[phenixbb] phenix.automr high zscore but too many clashes

[Georg Zocher]

Dear Zach,

are you sure about your spacegroup? And what about the matthews 
parameter (http://www.ruppweb.org/Mattprob/)?

Best Regards,
Georg



Andreas Förster schrieb:
> 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
>>
>>    0 accepted of 23 solutions
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>>
>>     
>
>   


-- 
Universität Tübingen
Interfakultäres Institut für Biochemie
Dr. Georg Zocher
Hoppe-Seyler-Str. 4
72076 Tuebingen
Germany
 
Fon: +49(0)-7071-2973374
Mail: georg.zocher at uni-tuebingen.de
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