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[ccp4bb]: AMORE question
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Dear CCP4 users,
I am now trying to solve a protein structure by MR using Amore. There are
four molecules in the au, based on the Matthews'coefficient and
self-rotation calculation.
The rotation and translation results are quiet puzzling. Here is the four
solutions for each molecules, after fixing them one by one
SOLUTIONTF1 1 77.01 90.00 271.21 0.1013 0.4771 0.3473 46.1 52.5 41.1 2 58.5
SOLUTIONTF2 1 15.47 48.52 87.74 0.4730 0.1005 0.1464 51.3 51.4 49.9 2 58.5
SOLUTIONTF3 1 72.38 32.04 96.38 0.8958 0.5205 0.3605 54.2 50.6 52.7 1 59.0
SOLUTIONTF4 1 81.25 38.07 83.60 0.0458 0.4842 0.3609 56.0 49.5 56.6 1 49.0
These solutions are the best,even though there is no clear gap.
After fiting, the CC and R-factor are also improved
TABLE Alpha Beta Gamma Tx Ty Tz Corr_F Rfac
SOLUTIONF 1 76.96 86.29 269.96 0.0895 0.4795 0.3503 57.2 47.8 57.3
SOLUTIONF 1 17.28 42.06 86.32 0.4720 0.1061 0.1464 57.2 47.8 57.3
SOLUTIONF 1 73.14 32.34 95.17 0.8981 0.5195 0.3576 57.2 47.8 57.3
SOLUTIONF 1 79.16 45.90 83.17 0.0539 0.4895 0.3601 57.2 47.8 57.3
Considering the model I used contains only 60% amino acids of my protein,
I think it is close to the solution.
But, problem appears when I check their packing. Molecules overlap to each
other, either directly or to their symmetry mates.
My questions are
1.Could someone know why such CC and R-f doesn't produce right
solution?
2. Does Amore check the molecular packing during translation search? How
to implement it?
I really appreciate it if someone can share their valuable experience on
this kind problem.
Wei
===================================================
Wei Zhang
Department of Biochemistry, Rice Unversity
Email: weizhang@rice.edu
===================================================