Michael,
Unfortunately PYMOL/dss doesn't generate quite enough
information to recreate PDB SHEET and HELIX records. PyMOL (like other
programs) simplifies the secondary structure concept down to a
per-residue property. There is no such thing as a sheet or helix in
PYMOL, but merely sets of proximal residues with a secondary structure
property (ss) of 'H' or 'S'.
load object-name.pdb
hide
show cartoon
dss object-name
Should be sufficient to get you a secondary structure representation for
any protein.
States represent multiple conformations -- you shouldn't need to worry
about them
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
> ad...@lists.sourceforge.net] On Behalf Of Michael Bovee
> Sent: Thursday, December 11, 2003 1:38 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] assign secondary structure?
>
> Hi,
> I have a 'raw' pdb file of atom coordinates only, and I'm hoping to
use
> the dss command in pymol to get helix and strand designations that I
> can paste back into the header space of the pdb so that I can model
> fancy helices and strands and so forth to get a nice picture in pymol.
> Then I can superpose features with homologous proteins for which this
> header info is available. I just didnt want to modify or create this
> header info 'by hand' if I didn't have to...
>
> But, I can't get dss to work in pymol (even the refman warns that this
> algorithm has not been rigorously validated). The refman says USAGE is
> dss selection, state
> Does this mean I need to first make a selection that encompasses some
> part (or whole) of the molecule, or should this work on the entire
pdb?
> I don't know what 'states' are so I just opted for '0' which is
> supposed to mean 'all states'.
>
> Thanks,
> --Michael Bovee
>
>
>
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