[phenixbb] difficulties with autoMR

Feldman III, George Franklin gfeldman at indiana.edu
Wed Sep 10 07:15:11 PDT 2008

I am trying to run phenix.automr on what I believe is perhaps a 
perfectly twinned data set, at 3A resolution. It is in space group 146 
and according to the matthews has 3 molecules in the asu. This is a 
mutant of an orriginally published structure in which only one residue 
has been mutated (but crystallizes in a different space group). When I 
give the autoMR the following input:

phenix.automr coords="MR.1.pdb" data=dtscale.ref resolution=0
component_type=protein identity="95" mass=13900 build=False copies=3

I get an LLG of 37 and the run goes quite quickly. The speed of the run
itself leads me to believe that I have a correct solution regardless of
the slightly low LLG, but when I open the .pdb output file there is
only one molecule in the asu. Am I doing something incorrectly? Why is
there only one molecule instead of 3 in the asu, and how can I go about
getting the other two to appear?

I did let the program go ahead run autobuild, this resulted in a 
structure with an r_work:.5448 and r_free:.6005. I am relatively new to 
crystallography, but these values seem rather high to be a good 
starting point for refinement.

I would appreciate any advice that might help me move on with my 
structure. Attached is the log file from phenix.xtriage in case it may 
be of any help. Thank you, in advance, for all of your help and advice.

Best Regards,
George F. Feldman

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