VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 17 2007 - 13:11:52 CDT

Philipp,
  If you want indices starting with "1", you'll need to use the
selection keyword "serial" rather than "index". I should also note
that neither serial nor index actually refer to the numeric key stored
in the PDB atom field, since people often edit these files or exceed the
legal number of atoms, thus rendering these values invalid.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 17, 2007 at 02:03:46PM +0200, Philipp Schoen1 wrote:
>
> Dear Alex
> thanks for your answer. I could perefctly usae your hints. However, there
> is still some issue:
> If I do something like set bin [atomselect top {2 <= x and x < 5}] I get
> all the wanted atoms of the water molecules (tested by writepdb test.pdb).
> But, if I chekc it by list $bin I see that the labeling (the integers of
> the index) is not correct. E.g.
> ATOM 9568 H2 TIP3 9250 4.264 10.733 -48.677 1.00 0.00 WT1
> H
> ATOM 9569 OH2 TIP3 5 3.668 10.176 13.191 1.00 0.00 WT2
> O
> ATOM 9570 H1 TIP3 5 3.224 10.545 12.387 1.00 0.00 WT2
> H
> ATOM 9571 H2 TIP3 5 3.092 10.473 13.913 1.00 0.00 WT2
> H
> The correct ones are index 9569, 9570 and 9571 (also shown in the test.pdb
> file). Calling the list $bin command, however results in 9568, 9569 and
> 9570. That is, all indices are reduced by one. Is it a bug?
>
> Gruezi Wohl!
> Philipp 

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