Hi Mahesh,
First of all, I risk going out on a limb here since I have no demonstrable experience concerning your topic. I was trying to solve a non-merohedral dataset for years, and I failed (like "failure" as defined in the dictionary). That is hardly a reference, but I got to read "a little" on the topic and maybe I got some comments that can be useful for you.
So, if you data would be twinned by non-merohedry, you would not have a valid solution by now. You would have only a fraction of the reflections indexed and a significant fraction in that index would be overlaps. The others would be partial overlaps/splits and the rest fully split reflections (singlets). Solving a non-merohedrally twinned structure requires developing an independent crystal rotation matrix for each twin domain, integrating in the correct point group, leaving all related reflections unmerged and with the original index, solving the structure and identifying the twin law (the one that describes the superposition of one twin domain on top of the other one) during structure solution/refinement. According to my knowledge, this has not been done with a novel structure as of now. (As for anything I say here, someone please educate me if I am wrong) The really mean part with non-merohedral data is, that you cannot even index the data properly, although a variety of indexing choices will give you reasonably well integration/merging statistics and you might not notice it in the beginning. It is very hard to identify the correct cell. A rough guideline is, that in many cases, crystals twinned by non-merohedry display a relationship of a~2b (2a~b, depending on choice) so you can try to double the axis for either a or b in a tetragonal cell and see if your predictions for a primitive cell with those dimensions overlap better with your reflections. The true space group of the lattice will emerge at a later point of time. The best way to do the indexing is supposedly using programs for small-molecule crystallography. When (=if) you have the two matrices, you can forward them to your protein x-ray crystallography software and integrate twice using one matrix at a time. A much better way to deal with non-merohedry is to make different crystals. Or to optimize the cryo.
If your data is twinned by pseudo-merohedry, most of the reflections will be overlaps with a very few splits, rather in higher resolution bins than in lower ones. In case your data is really twined, I suspect that is what you are dealing with here by looking at the diffraction patterns you showed before. This means you can solve your structure by integrating your data with only one crystal rotation matrix. However, your data might appear to be not only in a higher point group but also in a higher lattice system than it actually is. Your data then emulates a P422 but your structure does not generate the crystal by that symmetry relationship. Since there is no twin law for P422, phenix.xtriage can not help you there with merged data. Treating twinning by pseudo-merohedry is pretty much straight forward. You must process your data in the correct point group and later identify and apply the twin law. Start with P1 and work up if you have enough frames.
Also, if you have more than one molecule in the ASU, you might have simply overestimated the symmetry. I have seen this once in a monoclinic cell with two copies in the ASU where one angle was ~90.08, but not 90.00. It still merged reasonably well as an orthorombic cell, but it was not twined.
In either case, try processing your images in a lower point group first, and look carefully at your data.
Did your predicted reflections cover all the observed reflections? Did you predict reflections (entire lunes?) that are not there? How does your native Patterson map look like if you process your data in P1?
good luck,
s.
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