Slide 20 of 27
Things to check in mosflm.lp
Most importantly, check for occurrences of “WARNING”, “ERROR” and “SEVERE ERROR”.
- “WARNING”s are there to let you know that the program has detected a parameter which is not optimal and made an effort (usually successful) to correct it; you should not worry unduly about their presence, though it might be worthwhile checking to see if you can improve the data processing by taking a more active role.
- “ERROR”s occur when something has gone wrong in the processing which the program was unable to correct on its own. By and large these are problems of omission (e.g. is a file missing?) and can be avoided by taking careful note of the errors reported and taking action accordingly.
- “SEVERE”, “SERIOUS” and “FATAL” “ERROR”s cause the program to terminate. You should take careful note of what has caused the error and take steps to remedy it if possible. In some cases the only course of action is to contact the program’s authors and describe the problem to them.
- Having checked for those strings in mosflm.lp, look at the end of the file for a list of specific warnings about the data processing (look for the string “*** Warning messages ***”). All these messages (if any) contain advice about how to improve the data processing; take action accordingly, but bear in mind that Mosflm will probably have managed to cope well with these circumstances and reprocessing may not improve matters much.
- Having checked for warnings and errors, you should now check for rejected spots; if you processed interactively using the GUI, these will have been brought to your attention during processing, and there is (probably) no need to check now.
- Check the “Final rms residual” throughout mosflm.lp; for good data with low TDS on the images, expect it to be around half the pixel size (a little more for a lab source, often less for synchrotron data); this is a reasonably good indication that all parameters have been well determined and the spot positions have been predicted well.
- If the rms residual becomes high, first check that the “Total number” of reflections used in postrefinement has not dropped suddenly; it should rise through the first few images of data processing before becoming more-or-less stable.
Finally, check that I/sig(I) is significant in the high resolution shells (i.e. at least unity) and that the crystal was still diffracting at the end of the experiment (i.e. in the last image).