Re: [ccp4bb] mosflm and APS BM17
Hi I'd guess from the input file that the beam centre may be defined in a different reference frame to that which Mosflm expects in the image header; other possibilities are that the distance, wavelength, or something else (!) is wrong. Indexing is critically dependent on having the beam centre, distance and wavelength all being pretty close to the true values, though some indexing routines allow more latitude than others. My understanding (IMWBW) is that other programs (such as XDS or HKL2000) don't use the information in the image headers, and expect the parameters to be supplied by the user. With Mosflm, we try to make the user's life easier by trusting this information, especially from images collected at synchrotron beamlines; sometimes this trust is not warranted, and the user has to intervene! processing data collected on APS beamline BM17 on a MAR165 detector causes unexpected troubles. Even though the crystals are well-diffracting and the spots are sharp and well-resolved, indexing only works with a certain selection of frames, the refinement the goes totally hairwire. Probalby just a parameter or so set wrong. My input file in the attachment. The last three lines do not make much of a difference. Any ideas? Thanks! Cheers Jan mosflm.in: detector marccd directory ../Images template Image_0###.img image 001 nullpix 1 separation 0.95 0.95 close !LIMITS XMIN 0 XMAX 165 YMIN 0 YMAX 165 xscan 2048 yscan 2048 !SIZE 2048 2048 !PIXEL 0.07934 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] mosflm and APS BM17
Hi all, thanks a lot for all the responses! As anticipated, the solution is rather simple - the origin of the beam: denzo refines to: x=82.6 y=80.3 mosflm reads from header: x=80.0 y=84.0 - bad indexing etc mosflm works with: x=82.6 y=80.3 No swapping of x and y between denzo and mosflm in this case. Cheers Jan On 8/22/07, Harry Powell [EMAIL PROTECTED] wrote: Hi I'd guess from the input file that the beam centre may be defined in a different reference frame to that which Mosflm expects in the image header; other possibilities are that the distance, wavelength, or something else (!) is wrong. Indexing is critically dependent on having the beam centre, distance and wavelength all being pretty close to the true values, though some indexing routines allow more latitude than others. My understanding (IMWBW) is that other programs (such as XDS or HKL2000) don't use the information in the image headers, and expect the parameters to be supplied by the user. With Mosflm, we try to make the user's life easier by trusting this information, especially from images collected at synchrotron beamlines; sometimes this trust is not warranted, and the user has to intervene! processing data collected on APS beamline BM17 on a MAR165 detector causes unexpected troubles. Even though the crystals are well-diffracting and the spots are sharp and well-resolved, indexing only works with a certain selection of frames, the refinement the goes totally hairwire. Probalby just a parameter or so set wrong. My input file in the attachment. The last three lines do not make much of a difference. Any ideas? Thanks! Cheers Jan mosflm.in: detector marccd directory ../Images template Image_0###.img image 001 nullpix 1 separation 0.95 0.95 close !LIMITS XMIN 0 XMAX 165 YMIN 0 YMAX 165 xscan 2048 yscan 2048 !SIZE 2048 2048 !PIXEL 0.07934 Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 2QH
Re: [ccp4bb] mosflm and APS BM17
Is it possible that your crystal is not really a single crystal, or has multiple domains? I had a similar problem with an otherwise beautifully diffracting crystal (beyond 2.0 A) whose integration rapidly broke down after a few frames. On close inspection, it was possible to visualize multiple lattices in the diffraction images. At some rotation angles, these were not obvious and indexing was possible over a few frames. Apparently, my beautiful crystals were in fact stacks of plates slightly rotated with respect to each other. Jan Abendroth wrote: Hi all, processing data collected on APS beamline BM17 on a MAR165 detector causes unexpected troubles. Even though the crystals are well-diffracting and the spots are sharp and well-resolved, indexing only works with a certain selection of frames, the refinement the goes totally hairwire. Probalby just a parameter or so set wrong. My input file in the attachment. The last three lines do not make much of a difference. Any ideas? Thanks! Cheers Jan mosflm.in: detector marccd directory ../Images template Image_0###.img image 001 nullpix 1 separation 0.95 0.95 close !LIMITS XMIN 0 XMAX 165 YMIN 0 YMAX 165 xscan 2048 yscan 2048 !SIZE 2048 2048 !PIXEL 0.07934 -- Roger S. Rowlett Professor Colgate University Presidential Scholar Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED]
