It seems to me that this could be easily explained by there being a kink near the middle of the chain (so the bundle adopts a broad 'V' shape). Then fragments up to the length of the "arms" would each give two different but good solutions, but fragments longer than that would fall off. Have you tried asking Phaser to search for two copies of your 57aa fragment?
Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 30 Apr 2017, at 23:26, Dr A.A. Jalan <aa...@cam.ac.uk> wrote: > > Dear all, > > I have a two part question, > > I am trying to solve the structure of a collagen triple helix containing > 144aa. Phaser on models containing 21, 30, 39 and so on upto 120aa shows an > interesting trend. The TFZ and LLG scores peak at 57aa and then start to fall > off significantly. How should one go about explaining this. > > The second question is, phaser yields the following two solutions in the .sol > file using 57aa > > # CLUELESS_57 > SOLU RESOLUTION 1.36573 > > SOLU SET RFZ=9.7 TFZ=7.3 PAK=0 LLG=502 TFZ==11.1 LLG=1151 TFZ==16.6 PAK=0 > LLG=1151 TFZ==16.6 > SOLU HISTORY RF/TF(8/2:40)RNP(40:4)RNP(4:1)RNP(1:1) > SOLU SPAC P 1 21 1 > SOLU 6DIM ENSE ensemble1 EULER 86.543 77.471 296.818 FRAC 0.28741 > -0.00948 0.33176 BFAC -4.77330 #TFZ==16.6 # CLUSTER 2 > SOLU ENSEMBLE ensemble1 VRMS DELTA -0.4975 #RMSD 0.81 #VRMS 0.40 > > SOLU SET RFZ=9.3 TFZ=8.7 PAK=0 LLG=494 TFZ==11.3 LLG=1069 TFZ==16.4 PAK=0 > LLG=1069 TFZ==16.4 > SOLU HISTORY RF/TF(39/1:33)RNP(33:8)RNP(8:2)RNP(2:2) > SOLU SPAC P 1 21 1 > SOLU 6DIM ENSE ensemble1 EULER 353.101 26.529 183.602 FRAC 0.12571 > -0.00662 0.18389 BFAC -4.69482 #TFZ==16.4 # CLUSTER 1 > SOLU ENSEMBLE ensemble1 VRMS DELTA -0.4884 #RMSD 0.81 #VRMS 0.42 > > As can be noted, the solutions have fairly different coordinates. How should > one go about finding out which one is correct. > > Any inputs and suggestions are greatly appreciated. > > Thank you > > Abhishek > >
