Re: [Jmol-users] How to select atoms with names ending in '?'

[Robert H. <ha...@st...>]

OK, two threads of discussion here.

1) DO NOT poll the applet with a setTimeout(). This will occasionally crash
the applet and could cause one of the strangest bugs in Firefox -- while
polling, if you type in the address line, your text comes out sdrawkcab. No
kidding. I kid you not.

2) You need to get loadStructCallback working. If you can't, ask. It's
really the only way to go.

3) \? and \*. Great idea. I should be able to do that easily enough.

Bob

On Wed, Apr 15, 2009 at 9:37 AM, Chris Foley <chr...@st...
> wrote:

>  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.
>
>
>
>
> rg...@el... 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.
>
>
> th...@cc... 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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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


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