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 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. Otherwise, in the majority of cases, the user has to struggle to examine the SEQRES to coordinate mapping and carefully pick sequence numbers that have coordinates to succeed in selecting ranges. -Eric At 4/17/08, Rolf Huehne wrote: >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 /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Top Five 3D MolVis Technologies http://Top5.MolviZ.Org Biochem 3D Education Resources http://MolviZ.org See 3D Molecules, Install Nothing! - http://firstglance.jmol.org Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://workshops.proteinexplorer.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.proteinexplorer.org PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ------------------------------------------------------------------------- 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
