Just to add to Tim's reply, when you open the image with
iMosflm, you can Drag and drop the direct beam position in the
image display window. First, you have to click on the leftmost
icon in the row of icons under the image filename (a green
cross) which will display the direct beam position as read
from the image header as a green cross on the image. You can
then drag then over to where you think the beam position
should be (judging from the position of the backstop shadow).
If indexing still does not work, you can try doing a direct beam search
from the indexing pane, which will do a grid search +/- 2mm from the
However, you need to beware of one thing. I believe that the rotation axis
on the Sercat beamline goes in the opposite direction to most beam lines.
In such cases, indexing using more than one image will never work, because
the relative phi values will be wrong. You can try indexing with one
image, and then if that works, try predicting the next image. If that
prediction does not match, it is almost certainly because the rotation
direction is wrong.
To deal with this, choose the Settings->Experiment settings menu and click
on the "reverse phi" box. Then you MUST repeat the spot search for each
image being used in indexing, then it should all work.
> Dear All,
> We have collected a data for a protein crystal at SER-CAT Chicago and the
> detector is mar300.We are using mosflm to process the data.While
> indexing, the beamstop which it is taking is wrong, due to which it
> I am trying to define the beamstop manually using tools like mask and spot
> search area.
> (it might be wrong)
> It will be highly appreciable if someone can please suggest if this the
> method we should use to define the beamstop or there is any site
> definition file which has to be used, as it is available for HKL2000 or
> how we have to define the beamstop in mosflm.
> Sonali Dhindwal
> “Live as if you were to die tomorrow. Learn as if you were to live