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Revision as of 03:05, 3 November 2009 (view source) Igchoi (Talk | contribs) (→Phenix.automr) ← Older edit		Revision as of 03:14, 3 November 2009 (view source) Igchoi (Talk | contribs) (→Phenix.automr) Newer edit →
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	*2nd trial: try each model looking for the best solution		*2nd trial: try each model looking for the best solution
	**1V19A gave best solution		**1V19A gave best solution
		+	**resoltion 4-20 was enough to find the solution
		+	**judgement: LLG>100, Z-score>7
		+	**our solution was almost at edge
	<pre>		<pre>
	Solution annotation (history):  RFZ=5.2 TFZ=4.6 PAK=0 LLG=35 RFZ=5.6 TFZ=7.7 PAK=1		Solution annotation (history):  RFZ=5.2 TFZ=4.6 PAK=0 LLG=35 RFZ=5.6 TFZ=7.7 PAK=1

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Revision as of 03:14, 3 November 2009

MR

• get MR models (PDB homologs) - 1TZ6_A, 2V78_A, 1TYY_A, 2DCN_A, 3IQ0_A, 1V19_A (Top 6 PDBs) by Psi-blast
• superimpose them into 1TZ6_A (make multiple models & compare those structures) by UCSF chimera

Phenix.automr

• 1st trial: use multiple models
  • it didn't give good solution
• 2nd trial: try each model looking for the best solution
  • 1V19A gave best solution
  • resoltion 4-20 was enough to find the solution
  • judgement: LLG>100, Z-score>7
  • our solution was almost at edge

Solution annotation (history):  RFZ=5.2 TFZ=4.6 PAK=0 LLG=35 RFZ=5.6 TFZ=7.7 PAK=1
   LLG=92 LLG=92
Log likelihood gain for solution MR: 92.0433

Phenix.autobuild

• Going on to AutoBuild with this solution now

Model (overall_best.pdb) from: overall_best.pdb
Cycle: 7
R and R-free: 0.25 0.31
Map-model CC: 0.76
Model-building logfile (overall_best.log) from: overall_best.log
Model evaluation (overall_best.log_eval) from: overall_best.log_eval
Map coeffs used for build (overall_best_denmod_map_coeffs.mtz)
from: overall_best_denmod_map_coeffs.mtz
SigmaA map coeffs (overall_best_refine_map_coeffs.mtz) 
from: overall_best_refine_map_coeffs.mtz