On Mon, Aug 05, 2013, Boaz Shaanan wrote: > I teach many such students and it's fairly easy to explain to them where > to look in the PDB for particular pieces of information relevant to the > structure. I can't imagine how they'll cope with the cryptic mmCIF format.
For many purposes, it's not all that hard: the ATOM records in an mmCIF file look like a space-delimited version of the ATOM records in a PDB file: ATOM 1 O "O5'" . DC A 1 1 ? 18.935 34.195 25.617 1.00 64.35 ? ? ? ? ? ? 1 DC A "O5'" 1 ATOM 2 C "C5'" . DC A 1 1 ? 19.130 33.921 24.219 1.00 44.69 ? ? ? ? ? ? 1 DC A "C5'" 1 An awk script with /^ATOM/ as its selection is actually easier to write than the corresponding script for a PDB ATOM record, since the line can be split on white space. And hand-editing seems no harder than with PDB files. Note that if a student wonders what all the "?" entries mean, the answer is right there are few lines above in the mmCIF file. Seems easier (to me!) than having to memorize what goes in column 22 of a PDB record. Beyond this, everyone on this list will be long dead before the current PDB format really goes away. [And I think that includes those just entering the field.] ...dave case
