[phenixbb] Judging AutoSol Output

Petrus H Zwart PHZwart at lbl.gov
Sun Apr 30 09:40:07 PDT 2006

----- Original Message -----
From: agb838 at mail.usask.ca
Date: Monday, April 24, 2006 3:18 pm
Subject: [phenixbb] Judging AutoSol Output

> I have some basic questions about the output from Phenix. 
> Basically I
> have a data set that gave a solution, but I am not exactly sure 
> how to
> tell about the quality of the solution from the outputs. The overall
> score is 110. I am not sure exactly what that refers to or how 
> good/badit is. I have attached the AutoSol.output file. Any basic 
> suggestions at
> what I should be looking at, or if this is even the right file, 
> would be
> helpful. The resolve.mtz and resolve.pdb look alright. They are a good
> start, but much improvement is needed. If anyone has some 
> suggestions as
> to how to improve the output, that would also be helpful.
> I have also run the data through solve/resolve through the command
> prompt and it repeatedly locates four heavy atom sites (the data 
> set is
> SAD). Yet, when Phenix is used, 16 sites are found. Why the difference
> and how do I tell what is working better and why.
Autosol is finding sites using HySS and subsequently iterates phasing, 
solvent flattening with the use of difference maps to find more sites. 
Juding from your output, it find most sites in 1 go.
If you want to compare sites you find by Solve, Hyss, or famous 
programs from Buffalo or Goettingen, use 

iotbx.emma ha_from_autosol.pdb other.pdb

To get an idea how many sites are matching.

As far as I understand it, the overall score is a score relative to the 
other hand and other solutions and its absolute value is not so 
important, as long as it is (much) larger that any other solution.
In your case, solution 1 has a score of 110, solution has a solution of 
It is also finding NCS, which seems to be good (NCS correlation of 0.66 
early no allready).

Improvement of the pdb file is obtained by runnnig the modelbuild 
wizard I think.
The Autosol wizard only carries out a limit number of model building 
cycles and the modelbuild wizard does a more thorough job.



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