[email protected] wrote: > Hi Rich, > > >>> 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?'. >>> >> Is this construct a legal CIF atom_site_label Ian? As far as I am aware >> the CIF dictionary doesn't allow for that type of label. Or is this just >> for in-house use? >> > > I don't profess to be an expert on the CIF format (so I stand to be > corrected), but I don't think there's a problem with a CIF > _atom_site_label of this form. I found this reference: > > http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Iatom_site_label.html > Yes, this 2.4 dictionary is the current one and reading it with your specific construct in mind I can see where it would be allowed, even if strange. Since component 0 matches an _atom_type_symbol the next part is going to be assumed to be component 1 which will be 33? (in your example) and this is then the atom number (all other components require the presence of underscores). Technically this is overloading the atom number by including a character that is indicating disorder since that information would normally be incorporated in the CIF datanames defined for that (_atom_site_description, _atom_site_disorder_assembly, _atom_site_disorder_group). But, and especially if this is for in-house work, it doesn't break the CIF dataitem rules to have this kind of overloading encoded in the atom label.
> The use of trailing question marks here pre-dates my work on the project > in question and I believe it's a well-established practice at least within > my organisation. Even if this is not good CIF practice, for the purposes > of this question let's assume that it's for in-house use only and so > there's no problem! I'd really just like to know if what I'm trying to do > is possible in Jmol. > The problem may be in the CIF parser that Bob has written. Since ? is a valid CIF datavalue the parser may be treating that character in a special way which could make atom selection problematic. Bob will have to address that problem since I don't think anyone else has a good idea how it works. Generic CIF parsing is non-trivial (mine is in perl so isn't useful for Jmol) and special-case readers can get easily caught by uncommon constructs. Rich > I would be quite surprised if it's not possible to escape special wildcard > characters within Jmol, as per regular expressions etc. I assumed it would > be as easy as that. Maybe the Jmol scripting language instead prescribes > that atom labels cannot contain either '*'s or '?'s? > > Thanks for your help, > > ------------------------------------------------------------------------------ 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
