Dear Carlos and Dear Daniel
thank you so much for your response. As compared to standard pdb format,
my pdb has no definition for HELIX, SHEET etc it has only coordinates and I
am thinking to add them when I am going to submit my pdb to BMRB.
I have another question, I did try two days ago ksddp command in chimera,
but it didn't change my pdb representation. To use ksddp option in chimera
is it necessary to define the secondary structural region in pdb?.
I will try to go through the links and your suggestions.
Again, thank you so much for detailed info.
Have a good day..
thanks
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
> > _______________________________________________
> > AMBER mailing list
> > 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Dec 02 2015 - 12:30:04 PST
