VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 15 2002 - 09:58:43 CST

Robert,
  Thanks for the patch, that looks like a good idea.
I don't recall seeing your patch, but I'll try and get it
applied in the script library.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 15, 2002 at 10:58:02AM -0500, Robert Campbell wrote:
> 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 

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