Eric,
First, I was wrong. You cannot do that test to see if sequence numbers
are out of order. (You probably figured that out.)
Here's the deal:
select a-b
is not the same as
select resno >= a and resno <= b
because "a" may include an insertion code. For example:
load =1JGQ
$ select *^A
7 atoms selected
$ print {selected}.label()
[G]129^A:A.P #123
[C]186^A:A.P #181
[G]191^A:A.P #191
[C]998^A:A.P #976
[C]1028^A:A.P #1007
[G]1032^A:A.P #1013
[C]1362^A:A.P #1344
$ select 129^A-130
2 atoms selected
$ print {selected}.label()
[G]129^A:A.P #123
[A]130:A.P #124
$ select 129-130
15 atoms selected
$ print {selected}.label()
[U]129:A.P #122
[G]129^A:A.P #123
[A]130:A.P #124
[GLU]129:E.CA #6614
[ARG]130:E.CA #6615
[ALA]129:F.CA #6854
[VAL]130:F.CA #6855
[ASN]129:G.CA #7061
[GLY]130:G.CA #7062
[ILE]129:H.CA #7267
[ASN]130:H.CA #7268
[GLU]129:J.CA #7523
[GLY]130:J.CA #7524
[VAL]129:K.CA #7680
[GLY]130:K.CA #7681
My point here is simply that we can't just change one into the other in
general, because there is no way to generally translate the
residue+insertion code business into the <= / >= notation. Now, if we
said "OK, but if you don't use insertion codes, then "select a-b" should
mean something different than when you do," then I have a problem with
that.
So perhaps a compromise position is to introduce a flag:
set sequenceRangeChime
that dumbs down Jmol to ignore insertion codes and just use the residue
numbers in >= / <= mode. More like Chime/Rasmol.
Bob
When you write
Eric Martz wrote:
>I like Rolf's proposed solution very much, for the reasons he states.
>(Thanks, Rolf, for thinking creatively!)
>
>Bob, what do you think about it?
>
>This came up because when one writes simplified user interfaces to
>Jmol (as Eran Hodis is doing in Proteopedia), one wants to give the
>best reasonable result to a command like "select 10-20" without
>complicated explanations and requiring users to look up which
>residues lack coordinates. Sure, we can write code in Proteopedia to
>change the command to ">=/<=", but it seemed to me that this issue
>deserves to be handled better in Jmol itself. Again, Rolf's idea
>seems to me to fill the bill.
>
>-Eric
>
>
>
>
>>What do you think about the following solution:
>>
>>Only if one of the border residues is not present, the ">=/<="
>>selection mechanism is used instead. This would mean that nothing
>>would change with respect to numbering irregularities if one makes
>>sure that the border residues of a range are present. This is
>>currently already necessary in order to get a correct range selection.
>>If one of the border residues is not present, the selection is
>>currently not as desired in any case (nothing is selected). But by
>>using the other mechanism in these cases the selection would be
>>probably in >=95 percent as desired. So the overall failure rate would
>>be reduced. And the failure rate for cases with numbering
>>irregularities would not be increased. Only the type of the failure
>>would change.
>>
>>Regards,
>>Rolf
>>
>>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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