One of the most lucid explanations of how translational NCS results in peaks in a self-Patterson map is provided in Phil Evans’ classic paper, “Rotations and rotation matrices”, which is an Open Access publication. In particular, check out Figure 4, which illustrates a non-crystallographic dyad axis parallel to a crystallographic screw dyad.
Acta Christ. (2001) D57, 1355-1359. https://journals.iucr.org/d/issues/2001/10/00/ba5006/index.html Diana ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Feb 3, 2021, at 10:33 AM, Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote: EXTERNAL MAIL Hello, in the self-rotation function the peaks arising from the NCS rotation axes are good at hiding under the peaks for the crystallographic rotations, which is because they are actually translational NCS elements, I think. Also, sorry Eleanor, a double-check on wikipedia confirms the space group ambiguity is actually between I422 and your original choice I4(1)22. Did you do something special to get good anomalous to 2.7A e.g. wavelength, covalent modification, etc? Hope this helps. Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 3 Feb 2021, 13:59, Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote: I would look VERY carefully at your data processing. CCP4I2 report is a good place to start. The self rotation with the ring around the edge is hard to reconcile with two molecules in the asymmetric unit. Are the images clean or streaky? Do you have a photo of the crystal? And by the way - you cannot decide on spacegroup I422 or I 42 2 2 till you solve the structure.. Eleanor On Wed, 3 Feb 2021 at 12:12, Randy John Read <rj...@cam.ac.uk<mailto:rj...@cam.ac.uk>> wrote: Dear John, It’s hard to be absolutely certain from the reproduction, but it looks like you have equally high 2-fold axes all around the xy plane in the self-rotation function. Do you have an explanation for that? It would be helpful to know the heights of the Patterson peaks relative to the origin peak. However, assuming that the ones you have listed are all relatively high, this can be interpreted in terms of a commensurate modulation or, in alternative terminology, a multiple tNCS vector. All of the peaks are approximate multiples of the same translation vector, i.e. 1/2, 1/2, 1/6. 1/2, 1/2, 1/6 2/2, 2/2, 2/6, equivalent to 0, 0, 1/3 3/2, 3/2, 3/6, equivalent to 1/2, 1/2, 1/2 The next three in this series would be the same vectors in the opposite direction, i.e. related by the inversion operator in the Patterson. If the Matthews coefficient suggests 2 copies, you could probably have 3 in the asymmetric unit related by multiples of the same vector, but not 6. So in Phaser you would express this as TNCS NMOL 3 TNCS TRA VECTOR 0.5 0.5 0.169 Best wishes, Randy Read > On 3 Feb 2021, at 11:34, leo john > <ljohn16012...@gmail.com<mailto:ljohn16012...@gmail.com>> wrote: > > Sticking to the same doubt: > > Just to check the correct symmetry and space group, I have now processed my > data in P1 and I4 followed by running MOLREP for self-rotation function > (Figure attached). > > Can we conclude now on the correct space group and oligomeric state. > > Thank You all > John > > On Wed, Feb 3, 2021 at 8:34 AM leo john > <ljohn16012...@gmail.com<mailto:ljohn16012...@gmail.com>> wrote: > Dear All: > > I have a peptide that is crystallized in the space group I4122 with cell > dimensions 40,40, 200 Ang. > Mathews Coefficient suggests 2 molecules/ ASU. > Since I do not have a starting model for MR, I went for experimental phasing. > However, unsuccessful so far. > > Details about my dataset: > > 1) It has been collected at 2 Ang and has an Anomalous signal till 2.7 > 2) It has got Translational NCS. > 3) I checked the self-rotation function using MOLREP (figure attached), but > not able to make anything out of it. Please suggest. > 4) I got the translational and rotational peaks from the log file of MOLREP > > Peak 1: trans.vector /ort/ : 19.270 19.270 98.550 > trans.vector /frac/: 0.500 0.500 0.500 > Peak 2: trans.vector /ort/ : 19.270 19.270 33.326 > trans.vector /frac/: 0.500 0.500 0.169 > Peak 3: trans.vector /ort/ : -0.000 -0.000 65.224 > trans.vector /frac/: 0.000 0.000 0.331 > > Sol_Rf 1 0.00 0.00 0.00 0.00 0.00 0.00 0.4448E+06 > 4.53 > Sol_Rf 2 89.99 112.50 180.00 0.00 180.00 -45.00 0.3561E+06 > 3.63 > Sol_Rf 3 109.56 6.31 180.00 6.31 -140.88 173.69 0.4912E+05 > 0.50 > > These are unique peaks. > > My questions are: > > 1) How to read these MOLREP records and the plots to conclude something. How > can I guess the oligomeric state using the plot. Any link or suggestion will > be really helpful. > 2) How to specify the TNCS during phaser run. > > Thank You all > John > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > <SRF_P1_I4.png> ----- Randy J. 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