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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
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