-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear SDY,
if you can see extra density after MR into which you can even build or correct the model it is a good sign your chose the correct space group. Check the geometry of your model. I suppose it is very distorted - a matrix weight of 0.03 sounds high for 3.4A data - You can go down by a factor of 10 at least. You may need to run refmac for many cycles - I have used 200-300 cycles with weight matrix 0.001 and the LL would still not converge. Regards, Tim On 11/04/2012 04:03 PM, 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 - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQlpsuUxlJ7aRr7hoRAgUMAKCJNhlDW4q2Lgmer4lZJoi+GpxDmACg9sRW a5HeDN5HHK/Wdy1sEY+9vbE= =aefJ -----END PGP SIGNATURE-----
