Hi all. A brief comment.
The cif file contains only the asymmetric unit content. So, if a user wants to see "my molecule", only part of it will be displayed when opening a cif or res file in Avo, at present. This depends on the way connectivity is generated and is complicated by the fact that it may well be an infinite structure. In other words, displaying a crystal without taking site symmetries into account will produce incomplete coordinates for use in QM programs. Louis Le 10 nov. 2011 à 17:04, David Lonie a écrit : > On Tue, Nov 8, 2011 at 3:40 PM, Geoffrey Hutchison > <ge...@geoffhutchison.net> wrote: >>> Is the problem with a filled molecular crystal cell just that it's >>> difficult to see what's going on (too much info)? >> >> That's part of it, but also users often just want "the >> experimentally-derived" molecular structure. So maybe I synthesize a >> compound, get the x-ray structure and a CIF. I don't want the full unit cell >> -- I probably just want the molecule to paste into a manuscript or >> presentation, or maybe to submit to Gaussian. >> >> So there really are two different use cases -- I'm opening a file because it >> has x-ray defined coordinates of my molecule VS I'm opening a crystal and >> want to see the whole unit cell. >> >> Thus the need for a decent heuristic. It won't always work -- I might open >> benzene and want the whole unit cell, or I might want the primitive >> coordinates for YBCO. Fortunately, we have ways of handling that already. I >> just want the default experience to be good. > > Ok -- that works for me. My biggest concern with not showing the full > unit cell is that, as Avogadro is educational software, students may > not realize that they're only seeing part of the structure. So some > sort of notification may be useful here. A popup or slim dockwidget > with a "don't show me again" checkbox informing the user that a > reduced representation is being shown would be a nice touch. I could > add some API to the crystallography extension that would return the > Fill Unit Cell QAction, so that we could even give the option of > filling the cell from the popup. > > Dave > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > Avogadro-devel mailing list > avogadro-de...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/avogadro-devel > ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ Avogadro-Discuss mailing list Avogadro-Discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
