There are several questions here. 1) What is the point Group - P4 or P422. I find the pointless statistics which check all symmetry operators singly useful. If the 2 fold kh-l gives about the same CC as the 4 fold operators k-hl -h -k l -k h l then you probably do have point group P422. ( But check the twinning graph to see if twinning is likely - twinning in this space group can mimic the 2 fold k,h,-l ) and if it is present you should work in point group P4.
2) What is the space group? The absences make it look like P42 21 2 or P 43 21 2 except for the rogues 00 19 and 00 20 which maybe are just that - rogues - see Jims suggestions..) But do you have a non-crystallographic translation? this can be found by a native patterson peak search, and is part of the truncate output. If there IS a peak at x,y,z=1/4 say then that might mislead you be producing weak reflections along 0 0 l axis. 3) Find the MR solution - and that is easiest done using the Phaser command test alterspacegroups.. Eleanor On 4 Nov 2012, at 15:03, SD Y wrote: > Dear All, > I have few basic questions for which I need help. I have a 3.4 A data and I > have processed it to P4. > 1. I used pointless to find SG, it suggests P41 21 2. But I see two > strong intensities in systematic absences > Intensities of systematic absences > h k l Intensity Sigma I/Sigma > > 0 0 2 -0.7 0.3 -2.0 > 0 0 3 1.0 0.4 2.3 > 0 0 5 0.3 0.7 0.4 > 0 0 6 -0.7 0.9 -0.8 > 0 0 7 -0.4 0.9 -0.4 > 0 0 9 -0.2 0.9 -0.2 > 0 0 10 1.3 1.2 1.1 > 0 0 11 -0.8 2.1 -0.4 > 0 0 13 1.2 2.1 0.6 > 0 0 14 2.3 1.8 1.3 > 0 0 15 -1.0 1.9 -0.5 > 0 0 17 2.4 2.0 1.2 > 0 0 18 21.1 4.5 4.7 > 0 0 19 90.2 6.0 15.0 > 3 0 0 -0.1 0.2 -0.8 > 5 0 0 0.2 0.2 0.9 > 7 0 0 -0.3 0.2 -1.3 > 9 0 0 0.0 0.5 0.0 > 11 0 0 -0.2 0.6 -0.4 > 13 0 0 0.8 0.7 1.1 > 15 0 0 -1.2 0.6 -1.9 > 17 0 0 -0.3 0.8 -0.4 > 19 0 0 -1.4 0.6 -2.6 > 21 0 0 -2.2 1.2 -1.9 > 23 0 0 -0.8 1.3 -0.6 > 25 0 0 -1.2 1.1 -1.1 > 27 0 0 -0.9 1.6 -0.5 > 29 0 0 -0.4 1.7 -0.2 > 31 0 0 -7.1 1.3 -5.3 > 33 0 0 -2.4 2.1 -1.1 > 2. When I used phaser for MR, it gave weak solution in p43, so I > scaled data in p43 21 2 (this also two intesities high like above in > systamatic absences) and used for Phaser to get the following solution > SINGLE solution > > SOLU SET RFZ=4.5 TFZ=9.4 PAK=0 LLG=105 TFZ==10.1 RF++ TFZ=17.7 PAK=0 > LLG=282 TFZ==15.6 LLG=285 TFZ==12.4 > SOLU SPAC P 43 21 2 > SOLU 6DIM ENSE ensemble1 EULER 153.1 50.3 73.2 FRAC -0.11 0.03 -0.94 BFAC > -2.65 > SOLU 6DIM ENSE ensemble1 EULER 148.4 129.9 252.8 FRAC -0.32 -0.35 1.07 > BFAC 4.01 > Ensemble ensemble1 RMS variance(s): 1.13 > 3. I used this solution to further refine the model in refmac, using > local ncs, with/without jelly, optimized weight/weight of 0.03, map > sharpening with B=20 in several rounds. > > I noticed that R factor R factor stayed around 33% while R free keeps > floating around 42%. I could see some density for missing loop in the model > and I could build but the R work and R free moving apart. By reading, I > understand that this is very common for low resolution data unless I use > appropriate restraints. > > I am wondering if my space group is correct? I had understood that if it’s > right SG, high intensity reflections will not be found in systematic absences > but I started doubting if I have understood correctly. > > This is my first low resolution data, I want use this opportunity to learn > refmac well. So could you please let me know if my doubt is right regarding > SG and how do I troubleshoot. > > Thanks > SDY
