Eric Martz wrote: > Dear Bob, > > I'd like to suggest that "select 525-696:a" should select any > residues with coordinates in the specified sequence range, regardless > of whether residue 525 or 696 happens to have coordinates. For 2rd0, > where 525-696:a is a domain of interest in Figure 1 of the primary > reference, zero atoms are selected by Jmol because residue 525 lacks > coordinates. The same command works in Chime (all residues with > coordinates in the specified range are selected). > > Thus, I suggest that the above command should be equivalent to > > select :a and resno >= 525 and resno <= 696 > > which does work in Jmol. >
This would be ok if all residues were always numbered sequentially. But unfortunately there are a lot of entries with numbering irregularities within the PDB. Take for example entry '1A4K' (the numbering irregularities can be seen easily from the alignment view in our JenaLib atlas page for this entry: http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1a4k&EXPAND=alignment) and issue the following 2 commands in Jmol (http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1a4k): 1) select 27-28:A 2) select :A and resno>=27 and resno<=28 With command 1) 7 residues will be selected (27,1027,2027,3027,4027,5027,28). With command 2) only 2 residues will be selected (27,28). Since residues 1027,2027,3027,4027,5027 are structurally between residue 27 and residue 28 the result of command 1) is clearly what would be expected from a range selection command. Therefore I would argue strongly against simply replacing command 1) by command 2) in Jmol. But maybe it would help to reduce the problem Eric has described by restricting the replacement of command 1) by command 2) to cases without numbering irregularities. This would mean that Jmol would look for numbering irregularities while loading the file and set a flag if it has found any. 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
