hi BertThank you for your reply. Your are right about the values for your
Pattersons and NatFourier, but the systematic absences and pointless suggested
me to be P6122 and according to mathews coeff i get 1 molecule with
Vm= 2.06 solvent= 40.42. My protein has two SeMet sites so i
searched for two sites. I have just pasted few reflections which showed me P61.
then based on pointless i tried P6122 0 0
3 1.9
1.8 0.5 1.8
0 0 4
0.0 2.7
1.1 2.5 0 0
5 0.4 3.5
-0.5 3.3 0 0
6 427.5 33.6 399.9
30.3 0 0 7
14.3 5.9
4.0 4.8 0 0
8 1.5 5.8
-4.4 6.3 0 0
9 10.8 6.7
-2.1 7.5 0 0
10 7.0
7.3 1.5 7.2
0 0 11 -3.8
9.3 -2.7 8.4
0 0 12 201.7 19.1
198.6 19.8 0 0
13 22.5 9.6
12.5 9.9 0 0
14 2.9 10.7
0.0 8.5 0 0
15 -21.0 12.6
1.4 12.1 0 0
16 -1.6 12.6
10.8 12.3 0 0 18
6649.0 474.7 6423.4 460.5
0 0 19 -4.6
16.5 -8.5 15.1 0
0 20 -44.1 17.0
-16.3 16.7 0 0
21 34.6 20.7
61.8 18.5 0 0 22
-16.7 12.5 -15.4
15.9 0 0 23 -46.2
18.7 -35.9 18.2 pointless resultsBest
Solution space group P 61 2 2 Reindex
operator:
[h,k,l]
Laue group
probability:
1.000 Systematic absence probability:
0.963 Total
probability:
0.963 Space group
confidence:
0.949 Laue group
confidence
1.000thank youEthayathullaOn Thu, 21 May 2009 19:44:27 -0400 "Bert Van Den
Berg" wrote Re: [ccp4bb] MAD phasing Hi, My guess is that you
dont have the right space group. The values for your Pattersons and NatFourier
are way too low, especially the NatFourier you would like to be at least 2-3 or
so. In your assigned space group, do you have a reasonable value for the
matthews coefficient? Is there NCS? Are you finding the expected number of Se
sites? Again, I would try to investigate alternative SGs. Also it would be
a good idea to take the sites and refine them with SHARP. Good luck, Bert
On 5/21/09 6:38 PM, "Ethayathulla Abdulsamath" wrote: hello I am have
a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The
dataset is in P6 and based on pointless and absences it is P6122. Overall
Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i
used solve/resolve to find those peaks. I used datasets from 3.5 to 20A to find
peaks i got two good peaks of occ (1.4 & 0.92). I did analyze_solve and
refined those peaks. Then i tried resolve to autobuild and phasing but it didnt
work. The r-factor FC vs FP is 0.40 and FOM 0.6, although the results looks
promising i couldnt find proper phasing using phenix, resolve.autobuild.
i tried phenix.autosol also but it didnt work. how can i check the peaks
are real. can anybody suggest me how do I proceed further and what r the
mistakes i am doing.. Thank you Ethayathulla FROM SOLVE Site
x y
z occ
B -- PEAK
HEIGHT -- 1 0.386 0.986
0.050 1.449 60.000
23.82
2 0.623 0.997 0.046
0.921 60.000
22.11
Summary of scoring for this solution:
--
over many solutions-- -- this solution -- Criteria
MEAN
SD
VALUE
Z-SCORE Pattersons:
0.129
0.500
0.279
0.299 Cross-validation
Fourier: 4.83
2.62
41.8
14.1 NatFourier CCx100:
3.28
1.24
3.93
0.521 Mean figure of
meritx100: 0.00
7.16
53.5
7.48 Correction for
Z-scores:
-10.5
Overall Z-score value:
11.9
RESOLVE results CORRECTED OVERALL FIGURE OF MERIT OF PHASING:
0.61 *
* ESTIMATED FRACTION OF PHASE INFORMATION FROM
PRIOR: 0.39 * *
ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP:
0.61 * *
NOTE: The fraction from prior will be roughly
proportional to * Overall average CC:
0.5423778 Results of wilson scaling of model Fc to Fo :
Scale on I to apply to Fc = 1.934
B-value to apply to Fc= 1.971
Overall R-factor for FC vs FP: 0.404 for
3288 reflections Leaving out
1
reflections with FC=0 and correcting R-factor to 0.4036375
from 0.4035717 as only
99.96960 % of the reflections are ok
Writing overall R-factor 0.4036375
to "resolve.rfactor"
################################################### A.S.Ethayathulla,Ph.D.
Department of Biophysics All India Institute of Medical Sciences Ansari Nagar
New Delhi-110029 India. ###################################################
###################################################
A.S.Ethayathulla,Ph.D.
Department of Biophysics
All India Institute of Medical Sciences
Ansari Nagar
New Delhi-110029
India.
###################################################
