Donghyuk - testing your "twinning" in a lower symmetry space group can be misleading. Many checks look to see if twin related reflections are similar. But the twin laws are often the same as the symmetry operators, so if you have ignored the true symmetry, you will wrongly assume you have twinning.
In this case I would do the following. Look at the small trigonal cell in pointless/aimless etc. (134.223/2 134.223/2 182.666, 90, 90, 120) (You can just input the data integrated in C2 I think and pointless will check alternate cells. Your C2 data with these cell dimensions can be reindexed into a trigonal cell 67.2 67.2 182.9 90.0 90.0 120.0 ) Then pointless will check the likely pointgroup symmetrys - P3 ? P3/mmm ? P6? etc and give you a score for each symmetry operator. And since you now have no non-cryst translation you can believe the twin tests much more. OK? Eleanor On Tue, 15 Jan 2019 at 10:57, Donghyuk Shin <sdh...@gmail.com> wrote: > Dear all, > > Thank you very much for all of your constructive comments. > Based on all of your comments, I have done several treatment on my data > sets, and here are some questions related with both your comments and my > results. > > First of all, I would like to make a short note summarizing all of your > comments for the people who will have similar problem. > > 1) Twinning and tNCS has opposite effects to each other, and one should > carefully analyze the data if one of them present. > 2) Simple tNCS can be automatically analyzed and corrected during Phaser, > but if it does not work, you may try to lower symmetry, decrease the size > of the Uni cell, or turning off the tNCS option during phaser. > 3) If one think there is twinning in the crystal, to make sure whether > your data is twinned, it is better to take a look twinning test than seeing > the R-values from refinement with twin operators. Applying twin operators > always give you better R- values. > > Then, here are some questions related to my current analysis. > Q1. As many of you concerned and I also had speculation on my C2 cell > refinement with twin operators, I tried to analyze twinning of my datasets. > (ATTACHED) > As you can see the log file from truncate, I guess my crystal is twinned. > In addition to this, I also followed the discussion between Randy and Lan. > I wanted to make sure whether my refinement with twin operators is correct > or not. As Randy recommend and based on the paper from Garib N. Murshudov ( > http://www.ysbl.york.ac.uk/refmac/papers/Rfactor.pdf), I could see the > drop of R-values with twin operators is always possible, however, in this > paper, I could see the gap between refinements w/ or w/o twin operators is > quite smaller than my case. (0.49-> 0.41 or 0.58 -> 0.52 vs my case 0.39 -> > 0.23). Together, based on both twinning-test and good R-values, I now > believe C2 refinement with twin operators are true. What do you think? > > Q2-1. Because some of you asked me about the original spots and > re-indexing the data sets with high symmetry SG, I went back to mosflm, > and here are some images from my analysis. As you can clearly see there are > strong/weak spots in the frames, and if you increase the threshold you can > pick the strong spots (ATTACHED). Based on this, initially, I assumed that > my crystal has tNCS, because I thought this strong - weak pattern is caused > by tNCS. or Am I wrong? > > Q2-2. During new indexing, I choose two unit cells (large and small) and > integrated them into 2 SG (P31 1 2 or P31 2 1) as Lijun commented. (four > data sets) > All of these data sets indicated twinning, while smaller one showed higher > twinning fractions. Then, I ran phaser, and found that phaser only found > the solution from P31 2 1SG from both large and small cells. However, I > could see crash of molecules from large cell, and I decided to stick with > small cell again. Then, during refinement with twin operators the R-values > drops from (0.46/0.49) to (0.37/0.42), even the map looks already good. I > assume that applying high symmetry SG is not possible for this case, and > again C2 refinement might be correct. > > Q2-3. Related to Q1 and 2-1, Now, I think C2 (small cell) refinement with > twin operator is right solution. Then, here I have another question. > Based on the observations from frames, I guessed my crystal has tNCS, and > I only followed strong spots. (Maybe I am wrong ?) > Then, data sets with only strong spots suggests my crystal is twinned. > Together, I am thinking my crystal has both tNCS and twinning, and I could > solve the structure by following strong spots with twin operators. > > Again, I would like to express my special thanks to you all for giving me > valuable comments. > I hope this post will also useful for others in the future. > > Donghyuk > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
