I'm attempting a difficult molecular replacement using phaser and low resolution data (3.5A). There's almost certainly only one molecule in the asymmetric unit. Since the entire structure of a homologous multidomain protein doesn't work, I've broken it down in domains and have been attempting to find them sequentially.
The problem is the following. The solutions with the first domain work fine, pack, have ok Z-scores etc. They look fine visually. Then when I fix the first solution(s) and attempt to find the next domain, the packing function doesn't seem to work. When I look at the solution and generate symmetry mates, the 2nd domain invariably clashes with itself (but not with the 1st, nor does the 1st with itself). I don't remember seeing a similar problem when finding a 2nd copy of the same molecule. My suspicion is that phaser is using the wrong symmetry information for the 2nd molecule. Although why would the packing for the 1st molecule relative to itself remain the same (i.e. have no clashes)? Is this a known problem? Am I doing something wrong? The script file looks like this: MODE MR_AUTO HKLIn truncated.mtz RESOLUTION 3.5 LABIN F=F SIGF=SIGF COMPOSITION PROTEIN MW 75000 NUM 1 ENSEmble mol1 PDBFile helical.pdb IDENtity 0.20 ENSEmble mol2 PDBFile Cterm.pdb IDENtity 0.27 SOLU SET RFZ=2.7 TFZ=4.9 PAK=0 LLG=32 LLG=32 SOLU 6DIM ENSE mol1 EULER 13.345 119.350 196.414 FRAC -0.14439 1.86117 0.01283 SEARCH ENSEmble Cterm NUM 1
