[phenixbb] Reflection file editor. copying Free set from one to other mtz.

Nathaniel Echols nechols at lbl.gov
Fri Jan 23 11:06:40 PST 2015

On Fri, Jan 23, 2015 at 8:32 AM, Tarek DawoD <tkdawod at yahoo.com> 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.)

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