On Wednesday, August 07, 2013 04:00:16 pm Ed Pozharski wrote:
> On 08/07/2013 05:54 PM, Nat Echols wrote:
> > Personally, if I need to change a chain ID, I can use Coot or pdbset
> > or many other tools. Writing code for this should only be necessary
> > if you're processing large numbers of models, or have a spectacularly
> > misformatted PDB file. Again, I'll repeat what I said before: if it's
> > truly necessary to view or edit a model by hand or with custom shell
> > scripts, this often means that the available software is deficient.
> > PLEASE tell the developers what you need to get your job done; we
> > can't read minds.
>
> Nat,
>
> I don't think anyone here really means that the only way to change a
> chain ID is to write, say, a perl script. But an interpreter of the
> kind advocated by James (as much as I have hijacked/misinterpreted his
> vision) could indeed be very useful for people pursuing simple
> bioinformatics projects and new ways to analyse structural models.
We tackled this a while back for the then-current incarnation of mmCIF.
http://www.bmsc.washington.edu/parvati/mmLib.pdf
I suppose it will all have to be revisited so that it knows the quirks,
features, and foibles of the new and improved mmCIF.
Ethan
> While
> I understand your view that everyone should seek assistance from
> "developers" with every problem encountered, I also recall some
> reasonable idea about self-sufficiency that should cover scientific
> research (something like "give man a fish and you feed him for a day,
> teach him to fish and he starts paying taxes"... something along these
> lines ;). There is a difference betweens tools that allow to easily
> perform useful non-standard analysis and highly specialized tools that
> strive to cover every situation imaginable.
>
> Cheers,
>
> Ed.
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
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