Dear Andrew and all the people for their help, I am providing mosflm the right beamstop and now, I am able to do the indexing, refinement and indexing too.Then I run scala for the output mtz file and it shows Rmerge too high 0.58and also when examining the spots and predictions in the image, it seems like it is not picking a lot of spots, so missing large number of reflections.So, any suggestions to correct it or am i doing something wrong. Thanks again for the help and suggestions
-- Sonali Dhindwal “Live as if you were to die tomorrow. Learn as if you were to live forever.” --- On Thu, 22/3/12, Andrew Leslie <and...@mrc-lmb.cam.ac.uk> wrote: From: Andrew Leslie <and...@mrc-lmb.cam.ac.uk> Subject: Re: [ccp4bb] Defining beamstop and error during indexing- moslfm To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 22 March, 2012, 7:43 PM Dear Sonali, 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 current position. 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. Best wishes, Andrew > 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 > fails. > > 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 > forever.”
