Hi Fei, I assume you have edited the XDS.INP file to include the initially found space group and the first refined cell ? If not, then that would be my first choice to do. If that then still fails with the default parameters, then I would start fixing some values instead of refining all of them at the same time. The keywords to look for are the following: SPACE_GROUP_NUMBER= UNIT_CELL_CONSTANTS= REFINE(IDXREF)= REFINE(INTEGRATE)= REFINE(CORRECT)=
Once XDS successfully integrates your dataset coy GXPARM.XDS to XPARM.XDS and copy those values into the UNIT_CELL_CONSTANTS and rerun XDS.INP And more details on each of those can be found here: http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xds_parameters.html You should be able to take care of your problem as it doesn't sound severe. Jürgen On Jul 4, 2013, at 12:26 PM, Fei Li wrote: > Dear all, > > I recently collected some 10 degree wedges of data on a very small > membrane protein. The data processing so far is not working well. XDS > is the only software that process my data and give a space group and > cell parameters. However, I ended up with a merged dataset with low > completeness at low resolution. My data is not overloaded. This is a > very small protein shot with 5um mini-beam. I checked the FRAME.cbf > file and looks like XDS is not picking the spots at low resolution > correctly. It missed a good portion of my low res spots in every > datasets I checked and picked more at high res, which are weaker. Then > the indexing step will reject most of my spots for "too far away from > ideal position". imosflm was able to pick the spots correctly, but > does not index. I can send the FRAME.cbf file and the imosflm picture > if anyone thinks that will he useful to see. Any suggestion on how to > make XDS, or imosflm, correctly working for me is greatly appreciated. > Thanks a lot! > > Best regards, > > Fei > > > Fei LI > Graduate Assistant > 310 Biochemistry Building > Department of Biochemistry and Molecular Biology > Michigan State University > East Lansing, MI > 48824 ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
