Hi Mahesh You might find this paper useful for some background on types of twinning. It explains the difference between merohedral and non-merohedral twinning.
http://journals.iucr.org/d/issues/2003/11/00/ba5036/index.html Alice -- Alice Dawson WNH Lab Division of Biological Chemistry and Drug Discovery College of Life Sciences University of Dundee 01382 385744 From: Mahesh Lingaraju <mxl1...@psu.edu<mailto:mxl1...@psu.edu>> Reply-To: Mahesh Lingaraju <mxl1...@psu.edu<mailto:mxl1...@psu.edu>> Date: Monday, 26 August 2013 16:43 To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] Stuck rfree - possible non merohedral twinning ? Hi Juergen & other experts Thanks for the suggestions. I was under the impression that the twin laws/operators are to be used if the twinning is merohedral. In my case, it appears as if the twinning is non-merohedral and more over the data i have is processed as P422 which does not have twin operators ( probably because all the axial pairs are same anyway). Probably because of the same reason, xtriage did not give any operators for me to use. In such cases, do people usually try to process the data in another space group of lower symmetry which has a twin law and is there a definite way to distinguish twinning by merohedry vs non-merohedry other than just looking at the diffraction pattern ( is it crucial to make that differentiation ?) ? Thanks Mahesh On Sun, Aug 25, 2013 at 10:24 PM, Bosch, Juergen <jubo...@jhsph.edu<mailto:jubo...@jhsph.edu>> wrote: Hi Mahesh, if you use Refmac, then you can tell it to refine the twin fraction, no need to tell it the twin law as Refmac will figure it out. If you use phenix, you explicitly tell it the twin law and refine then with it. You can get the possible twin laws by running phenix.xtriage and looking at the log file. For a 1.7 Å dataset you should see excellent holes in the Phe and Tyr, even though your Rfactors are high. If that is the case then you are likely correct with the twin (if nothing else is wrong, Cbeta, Ramas etc). And you did add some waters to your structure already right ? if not the go water picking via Coot. Have you been converted to XDS now ? Welcome to the club. Jürgen On Aug 25, 2013, at 8:35 PM, Mahesh Lingaraju wrote: Hello everyone, I collected a dataset which looked like it is twinned ( or a really long axis in the cell) and did not process in HKL2000 and MOSFLM but with some of help and suggestions from CCP4BB, XDS was able to process it. The data looks good upto 1.7 Å. However, the rfree is stuck at 0.34 even though my model is almost complete. I am beginning to wonder if the data is really twinned as it has the characteristics of non- merohedral twinning: In the images some of the reflections are sharp while some are split and one of the axis in the cell is usually long ( the cell is a= 46.78 b= 46.78 c= 400.34; 90 90 90) is there anyway to work around this ? or collecting better data is the only solution ? Any help is deeply appreciated Thanks Mahesh ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742<tel:%2B1-410-614-4742> Lab: +1-410-614-4894<tel:%2B1-410-614-4894> Fax: +1-410-955-2926<tel:%2B1-410-955-2926> http://lupo.jhsph.edu The University of Dundee is a registered Scottish Charity, No: SC015096
