I have committed this for testing as 11.5.31_dev. It turns out the
original rewrite of the sequence range code was done by Miguel in
Sept/2005 in response to a request by Rolf relating to a strange PDB
file (1t0n) that had duplicate numbering and no chain designations. As
far as I can see, that particular PDB file has been fixed, and the
problem is a non-issue. So the way the (proposed) code works now, is this:
Given two sequence+insertion codes A and B...
For each chain...
1) look for A.
2) if A is not found, find the code numerically closest to it and
larger
3) if no such code exists, return 0 atoms
4) if B is missing ("select 1-")
select the last group of the chain
else
look for B at or after A in the file
5) if B is not found, find the code numerically closest to it and
smaller
6) if no such code exists, return 0 atoms
7) return all atoms physically between and including codes A and B
How does that sound?
Bob
Bob Hanson wrote:
>OK, upon rereading this thread, especially Rolf's earliest post, and
>thinking more about what SELECT a-b should mean, and what insertions
>are, and all that, I do agree that the first solution I had in mind and
>put into 11.5.30 is not a good idea. What if we just went with Eric's
>initial idea, but not in the sense of resno >=/<=. I agree with Rolf
>that that will really mess up scripts, and I agree with Eric that what
>we have now is not intuitive. But I disagree with Rolf that the behavior
>should be different depending upon what the file is like. That to me
>seems like it would be totally opaque behavior to a user.
>
>It seems to me what we have now is just about right, except we should
>allow for missing end groups. Then no scripts will be affected, because
>surely no one has a script that selects 0 atoms (11.5.29 behavior) or
>expects that.
>
>Taking Eric's example (2rd0):
>
>(505,528,529,530)
>
>Do we all agree that
>
>select 520-530 should select 3 groups (as Rasmol)?
>
>Taking Rolf's example with 1ak4:
>
>(27,1027,2027,3027,4027,5027,28)
>
>
>Do we all agree that
>
>
>select 27-28 should select all of these?
>
>select 27-2027 should select just the first three?
>
>select 5027-28 should select the last two?
>
>
>And insertions (1jgq):
>
>(1031,1032,1032^A,1032^B,1033)
>
>Do we all agree that
>
>select 1031-1033 should select all?
>
>select 1031-1032^A should select just the first 3?
>
>select 1031-1032^C should select... what? perhaps the first 4?
>
>
>If so, I will just make Jmol do that, that's all.
>
>Bob
>
>
>
>
>
>
--
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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