From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 11 2005 - 16:19:57 CDT

Hi,
  I forgot to get this done for VMD 1.8.3, but I've
just added a "serial" atom selection keyword which uses
a 1-based indexing scheme that matches the PDB, NAMD's internal
numbering, and many Fortran-based simulation programs.

I chose to name the keyword "serial" as suggested by Andrew as this
matches the term used in the PDB docs, and it seems unlikely to be
confused with something else. Thanks to Axel for reminding me about
this a few weeks ago with his own similar patch.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 07, 2005 at 04:36:50PM -0700, Andrew Dalke wrote:
> John wrote:
> >I could definitely see adding a new selection keyword to allow
> >selection
> >by the index values from the original file, though the responsbility
> >of watching out for the items I list above would then be on the
> >shoulders
> >of the user. I don't have time to mess with this for VMD 1.8.3, but
> >that
> >might be worth doing for a subsequent revision.
>
> One thing to point out is the PDB spec regards that as a serial number
> field where the first record is 1 and the numbers proceed sequentially.
>
> As such the difference between "serial" (the hypothetical name
> used for this field) and "index" (the 0-based version of that field)
> is always 1.
>
> It's possible for someone to use a different numbering scheme for
> those fields but as John pointed out those numbers are best ignored.
> I don't think there should be a field to access those number exactly
> as given. (Should "00001" be considered the same as " 1"?)
>
> So I think the solution to pl's problem could be to just add a
> new integer function to the atom selection code to handle "serial".
>
> Andrew
> dalke_at_dalkescientific.com

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