Warren wrote:
> Miguel,
>
> This is definitely one of the more un-dealt-with issues in macromolecular
> structure, and I don't know of any satisfactory solution.
Thanks for speaking up on this issue.
> PyMOL's
> approach is to treat alternate conformations as distinct atoms which share
> all identifiers except for the one-letter alt-conf identifier, which is
> blank ('') for an atom which has no alternative conformation. Thus, in
> PyMOL's atom selection language:
>
> an all A selection: alt ''+A
> an all B selection: alt ''+B
> or a specific mixed A/B selection: alt '' or (resi 120 & alt A) or (resi
> 130 & alt B)
>
> etc.
OK
You said that PyMOL treats them as distinct atoms ...
Q: Are these distinct atoms in the same 'model' or in different 'models' ?
> Food for thought. Before choosing an implementation, I suggest
> taking a look at how O, VMD, and DSViewer handle these as well.
Excellent idea. Perhaps someone on the mailing list is familiar with how
some of these packages try to deal with the issues.
Miguel
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