Hey Zach, remove the loops from your search model and rerun the MR. Alternatively, increase the maximum number of clashes allowed until you get a solution written out. See where your solutions clash. Again, if it's in a loop region, cut the loop and rerun. Your z-scores look great. (Notice that you have zed-scores when you run phaser through ccp4i and zee-scores when you run phaser through phenix.) Andreas zach powers wrote:
Hi,
I have a problem and i wonder if someone has had a similar experience. I have been using phenix.automr program to find an MR solution for a protein. When I ask Phaser to use copies=2 I find a number of solutions with poor z-scores (3-4). When I ask it to use copies=3, I get great Z-scores (see below) but no solution due to the high number of clashes (>100!).
As an x-ray newbie I am a bit perplexed of what to make of this: the solution is not good because there is not enough space in the unit cell to comfortably accommodate all three molecules yet the Z-score indicates the structure is good.
My structure does have several loops and these may be contributing to the clashing residues. As a newbie I have a newbie question - what does this mean (great z-score but no solutions)? Is this non-solution a possible solution if I play with it, or is the packing simply too tight and the Z-scores are not valid?
In the meantime I am chopping my protein into sub-domains as recommended in the Phaser documentation, but if anyone has seen something like this before, any suggestions are welcome.
thanks zach charlop-powers
Packing Table: Space Group P 3 ------------------------------ Solutions accepted if number of clashes = 135 (lowest number of clashes in list) provided this number of clashes <= 10 (maximum number of allowed clashes) # #Clashes # Accepted Annotation 1 188 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=10.4 2 156 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=10.2 3 151 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.8 4 146 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.7 5 187 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=10.5 6 202 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.2 7 170 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.1 8 144 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=10.2 9 177 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=9.1 10 153 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.9 11 150 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.8 12 217 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.6 13 182 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.6 14 135 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.5 15 175 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 16 159 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 17 192 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.3 18 165 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=9.2 19 169 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=9.1 20 158 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.0 21 173 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=8.0 22 154 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=16.3 TFZ=8.9 23 206 NO RFZ=20.3 TFZ=18.2 PAK=10 LLG=431 RFZ=18.5 TFZ=7.8
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-- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk