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
