nevermind. The proposed algorithm is:
For each model...
For each chain in the model...
While not done...
Given two sequence+insertion codes A and B...
1) look for (another) A.
2) if A is not found...
2a) find the code numerically
closest to it and larger
2b) if no such code exists, return DONE
2c) set INEXACT
3) if B is missing ("select 1-")
3a) select the last group of the chain
3b) set INEXACT
else
3c) look for B at or after A in the file
3d) if B is not found...
4a) find the code numerically
closest to it and smaller
4b) if no such code exists, return DONE
4c) set INEXACT
5) select all atoms physically between and including codes A and B
6) if INEXACT, return DONE, else return NOT DONE
Bob Hanson wrote:
>In addition, I note that if there are two blocks of groups having the
>same group numbers (as in the old 1t0n or 1blu files) in the same chain
>(in my observation, protein and water), then the first matching range
>(the protein) is selected.
>
>Bob
>
>Bob Hanson wrote:
>
>
>
>>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
>>
>>
>>
>>
--
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
-------------------------------------------------------------------------
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
