Dear John, It is not the sequence identity/similarity that counts, but how similar the protein folds are. For many protein families, the fold is identical although the sequence identity is very low. With 25% sequence identity and presumably a protein from the same family, I give you a good chance that e.g. Phaser will find the solution. However, if there is a hinge movement, or some other deformation, you may not find a solution despite very high sequence identity.
Concerning your twinning: with 25% twinning fraction, you could try to detwin using Yates algorithm, but I would just try Phaser first with the data as is. I have done this with data sets with a twinning fraction close to 50% and what happened was that phaser would find two solutions, one for each twin orientation. The "raw" electron density map using this twinned data was amazingly good, presumably because the data of the twin fraction with the same orientation as the molecule used for phasing would produce very nice electron density, while the data of the the twin fraction with the other orientation would just produce noise, because for this data phases would be more or less random. So the bottom line: I would just run Phaser with the P6x data as is (with SGALTERNATIVE ALL) and only if that does not work try more elaborate methods. Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of john peter Sent: Tuesday, August 30, 2011 9:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] twinning in hexagonal system Hello All, This is regarding twinning in a data set. I collected a native data set to resolution, 1.8 A. I used XDS suite to process and scale the data set. It scaled well in P622 and I found systematic absence (l=6n present). Hence thought the space group may be P6122/P6522. SFCHECK did not show any twinning and also it did not detect pseudo-translation. Twin test in http://nihserver.mbi.ucla.edu/pystats/ ( Merohedral Twin Detector: Padilla-Yeates Algorithm ) showed perfect twinning. Scaled in P61/65 and SFCHECK reported twinning fraction 0.272 & no pseudo-translation. http://nihserver.mbi.ucla.edu/pystats/ ( Merohedral Twin Detector: Padilla-Yeates Algorithm ) showed perfect twinning. Another server from ucla http://nihserver.mbi.ucla.edu/Twinning/ showed partial twinning with twin fraction 0.23 as follows. 2 along a, b, a*, b* No. Twin Law Related Reflections = 18033 (pairs) No. Twin Law Pairs Considered = 9016 <H> = 0.266149 <H2> = 0.095303 Twin Fraction = 0.233249 +/- 0.000602 (SHELXL Commands: TWIN 1 0 0 -1 -1 0 0 0 -1 and BASF 0.233249) In P61/65, I got the following matthews-coeffs mol/asym Matthews Coeff %solvent P(1.73) P(tot) _____________________________________________________________ 1 9.75 87.39 .00 .00 2 4.88 74.79 .00 .01 3 3.25 62.18 .06 .14 4 2.44 49.57 .57 .63 5 1.95 36.97 .36 .21 6 1.63 24.36 .00 .00 7 1.39 11.75 .00 .00 _____________________________________________________________ May I ask what could be the real twin fraction and what is the likelihood of solving the structure by molecular replacement by models with 25 % sequence identity and 30 % sequence similarity. Thank you so much for reading this mail during your busy hours and all suggestions, comments would be gratefully welcome & appreciated. thank you ccp4 mailing list. John
