[phenixbb] phenix automr

Thomas C. Terwilliger terwilliger at lanl.gov
Sun Mar 29 17:34:01 PDT 2009

Hi Shya,

It sounds to me as though phaser and automr are doing what they are
supposed to do. The space group P41212 has the same point group as P43212
(and the same systematic absences) so from your raw data it is not
possible to tell which (if either) is correct.  Phaser evidently did not
find a great solution as your LLG is negative and the map poor.

Randy or others may give you some more detailed suggestions but here are
some ideas:

1. Try a different search model (a different structure, a combination of
models, trim off poorly-related parts)

2. Try changing the anticipated RMSD if you have set it instead of
sequence identity. This could affect the calculation of the LLG.

All the best,
Tom T

>> Hi all,
>> I tried to use phenix automr by using the gui and also I am using the
latest version of phenix (courtesy of the phenix development team). I
asked it to search for two molecules in the asymmetric unit but it
>> just one also I am getting negative (-29) LLG value for the final
solution. The map also does not look good. I also asked it to search
>> all possible space group, although I processed the data with P43212
>> automr finds a different one P41212.Will fixing the space group fix the
problem? Does anyone know what is going on? I tried running phaser
separately through ccp4 and phaser did find two molecules although the
>> did not look good in this either.
>> Shya
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