Hi Young-Jin,
As my recent data did not give me perfect statistics, I was wondering what the problem was (one of things is ice ring though). When I ran Xtriage with my struggling current data set and looked like I got twinned data. I reran PHASER as was suggested and confirmed that current space group is right. My question is now how I can handle this problem. First, as was recommended I input twin_law, however not all the cases (I have a couple of data sets) were working. One favorite(!) error message was as following:
"Map type 'Fc' not supported for twinned structures. Allowed types: Fo-Fc, Fobs-Fobs-Fmodel, 2mFo-DFc, 2mFobs-DFmodel, mFo-DFc, mFobs-DFmodel, gradient, m_gradient." I got this from both GUI and shell environment.
in the command line all you need to to give phenix.refine the twin law: phenix.refine model.pdb data.mtz twin_law="-h,l,k " as it is explained in the manual: http://www.phenix-online.org/documentation/refinement.htm#anch34 If you are using the GUI then also you can input the twin law information, and if it then crashes then Nat is the best person to explain it.
1. Now from now on, whenever I want to phenix.refine, should I include twin_law command such as 'twin_law=-h,l,k'?
Yes.
2. In this case, what do I expect to see such as lowering Rfree or else? If it doesn't help lowering Rfree,
Typically, after discovering twinning and taking it into account the R-factors should drop by 3-10% or so.
what to do next?
I guess just finalize your model and make sure it's right -:)
3. Do I have to report I did with twinlaw option in case of preparing a paper or presentation?
Yes. And the relevant information is printed in REMARK 3 records of your refined model. IMPORTANT: make sure this information is preserved when you PDB deposit your model.
How much can I convince my refinement is OK with twined data?
The rock-solid way is to show result of refinement with and without considering twining (showing R-factors may be enough). I almost forgot... Once you decided to use twinning make sure the Free-R flags are generated in PHENIX so you will not get biased Rfree.
Additionally, I checked other data, and applied twin_law but the result R/Rfree were exactly same as the one I refined without twin_law option, it this normal case?
If using twin information doesn't change anything then it's not worth of using at all. Finally, run: phenix.model_vs_data mode.pdb data.mtz Does it tell your data is affected by twining? If not - forget about it. Pavel.