Bill: From earlier COOT mail:
===== -----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. ===== However, a colleague and I have found an error in what COOT writes out and, at least at the GRC on Diffraction Methods, Paul agreed was problem, but noted that he had not yet fixed it. In an email that I sent to Paul on 1 July 2014: You state “The vector after the & shows the necessary origin-shift needed to bring the molecule close to the origin.” However, in a real life example, we found the center-of-mass of a molecule at 0.45, 0.55, -0.10 unit cell translations, but in COOT after the “&” we found {0 1 0}. We would have thought in this situation based on your explanation below that it should have been {0 -1 0}. ===== Steven -----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[email protected]] On Behalf Of William G. Scott Sent: Saturday, August 30, 2014 10:03 AM To: [email protected] Subject: symmetry operator notation question Hi folks: What is the meaning of the last field — the one in curly brackets -- that describes the symmetry transformation of a given atom in coot? For example, for a given X Y Z, coot displays the symmetry transformation of an equivalent position as " Y+1/2, -X+1/2, Z + (0 -1 1) & { 1 0 1 }”. Thanks. Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
