Why limiting ourselves saying that we read models, or produce models, or do whatever with models? It is auto-destructive. We read, produce or treat STRUCTURES, and that is what a PDB contains, a chemical structure. And that is the term that I am proposing instead of UNIVERSE (which is confusing).
Daniel's alternative of reading Hierarchies.Residues is clearly less understandable that my proposal Structure.Proteins.Residues.Atoms.
My proposal, by the way, is Dina's 4 levels with more adequate chemical terms, imho. Substitute Proteins for Nucleic acids or whatever is adequate, of course.
On Thu, Oct 8, 2009 at 8:11 PM, Daniel Russel <">> wrote:
> On Oct 8, 2009, at 7:03 PM, Ben Webb wrote:
>> On 10/08/2009 06:55 PM, Daniel Russel wrote:
>>> We need to clean up what happens when multiple molecules are loaded from
>>> a PDB.
>> Do you mean multiple chains in one model (potentially, but not
>> necessarily, separated by TER records), multiple models separated by ENDMDL
>> records, or both?
> Within one PDB MODEL record. Not just multiple chains of protein but
> heterogens too.
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