Dear Angel,
Thanks for the reply. I understand atomNo and atomIndex and would like to
know how jmol index the periodic crystal. For example, there would be 27
atoms if "load 1000041.cif {1,1,1}". It is easy to understand the indexing
of atomno 1 and atomno 2. I was wondering how jmol determine which atoms
should be atomno=3? Which atom goes to the next? Is there an algorithm
about this indexing rule and the rule regarding to periodic crystal?
Jing
On Mon, Dec 29, 2014 at 2:04 PM, Angel Herráez <angel.herr...@uah.es> wrote:
> Jing,
>
> It may depend on the file format. My experience with crystal formats is
> null. This is what I
> know from other formats:
>
> If the file provides atom numbers (like PDB), Jmol will obey them. The
> atomIndex starts at
> zero, so it is usually atomNo minus one.
>
> Otherwise, i guess that atoms are numbered in the order they are read from
> file.
>
> One important difference is that atom numbers may be dupicated, e.g. when
> several models
> are loaded (or a SDF or XYZ file that holds several models in one file).
> However, atom
> indexes are sequentiallly incremented across all models and so they are
> unique.
>
> If the model is repeated to generate the crystal, that's more complex;
> others may be able to
> tell you.
>
>
> ---
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