A source of confusion is that we are using two different definitions of "origin". In the a graphics program sense (coot, pymol), the origin is always at xyz coordinate (0, 0, 0). I think that's what Napo means by "present the same cell and origin."
However, imagine a crystal upon which we put a unit cell box with one corner labelled (0, 0, 0) and the opposite corner labelled (1, 1, 1) in fractional coordinates. We can use the unit cell box as a "ruler" to read out positions in the crystal. Within the crystal are our molecules in a repeating lattice. Now suppose we move our unit cell box around the crystal while keeping the molecules fixed in the lattice. Do you see how the relative coordinates of the molecules with respect to that unit cell box will change even though the crystal does not change nor do the molecules in the crystal? I know this doesn't explain everything about "origins" as not every point in most crystal lattices can be an origin, but I will save that concept for another day. I just wanted to note the apparently different definitions of origin in this thread. Jim ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of Napoleão Valadares [[email protected]] Sent: Sunday, November 20, 2011 9:57 AM To: [email protected] Subject: Re: [ccp4bb] 1.95A, different phases, maps look the same, R/Rfree 22/24, wrong space group? - No alternative origin .... About the same origin: The pdbs of both Solution-1 and Solution-2 present the same space group and cell, as observed opening the pdbs as text files or in pymol. When I open both maps on coot they are not superposed but present the same cell and origin.
