Thanks. :)
Similar to Bob's suggestion, how about:
select C33? and not
(C33,C330,C331,C332,C333,C334,C335,C336,C337,C338,C339)
Are letters allowed?
select C33? and not
(C33,C330,C331,C332,C333,C334,C335,C336,C337,C338,C339,C33a,C33b...........)
Clumsy but easily generated.
As a suggestion for Jmol developers, giving access to Java's regex API
(or a third party OS regex if backwards compatibility is an issue)
would give loads of flexibility for any type of string matching. Not
sure how feasible that would be.
Chris.
[email protected] wrote:
This is a good suggestion Chris. For Ian's problem (since it is a
well-defined in-house setup) the preprocessing could change the ? of an
atom name to "disordered" (no need to stick with one character).
Rich
On Wed, April 15, 2009 9:05 am, Chris Foley wrote:
Again, this won't solve the "?" problem but it may be a way of avoiding
the issue. A simple script to change all "?" characters in atom names to
"$" (or whatever character might be legal in CIF files and convenient in
Jmol scripts) would be an easy solution. If you don't want to alter your
CIF files, this could be done on the fly with a PHP script that serves a
modified version of the CIF file specified in the URL. For example:
http://www.mysite.com/jmol-friendly.php?file=myfile.cif could serve a
modified copy of myfile.cif.
Just a suggestion. Hope it helps.
Cheers,
Chris.
[email protected] wrote:
Hello,
I'm sure there's a really easy way to do this but as a new Jmol scripter
I'm struggling to see how! I need to write a Jmol script to select all
atoms with names ending in '?'. My input file is a CIF and the presence
of
a trailing question mark in the atom name indicates a disordered atom,
e.g. 'C33?'.
The trouble is a '?' is used as a wildcard in Jmol scripting, and I
cannot
find a way of escaping it to prevent it from matching any single
character.
I have successfully written a _javascript_ solution that uses the
following:
var atomList = jmolGetPropertyAsArray("atomInfo", "all");
to get a list of atom objects and then uses the 'info' field to get at
the
atom labels. However, due to some kind of race condition that I don't
fully understand yet, the script sometimes fails as Jmol hasn't fully
initialised when it runs so the atomInfo property is empty. This is not
my
preferred solution anyway...
I'd much rather tackle this the easy way using a standard Jmol selection
_expression_. Is there any way I can do this please? Sorry if it's
obvious.
Thanks in advance,
Ian
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