On the whole it is good practice to refine the 7 molecules you have - correct sequence etc etc, all with NCS restraints a 3A, then if you like use one of your improved molecules as the search model. But don't you have some NC symmetry such as dimers or tetramers - if so take one of the complete units and fit over the partner of the missing molecule - it is very probable then that you have positioned the lost one. Or if you want to be completely automated - use the dimer/tetramer whatever as the search model.. Eleanor MOLREP is good at this -
On 30 Oct 2012, at 14:53, Mark J van Raaij wrote: > if you are sure about it's position, why not put the 8th molecule by hand? > why believe what a program does more than you can see by eye? > (this is nothing against Phaser, it is a great program) > > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > > > > On 30 Oct 2012, at 15:44, Jacob Wong wrote: > >> Dear all, I have this (3.0 A) structure that has 8 molecules per ASU - >> Phaser was able to find 7 molecules correctly, but not the last one, as >> indicated by the .sol file (TFZ=5.1) below and the resultant density map. I >> tried to delete the entry of the last molecule and give the truncated .sol >> file for another round of MR but Phaser returned with the same solution that >> has the 8th molecule misplaced. I am tempted to place the 8th molecule by >> hand but before that would like to learn from you a better way of handling >> it. One thing I could think of is to refine/rebuild the partial structure >> with the 7 molecules so as to resolve any potential packing clashes due to >> model/structure variations and then let Phaser find/position the 8th one for >> me, but it appears that Phaser doesn't accept .pdb file for a "MR with >> partial solution" routine? Thank you, Jacob >> >> # [No title given] >> SPACEGROUP P 21 21 21 >> SOLU SET RFZ=3.7 TFZ=8.2 PAK=0 LLG=78 RFZ=3.7 TFZ=16.0 PAK=0 LLG=248 >> TFZ==17.2 RFZ=3.7 TFZ=17.8 PAK=0 LLG=463 TFZ==19.7 RFZ=2.9 TFZ=23.0 PAK=0 >> LLG=765 TFZ==23.2 RFZ=2.8 TFZ=28.6 PAK=0 LLG=1201 TFZ==30.0 RFZ=3.9 TFZ=23.1 >> PAK=0 LLG=1537 TFZ==24.3 RFZ=2.6 TFZ=19.5 PAK=1 LLG=2096 TFZ==32.1 RFZ=3.0 >> TFZ=5.1 PAK=1 LLG=1945 TFZ==7.0 >> SOLU 6DIM ENSE ensemble1 EULER 333.533 143.979 14.880 FRAC -0.30547 0.22985 >> -0.12420 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 287.095 31.031 200.132 FRAC -0.01202 0.48107 >> -0.12591 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 220.563 33.756 203.275 FRAC -0.33196 0.18927 >> -0.27514 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 125.978 23.511 167.527 FRAC 0.36411 -0.45096 >> -0.17121 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 148.925 162.593 356.498 FRAC -0.41711 >> -0.09462 -0.07282 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 323.033 34.903 192.073 FRAC -0.53201 -0.04754 >> -0.02533 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 113.904 157.019 345.596 FRAC 0.09892 -0.60041 >> -0.17986 BFAC 0.00000 >> SOLU 6DIM ENSE ensemble1 EULER 79.967 95.631 1.727 FRAC -0.41239 0.07915 >> -0.05760 BFAC 0.00000
