[ccp4bb] MAD phasing

Ethayathulla Abdulsamath Thu, 21 May 2009 16:13:27 -0700

helloI 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 &amp; 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.&nbsp; i tried phenix.autosol also but it didnt work. how can 
i check the peaks are real.&nbsp; can anybody suggest me how do I proceed 
further and what r the mistakes i am doing..Thank you EthayathullaFROM 
SOLVE&nbsp; Site&nbsp;&nbsp;&nbsp; x&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
y&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; z&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
occ&nbs!
 p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; B&nbsp;&nbsp;&nbsp;&nbsp; -- PEAK&nbsp; 
HEIGHT --&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp; 0.386&nbsp;&nbsp; 0.986&nbsp;&nbsp; 
0.050&nbsp;&nbsp; 1.449&nbsp; 
60.000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
23.82&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 0.623&nbsp;&nbsp; 0.997&nbsp;&nbsp; 
0.046&nbsp;&nbsp; 0.921&nbsp; 
60.000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
22.11&nbsp;Summary of scoring for this 
solution:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 -- over many solutions--&nbsp;&nbsp;&nbsp; -- this solution 
--&nbsp;Criteria&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 MEAN&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
SD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; VALUE&nbsp;&nbsp;&nbs!
 p;&nbsp;&nbsp;&nbsp;&nbsp; Z-SCORE&nbsp;Pattersons:&nbsp;&nbsp;&nbsp;&
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 0.129&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
0.500&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
0.279&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.299&nbsp;Cross-validation 
Fourier:&nbsp;&nbsp;&nbsp;&nbsp; 
4.83&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
2.62&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
41.8&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 14.1&nbsp;NatFourier 
CCx100:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
3.28&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
1.24&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
3.93&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0.521&nbsp;Mean figure of 
meritx100:&nbsp;&nbsp;&nbsp;&nbsp; 
0.00&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
7.16&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
53.5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.48&nbsp;Correction for 
Z-scores:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb!
 
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 -10.5&nbsp;Overall Z-score 
value:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 11.9RESOLVE results&nbsp;CORRECTED OVERALL FIGURE OF MERIT OF 
PHASING:&nbsp;&nbsp; 
0.61&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
*&nbsp;*&nbsp;&nbsp;&nbsp;&nbsp; ESTIMATED FRACTION OF PHASE INFORMATION FROM 
PRIOR:&nbsp; 0.39&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
*&nbsp;*&nbsp;&nbsp;&nbsp;&nbsp; ESTIMATED FRACTION OF PHASE INFORMATION FROM 
MAP:&nbsp;&nbsp;&nbsp; 0.61&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
*&nbsp;*&nbsp;&nbsp;&nbsp;&nbsp; NOTE: The fract!
 ion from prior will be roughly proportional to&nbsp; *&nbsp;&nbsp;&nbs
p;  Overall average CC:&nbsp;&nbsp; 0.5423778&nbsp;Results of wilson scaling of 
model Fc to Fo :&nbsp;Scale on I to apply to Fc =&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
1.934&nbsp;B-value to apply to Fc=&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
1.971&nbsp;Overall R-factor for FC vs FP: 0.404 
for&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3288 reflections&nbsp;Leaving 
out&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp; 
reflections with FC=0 and correcting R-factor to&nbsp; 0.4036375&nbsp; 
from&nbsp;&nbsp; 0.4035717&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; as only&nbsp;&nbsp; 
99.96960&nbsp;&nbsp;&nbsp;&nbsp; % of the reflections are ok&nbsp;Writing 
overall R-factor&nbsp;&nbsp; 0.4036375&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; to 
"resolve.rfactor"



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A.S.Ethayathulla,Ph.D.
Department of Biophysics
All India Institute of Medical Sciences
Ansari Nagar
New Delhi-110029
India.
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[ccp4bb] MAD phasing

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