----- Original Message ----- From: [email protected] 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 63. 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. HTH Peter _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb