VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 10 2005 - 18:38:51 CST

Andrew,
  That would certainly be the simplest way to make people happy without
changing existing behavior or dealing with the string problems you mention.

  John

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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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