I wrote a little jiffy program for doing things like this: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com
you run it like this: origins.com rigthorigin.pdb wrongorigin.pdb I222 correlate This will shift "wrongorigin.pdb" by each of what I think are the "allowed origin shifts", calculate an electron density map using SFALL, and compare that map to the one made from "rightorigin.pdb". The shift that gives the best correlation coefficient will then be applied to "wrongorigin.pdb" and output as "neworigin.pdb". There are plenty of faster ways to do this, such as phenix.emma, but I still like to use this script when I feel like being puerile (which is often). Now, the list of origins (at the bottom of the script) is something I derived empirically by generating random atoms in a random cell and applying random fractional shifts, searching for cases where the structure factors are the same as the no-shift case. Again, I did it this way to avoid thinking about it. My list has 8 different allowed shifts for I222, but I assume this is because the 0,0,1/2 shift is part of a symmetry operator. I guess it is a matter of semantics as to wether or not that is an "allowed shift"? -James Holton MAD Scientist On Tue, Oct 11, 2011 at 2:58 PM, George M. Sheldrick <gshe...@shelx.uni-ac.gwdg.de> wrote: > There are 4 possible origins in I222. There is a simple but inelegant way to > check. Run the SHELXE job for the second dataset four times, first with no > MOVE > instruction, then with one of the following MOVE instructions inserted between > UNIT and the first atom in the *_fa.res file from SHELXD: > > MOVE 0.5 0 0 > MOVE 0 0.5 0 > MOVE 0.5 0.5 0 > > one of these should give you phases with the same origin as your first > dataset, > so if you display both maps from the .phs files in COOT they will superimpose. > > George > > On Tue, Oct 11, 2011 at 11:29:14PM +0200, Klaas Decanniere wrote: >> >> >> Hi, >> >> I have two solutions from the ShelX C/D/E pipeline I would like to compare >> (different datasets, same protein). They seem to have different origins. >> Space group is I222, with a choice of 8 origins. >> How can I find and apply the correct shift to have the phase sets on a common >> origin? >> The information on http://www.ccp4.ac.uk/html/alternate_origins.html and >> http:/ >> /www.ccp4.ac.uk/html/non-centro_origins.html explain it very well, but thy >> don't point to the tools to use. >> Is it a matter of reindex and trying all 8 possibilities? >> >> thanks for your help, >> >> Klaas Decanniere > > -- > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 >
