I would appreciate thoughts on this:
There was a bug in the chain case sensitivity that forced "select :a" to
not match "A" in a PDB file chain designation, and that is fixed, but
besides that there is an issue for which all should be aware and for which
I would like your thoughts.
Nine years ago Miguel introduced
set chainCaseSensitive (default FALSE)
[http://ehc.ac/p/jmol/mailman/message/10315720/]
That was then. Now we have multiple-character chains and lots of overflow
from upper case A-Z to lower-case a-z in PDB chain designations. I am
trying to create an algorithm that respects old situations and still
doesn't require this special flag for new structures that are starting to
have lower-case letters for chains (1S5L, 1VSP, others?).
My idea is this:
(1) If files loaded have no lower-case chain labels and all are
single-character, match them as always, based on the setting of
chainCaseSensitive; default for which is FALSE:
load =1d66
select :a
468 atoms selected
select :A
468 atoms selected
The idea is that the original idea of chainCaseSensitive was to allow ":a"
to match "A" in a PDB file, not so much to allow ":A" to match "a" in the
PDB file.
Correct?
(2) If any one of the current files loaded has lower-case chain characters
or multi-character chains, then it seems to me Jmol should disregard the
setting of chainCaseSensitive and just consider its value to be TRUE. This
is because if there really is a lower-case chain, then why NOT be
case-sensitive? Surely it means there are A and a, and those are totally
different chains. And if there are multi-character chains, then we are in a
new world, and we should respect those letter cases and just say "it's case
sensitive for them".
Thus:
(1) When any currently loaded files have lower-case or multi-letter chain
identifiers
--> chainCaseSensitive ignored
(2) When all currently loaded files have non-alphabetic or only upper-case
chain identifiers
--> chainCaseSensitive respected
Bob
On Tue, Sep 9, 2014 at 12:11 PM, Angel Herráez <angel.herr...@uah.es> wrote:
> There is also a problem with numeric chain IDs:
>
> load =1LMB;
>
> select *:1; //selects chains 1 and 2
> select *:2; // same atoms
>
> select *:3; //selects chains 3 and 4
> select *:4; // same atoms
>
> I notice that hover display quotes around the ID, like
>
> [DG]37:"2".O3'
>
> so I tried
> select *:"1"
> without change
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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