Mo;lecular replacement can choose any suitable origin so you cant predict.
The easiest way is to run superpose molecules
Match all residues to each other.
You should get a rotation matrix -1 0 0 0 0 1 / 0 1 0 with some
translation which sjould be very c;lose tpo components of 0, or 1/2
along
James Stroud wrote:
... What is the
operation to reindex such that real space is rotated 180 about z? These
are in P212121.
Isn't that the 21 along z in your orthorhomic space group? Just apply it
to your MR solution instead, and add an affine normaliser if needed to
superpose the
If you were lazy you'd just run phaser ;-)
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Fri, 17 Apr 2009, James Stroud wrote:
Update:
The pounding I am beginning to feel in my head is reminiscent of a pounding I
felt while
Update:
The pounding I am beginning to feel in my head is reminiscent of a
pounding I felt while working in p43212 a while ago. I think this is
an alternate origin issue. Now I just need to figure out how to
redefine the origin.
James
On Apr 16, 2009, at 9:38 PM, James Stroud wrote:
Dear James,
yes, this reminds me of a problem long time ago: since the origin in
P212121 is defined as the midpoint of non-intersecting screw axes (I
hope that's right - I don't have the tables at hand), you have to add
(1/4*a,1/4*c,1/4*b) after re-indexing, if I'm not mistaken.
Best
when reindexing p212121 with -h,l,k, you get
P 21 21 21 (a+1/4,b-1/4,c-1/4)
so you should subtract 1/4 from x and add a quarter to y and z.
some tools in the cctbx are available that make this go easy
(reindexing and moving things back to a standard setting). Reruning
phaser might be the least
James,
If you still have the raw images on line, you can use a new feature in
LABELIT to take care of matching the 2nd dataset indexing solution
against the isomorphous atomic model from data set 1, and then
re-integrate.
Usage:
labelit.index data set 2 first image data set 2 90-degree
For the sake of completeness I also thought that the REFERENCE_DATA_SET
card in XDS does the same thing.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Fri, 17 Apr 2009, Nicholas K. Sauter wrote:
James,
If you still have the
Hello All,
I have two crystals (that I'll call data set 1 and data set 2)
that seem to be isomorphic, but y and z are transposed between the two
data sets. Reindexing data set 2 with the operators
h = -h
k = l
l = k
makes the axes match data set 1, but running MR with the previous
