Hi
This was indeed the issue - on this beamline (I think it's 19-ID-D at APS, but
I'm waiting on confirmation of this) the phi axis rotates the opposite way to
"usual", so Mosflm needs to be told.
(As an aside, in the most recent release we automatically check the serial
number of the detector to see if it's in a list where we know this is done -
but our internal list is not comprehensive [and some detectors don't record
this information in a useful way...]. We'll add the detector from Jan's
dataset to our list)
The best way to check if this is the problem is to -
(1) index in the normal way using two images. If
(a) the predictions don't look right
and
(b) the sigma(x,y) (the column to the right of the cell dimensions) is
more than you would normally expect (say, for a good looking crystal if it's
more than ~0.1mm)
(c) the cell is not close to what you expect
then this may be the issue.
(2) Index from the first image chosen by Mosflm and see if the predictions
match and sigma(x,y) is much smaller than in (1b)
(3) Index from the second image chosen by Mosflm and check predictions (for
this image) and sigma (x,y)
If (2) and (3) look "good" but (1) is bad, there's a good chance the phi is
rotating the opposite way to that which Mosflm expects. In this case, check the
setting box in the "Settings -> Experiment Settings -> Experiment" window and
try (1) again - remembering that if you do this you need to repeat the spot
search.
The orientation of the displayed image has no bearing on the beam centre used
by Mosflm as read from the image header. Some beamlines record the beam centre
in the Denzo frame, some in the Mosflm frame, some in both (and possibly some
do in some other frame - there's a wide choice!).
In iMosflm, the image is displayed with respect to the internal Mosflm frame -
so it's consistent with how we treat the images computationally. Other programs
(probably?) display the image as thee detector software displays it.
On 18 Oct 2012, at 22:12, Ben wrote:
> I had a very similar problem with data collected on a particular beamline.
> The issue was that I had to reverse the spindle direction in imosflm
> settings. Also, when I load data from this beamline into imosflm the program
> rotates the images by 90 degrees for some reason (this does not happen in
> HKL2000). Because of this rotation, the beam center that I used in HKL2000
> was different than the beam center position for imosflm.
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road,
Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic
Computing)
