Hi Bob, That's excellent - thanks very much for looking into it. I'll give the '\?' a go soon. When will this be included in a publicly available build, and which build(s) will it go into?
Thanks again, Ian Robert Hanson wrote: > OK, the \? is in and has been tested with CIF files. Jmol doesn't > allow * at the beginning of atom names, and some PDB atom names > already have * in them, so \* is not an option. But what you can do is > match specific numbers of characters, and make that wide enough to > encompass all reasonable possibilities: > > select ?\? or ??\? or ???\? or ????\? > > for example. > > This is illustrated at > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > with files in > > http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip > > Bob > > > On Tue, Apr 21, 2009 at 4:30 PM, Robert Hanson <[email protected] > <mailto:[email protected]>> wrote: > > 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 > <[email protected] > <mailto:[email protected]>> 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. > > > > > [email protected] <mailto:[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] <mailto:[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 >>>> >>>> >>>> LEGAL NOTICE >>>> Unless expressly stated otherwise, information contained in this >>>> message is confidential. 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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 > > > > > -- > 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 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. 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