Questionable practice is writing an interpretation program for
operations that can be handled simply at the command line. Programs
that use the API that Eugene implicitly refers to are no panacea, e.g.
Coot has strange restrictions on things like changing the chain label
that can be fixed in a matter of seconds by editing the PDB file in e.g.
xemacs. Which means that when I'm building a large structure with
multiple chain fragments present during the build process, I've edited
those intermediate PDB files tens of times in a single day.
While alternative programs exist to do almost everything I prefer
something that works well, works quickly, and provides instant visual
feedback. CCP4 and Phenix are stuck in a batch processing paradigm that
I don't find useful for these manipulations.
While PDB is limited and has a lot of redundant information it's for the
latter reason it's a rather useful format for quickly making changes in
a text editor. It's certainly far faster than using any GUI, and it's
also faster than the command line in many instances - and I have my own
command line programs for hacking PDB files (and ultimately whatever
formats come next)
Using mmCIF as an archive format makes sense, but I doubt it's going to
make building structures any easier except for particularly large
structures where some extended-PDB format might work just as well or better.
Phil Jeffrey
Princeton
On 8/5/13 9:53 AM, Pavel Afonine wrote:
Editing (for example, PDB files) by hand is a questionable practice. If
you know programming use either existing reliable parsers (available for
both, PDB and CIF) or write your own jiffy.
