First - test other spacegroups - your solutions have lots of 60 degree angles - and the space group is hexagonal - there can be confusion between cryst symmetry and homo-dimer symmetries.
If you go back to the data processing and read the pointless output carefully for point group clues- Qs to check. Are the CCS for all crystal symops approximately equal? Could it be lower symmetry? trigonal ? or the two fold axis generated from the dimer?? Then are there absences along c indicative of P61 ? :P 62? or is there a non-cryst translation which could also generate absences? Then I always run the MOLREP self-rotation to see in this case is there a dimer two-fold somewhere different from the crystallographic ones? These cases with lots of model symmetry in high symmetry spacegroups are often tricky but neat fun when you get it sorted! Eleanor On Wed, 6 Jan 2021 at 08:56, Randy John Read <[email protected]> wrote: > Dear Luca, > > I think all of those orientations are symmetry-related copies of the same > orientation. This would imply that there is tNCS, but it doesn’t look like > Phaser is applying tNCS. The second and fourth molecules are in the same > orientation, but differing by 1/6 of the a-axis cell translation. Is there > a large off-origin native Patterson peak, perhaps at 1/6,0,0? > > Also, when there is tNCS it can be difficult to disentangle > crystallographic and non-crystallographic symmetry. Did you try all the > space groups in the same point group? > > Marc makes a good point about the number of copies. The Matthews volume > only gives you a rough estimate of the true number of copies, and the > signal in placing the fourth molecule is very unconvincing compared to the > first three. > > Best wishes, > > Randy Read > > > On 6 Jan 2021, at 07:38, Luca Mazzei <[email protected]> wrote: > > > > Hi all, > > > > I am struggling with the MR of a homo-dimer using Phaser. Matt_coeff > strongly suggests the presence of 4 mol per asym unit (space group P6222). > The results after a search of 4 mol per asymmetric unit of my monomer are > the following: > > > > ** SINGLE solution > > > > ** Solution written to SOL file: phaser_3f6v_A1_MOLREP.sol > > > > ** Solution written to PDB file: phaser_3f6v_A1_MOLREP.1.pdb > > ** Solution written to MTZ file: phaser_3f6v_A1_MOLREP.1.mtz > > Solution annotation (history): > > SOLU SET RFZ=3.9 TFZ=8.5 PAK=3 LLG=65 TFZ==10.0 RFZ=2.6 TFZ=17.0 > PAK=3 LLG=326 TFZ==29.8 (& TFZ==22.5 & TFZ==19.7) > > LLG+=(326 & 529 & 593) LLG=795 TFZ==5.4 PAK=5 LLG=795 TFZ==5.4 PAK=5 > LLG=795 TFZ==5.4 > > SOLU SPAC P 62 2 2 > > SOLU 6DIM ENSE autoMR EULER 125.3 60.8 300.2 FRAC 0.17 -0.13 > 0.08 BFAC -9.34 #TFZ==10.0 > > SOLU 6DIM ENSE autoMR EULER 305.4 60.8 300.2 FRAC 0.27 -0.16 > 0.08 BFAC -5.29 #TFZ==29.8 > > SOLU 6DIM ENSE autoMR EULER 294.7 119.1 120.3 FRAC 0.45 0.01 > 0.26 BFAC 0.34 #TFZ==22.5 > > SOLU 6DIM ENSE autoMR EULER 305.5 61.6 300.1 FRAC 0.11 -0.16 > 0.08 BFAC 29.19 #TFZ==5.4 > > SOLU ENSEMBLE autoMR VRMS DELTA -0.2463 #RMSD 0.93 #VRMS 0.79 > > > > It seems (also looking at the maps) that it correctly places three > monomers out of four. How can I use this information to improve the search > of the fourth monomer using the same template model? > > > > Thanks in advance for your help, > > > > Best regards > > > > Luca Mazzei > > > > Luca Mazzei - PhD > > Laboratory of Bioinorganic Chemistry > > Department of Pharmacy and Biotechnology (FaBiT) > > Alma Mater Studiorum - University of Bologna > > Viale Giuseppe Fanin, 40 - 40127, Bologna - Italy > > Tel: +39 0512096235 > > > > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 > 336827 > Hills Road E-mail: > [email protected] > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
