Hi Paul, Thanks for the explanation. Yes, it would be great if Coot can write out the operator in matrices when one writes out a symmetry-related molecule as the matrix form is easier to pass between different programs.
Yong -----Original Message----- From: Paul Emsley [mailto:[email protected]] Sent: Tuesday, February 11, 2014 9:43 AM To: Yong Wang Cc: [email protected] Subject: Re: symmetry operator style in new coot On 10/02/14 21:46, Yong Wang wrote: > Dear Coot users, > > The symmetry operator in the new Coot (0.7.2) has a different style from that > in the older version. For example, the current symmetry operator (based on > the label) would have something like -X+Y,-X,Z+(1 1 0)&{0 1 0} and the saved > coordinates file would be named xxxx_symmetry_3010100.pdb. The translational > part does not look as simple as the old style. Could someone explain the > part "+(1 1 0)&{0 1 0}"? Is there a command to export the matrix out? > Dear Yong, I don't know how other programs do symmetry expansion, but Coot moves the molecules close to the origin (by cell translations), does the symmetry expansion there and then moves everything back around where the origin molecule was placed. The vector after the & shows the necessary origin-shift needed to bring the molecule close to the origin. In the past, the atom symmetry label was the sum of the actual translation (due to symmetry operator) and the pre-translation. Some time ago I decided that that, although shorter, was confusing. I don't think that there is a function to write out symmetry matrices explicitly, but I suppose that it would be straightforward to write to the screen the symmetry operator of the selected symmetry molecule when you write a symmetry related file. Would that do? Paul.
