -Dan
>
> 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 <vin.vasanth.gmail.com> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Wed Dec 02 2015 - 13:00:03 PST
