[Jmol-users] Bug? in select by atom number?

[Gutow, J. H <gu...@uw...>]

I am trying to explain how the select statement in 12.2.28, works to one of my students and am confused by the following example.

load =1lcd
select ({553:559})

This selects the carbons in a phenyl ring plus the C it is attached to.   Here's what has me confused.  The atoms selected are:

#556, #557,#558,#559, #560, #561, #562

These are clearly not within the selection range indicated.  My first interpretation is that it maybe this is based on connectivity, because it selects atoms connected to #553 following bonds to #559.  But that's not what it is doing either.  If you try:

select ({557:559})

You get three atoms selected #560, 561 and 562.  It certainly is three atoms, but why these three and not #558, 560 and 561, which are nearest neighbors in the ring to #557 rather than 559?

How is Jmol interpreting these select statements?  I'd like to be able to explain this too him.

Thanks,
Jonathan 
                        Dr. Jonathan H. Gutow
Chemistry Department                                 gu...@uw...
UW-Oshkosh                                           Office:920-424-1326
800 Algoma Boulevard                                 FAX:920-424-2042
Oshkosh, WI 54901
                http://www.uwosh.edu/facstaff/gutow/