Re: [cctbxbb] Fail to extend space-group with centring translations
Luc, This is a key item in Ralphs reply:
"You cannot change the rotation denominator (fixed at 1) for the matrices processed by sgtbx.space_group. Therefore you cannot work with, e.g. the pseudo-orthorhombic C-centered setting of a hexagonal space group. However, I never came across a situation where this was interesting."
If the design of the toolbox is too restrictive to permit the user to invent any closed set of operators they want - well thats the end of it. As we say in the UK, C'est la vie.
Could you please outline a plausible example where the current implementation is a serious limitation?
There were lots of things we would have liked to add to CRYSTALS, but there was no room in Bob Carruthers database, and extending it would have been a major hasle.
I am sure the cctbx is more flexible.
As you pointed out, there are work-arounds that can be applied by a clever crystallographer, and the less clever ones won't even try to do anything clever. It's a self-limiting situation! Much of what crystal enginners want could be done if Oleg lets the user create an extended atom parameter list, and put this into a new unit cell in P1.
You can create any P1 cell you want, it is totally trivial: first use e.g. xray_structure.expand_to_p1(), then loop over the translations you want to duplicate the atoms. We can easily add methods to do it in one call. Note that the cctbx is open source, with the possibility of write access to the main source repository. Cheers, Ralf ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com
Hello Since none of you guys have come across the need for dreamed-up space groups, I guess the need is somewhat limited. These artifacts are tools used to help in the understanding of crystal (not molecular) structures so rarely get published.
Could you please outline a plausible example where the current implementation is a serious limitation?
I believe Ralph can handle C-1 so the attached example would not be a problem, but it demonstrates the situation. Table 3 gives basic parameters for four compounds. It is evident that I and II are related, and that III anf IV are related. What is not evident without computation is that all four CRYSTAL STRUCTURES are related. This becomes evident if you transform I and II to the correct C-centred cell. In each pair of tables 4 & 5 and 6 & 7 atomic parameters can be compared directly. If the P to C transformation is made, all four tables can be compared by inspection. In this case, the referees and editors refused to accept a non standard SG, so the text of the paper becomes laborious, explaining what would otherwise have been obvious. In higer symmetry SGs it may be easier to compare structures if even more bizzare SG are invented, or if non-standard origins are used.
You can create any P1 cell you want, it is totally trivial: first use e.g. xray_structure.expand_to_p1(), then loop over the translations you want to duplicate the atoms. We can easily add methods to do it in one call. Note that the cctbx is open source, with the possibility of write access to the main source repository.
Im sure this will be true, and that someone will provide the user-interface for generating the basis vectors form the new (probably enlarged) cell and new atomic parameters after the expansion. Im sure the SM-tbx folk have more pressing problems to deal with than worrying about this minority application Best wishes David
participants (2)
-
David Watkin -
Ralf W. Grosse-Kunstleve