Nat,
I agree that deep understanding of column-formatted text isn't really
necessary (there's not much internal complexity there).
I was attempting to point out that the general rule of not re-inventing
the wheel doesn't always apply. Even when we're addressing biological
questions, if we're using computational tools then I feel it's helpful
to understand how those tools work (and possibly more importantly, how
to tell when they fail to work as we would expect).
Just my 2 cents...
Pete
Nat Echols wrote:
> On Fri, Jun 7, 2013 at 8:37 AM, Pete Meyer <[log in to unmask]> wrote:
>
>> On the other hand, programming an implementation of something is a good
>> way to make sure that you really understand it - even if you end up using
>> another program.
>
>
> I would argue that it's not really necessary to understand the column
> formatting of a PDB file, any more than it's necessary to understand how
> binary data is arranged in an MTZ file. (Especially since the long-term
> plan is to migrate to mmCIF, which is more flexible and can store far more
> information.) We're ultimately trying to answer questions of biology and
> chemistry, not informatics, and writing a parser that actually handles all
> of the variety in the PDB (let alone the garbage produced by some programs)
> is far more difficult than it sounds.
>
> -Nat
>
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