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 >> >> >> LEGAL NOTICE >> Unless expressly stated otherwise, information contained in this >> message is confidential. If this message is not intended for you, >> please inform [email protected] and delete the message. >> The Cambridge Crystallographic Data Centre is a company Limited >> by Guarantee and a Registered Charity. >> Registered in England No. 2155347 Registered Charity No. 800579 >> Registered office 12 Union Road, Cambridge CB2 1EZ. >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by: >> High Quality Requirements in a Collaborative Environment. >> Download a free trial of Rational Requirements Composer Now! >> http://p.sf.net/sfu/www-ibm-com >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------------ This SF.net email is sponsored by: High Quality Requirements in a Collaborative Environment. Download a free trial of Rational Requirements Composer Now! http://p.sf.net/sfu/www-ibm-com _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
