dear all ... beyond iupac nomenclature ...
the remediated pdb sounds very nice, so i had a short look at the formats they provide and found this: mmcif, pdbxml, and pdb and http://biomol.dowling.edu/WPDB/ has a very nice discussion of advantages and disadvantages of the various formats ... it sounds to me like mmcif would be the best way to go, but i do understand that is less amenable to quick and dirty processing with grep, sed and awk etc ..., and therefore users have been reluctant to use it. but i think i would be willing to put up with having to add another 10 lines to my <add your favourite shell here> scripts to process mmcif, if that allows me to take home all the other advantages. the biggest problem at this point is, as far as i know (and this is also what the above website states), that my favourite refinement program does not really work with anything but pdb, so i am not really sure whether it is the users who are reluctant to use mmcif (as above website states) ... wouldn't it be nice to try and teach our favourite refinement programs mmcif ? ingo
