From: Robert Campbell (rlc_at_k2.med.jhmi.edu)
Date: Fri Nov 15 2002 - 09:58:02 CST

Hi John,

On 2002-11-14 16:02 you wrote:
> VMD uses the program "Stride" for its secondary structure determination
> and cartoon representations. This Tcl script should allow you to use
> the secondary structure information in a PDB file instead of what
> Stride calculates. Also, you could use this script as a guide in
> writing your own script routine to customize the secondary structure.
> http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/vmd_use_pdb_ss/

I previously (~2 years ago?) suggested a patch to this script that
nobody thought fit to apply I guess. The problem with the original
script is that secondary structure (helix or beta-strand) that has been
already assigned by a previous run of stride, but is not specificied in
the PDB file (i.e. it is "coil" according to the PDB file) will not be
reset to coil. So my modification does that first -- set everything to
coil and then apply the secondary structure from the PDB.

  *** /home/rlc/vmd_use_pdb_ss.txt Fri Nov 15 10:52:13 2002
  --- /prog/vmd/scripts/vmd_use_pdb_ss Thu Mar 14 11:26:23 2002
  ***************
  *** 31,33 ****
            # also, if read ATOM then there are no more def's
  ! if {$str == "ATOM "} {
                break
  --- 31,33 ----
            # also, if read ATOM then there are no more def's
  ! if {$str == "ATOM " || $str == ""} {
                break
  ***************
  *** 48,49 ****
  --- 48,54 ----
        if {$ssdata == {}} {return 0}
  +
  + #rlc's modification: first, reset everything to coil as a default
  + set sel_all [atomselect $molid "all"]
  + $sel_all set structure coil
  +
        # Go through each of the element
  ***************

Cheers,
Robert

-- 
Robert L. Campbell, Ph.D.               http://biophysics.med.jhmi.edu/rlc
rlc_at_k2.med.jhmi.edu                                    phone: 410-614-6313
Research Specialist/X-ray Facility Manager
HHMI/Dept. of Biophysics & Biophysical Chem., The Johns Hopkins University
    PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2