Hi George, > It seems to me that column 21 of an ATOM or HETATM instruction > is always blank, and column 22 is the chain ID. So if we put a > two-character chain ID right justified in columns 21 and 22, for the > vast majority of structures there would be no change, and it would > be relatively easy to change MMDB, Coot etc. to accomodate the > increase in the possible number of chains from 26 to (say) 36^2 = > 1296 (if digits are allowed too).
I really like this idea and I will make phenix/cctbx work this way. > The next problem is of course the 5-digit atom serial number in columns > 7 to 11, which limits the total number of atoms in the structure to a > paltry 99999. Many programs ignore this number, but it is used by the > CONECT, SSBOND and CISPEP records in the PDB. However column 12 also > appears to be blank, I think that using it (e.g. with A for atoms > 100000 to 199999, B for atoms 200000 to 299999 etc.) would enable the > sequence numbers to be recycled and would again require no change for > the vast majority of PDB files. I personally think that this is a much > better solution than what the PDB currently does for more than 99999 > atoms (they spread the structure over several PDB files with different > PDB-IDs!). The solution to this problem is to simply treat the serial numbers and residue numbers as strings. X-PLOR/CNS has been doing this forever, maybe other programs, too. Implementations to generate intuitive, maximally backward compatible numbers can be found here: http://cci.lbl.gov/hybrid_36/ This includes a Fortran-77 implementation without any external dependencies, heavily tested with a large variety of compilers. I think these simple tricks will be sufficient until we are all retired! Cheers, Ralf ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469
