Eric Martz wrote: > Dear Rolf, > > Your point about sequence numbering irregularities is well taken. > Regarding your proposed solution, I'm not sure how enthusiastic Bob > is about checking for such irregularities within Jmol. > > If he is not enthusiastic, and if it has to be one or the other for > all cases (having "select 100-200" be equivalent to "select > resno>=100 and resno <= 200", or not), I am still in favor of having > "select 100-200" be equivalent to "select resno>=100 and resno <= 200". > > My reasoning is that, in my experience, sequence numbering > irregularites occur in a very small percentage of PDB entries. (Does > anyone know the percentage?) On the other hand, residues without
I could not count all irregularities yet, but if you look for example only at the insertion codes there are currently affected about 4 percent (2138 of 51160, including theoretical models) of the PDB entries. > coordinates occur, I think, in the majority. So I prefer to handle > the majority case correctly, and leave the struggle to the minority of cases. > But this will give a lot of trouble to all those people that work with all PDB entries (like we at the JenaLib). And it is much more complicated to cope with those irregularities than just replacing a very small selection command by a slightly longer one. If there really would have to be made a choice for all cases there should at least be a configuration option for selecting one of the methods. Regards, Rolf ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
