Miguel wrote:
Rolf wrote:
As an example, let us assume that we have a chain with the following 10
residue sequence numbers.
1 2 3 4 5 1 2 3 4 5
Q: If I say 'select 1-5' should all 10 residues be selected?
Generally I would expect all 10 residues to get selected.
I think that you are thinking all 10 residues for a different reason than
I was thinking.
I was thinking that there were two ranges from 1-5.
I agree, non greedy but global
You were thinking of one range that ran fromm the first 1 to the last 5.
no, because this case must be two different chains with a TER record in
between.
> Q: If I say 'select 2-3' should 4 residues be selected?
>
This is even more complicated, because you have 3 alternatives:
2 or 4 or 7 residues
Correct.
Jmol today will return 2 in this case because the implementation assumes
that residue numbers are unique.
only the atom number is unique in a PDB file, therefore again we have
two sets (from two chains, or hetero) with two members each, 4 residues
should be selected.
It raises the additional question if the range should be considered as
local (2,3 and 2,3) or as global (2,3,4,5,1,2,3).
As a default I would expect it to be considered as local and greedy.
I disagree! I vote for ((2,3) , (2,3)) and regard this as non greedy but
global (all occurrences)
ignoring the chain structure in the PDB file would be a very bad idea.
Please Miguel, don't do that.
With kind regards, Jan
OK
Well that is the answer that will give you the behavior you want with the
file that caused all these problems.
I will see what I can do.
Miguel
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