On Fri, Jan 23, 2015 at 8:32 AM, Tarek DawoD wrote:

1- if i have 2 myfile-data.mtz files (for the same structure but 2 different ligands, one of them 1.9 A and the other 1.6 A) and i want to copy free set from one to the other. so i have in the (ALL Input Arrays) 2 intensity and 2 R-free flag. so what i did is to add in the (output array) one of the intensity which belongs to one and one R flag which belong to other. i was not sure how to use the other output options??? what should i check or uncheck in this particular case???

You should be able to leave the other options alone. Just make sure that the output symmetry is taken from the input file with the intensities, not the file with the R-free flags. (There is a button in the first tab that lets you select a file to extract symmetry from.) If you're copying flags from the 1.9Å dataset to the 1.6Å dataset, the extra reflections will have new flags generated automatically (the checkbox labeled "Extend..." etc. covers this). One big caveat: make sure that the input files are indexed identically - for example if one file has this symmetry: P221212 30 40 50 90 90 90 and the other has this: P21212 40 50 30 90 90 90 the editor (and other programs) will not handle the difference in indexing automatically. (It will usually - but not always - be reasonably obvious whether this is a problem or not.) 2- How this works? suppose i have h k l (6 7 21) has flag 1 in the data.mtz

file (the one i used to copy the free set to other mtz), if i will copy this to other mtz (which has no R flag of course), the program will look for (6 7 21) h k l in the other mtz to give it also flag 1. Am i right.???

This is not exactly how it works in the actual code, but the result is essentially the same. It will automatically account for differences in reciprocal-space ASU (but not indexing!), anomalous vs. non-anomalous, and reflections present in one dataset but not the other. 3- if i am right in number 2, Suppose the other mtz has no (6 7 21) h k l

what will happen? if it is just ignoring it or assign flag 1 for other h k l which did not exist in the first data.mtz. this means it is impossible to get 100% free set similar between say the 2 mtz files in this case.

Using default settings, any reflection in the output file for which you have an experimental observation will also have a corresponding R-free flag. This implies that if you have slightly different sets of experimental observations, the resulting arrays of flags will not be identical - but they *will* be 100% identical for all reflections in common if you use the editor as intended. (I think the current behavior is to keep flags from the input even for reflections that don't have experimental observations - this can also be toggled. Either way, however, it should not cause problems for any of the other tools in Phenix.) -Nat