Hi Vandna,
Almost...
Yes you should use overall_best_refine_data.mtz for refinement. You don't need exptl_fobs_phases_freeR_flag.mtz as it is identical to overall_best_refine_data.mtz.
Yes you can provide autobuild or Coot with overall_best_denmod_map_coeffs.mtz as information for calculating a map.
Note that you provide this to autobuild with "input_map_file=overall_best_denmod_map_coeffs.mtz" and you also need to provide autobuild with "data=overall_best_refine_data.mtz?".
All the best,
Tom T
________________________________
From: Vandna Kukshal
Sent: Sunday, March 13, 2016 8:28 AM
To: Terwilliger, Thomas Charles
Cc: PHENIX user mailing list
Subject: Re: [phenixbb] phenix autosol
thank you very much for your reply.
so as i understand that for further refinement I have to use overall_best_refine_data.mtz as well as exptl_fobs_phases_free R_flag.mtz file (which include exptl phases with Free R ).
and in auto build i have to give overall_best_denmod_map_coeffs.mtz as well as in coot i have to use same.
After solving fromSAD i have trouble understanding all these files.
let me know if i understood correctly.
thanks for your valuable reply.
On Fri, Mar 11, 2016 at 10:48 PM, Terwilliger, Thomas Charles mailto:[email protected]> wrote:
?Hi Vandna,
I'm sorry there are so many files from autosol...I know it is not obvious what to use.
You want to use:
overall_best.pdb as your best working model
overall_best_refine_data.mtz as your refinement data and
experimental phase information also used in refinement
overall_best_denmod_map_coeffs.mtz as your best working map coefficients.
Let me know if that doesn't do it!
All the best,
Tom T
________________________________
From: [email protected]mailto:[email protected] mailto:[email protected]> on behalf of Vandna Kukshal mailto:[email protected]>
Sent: Friday, March 11, 2016 5:52 PM
To: PHENIX user mailing list
Subject: [phenixbb] phenix autosol
Hi ,
I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing.
autosol gave me many different output MTZ files .
for building further in coot which MTZ file i should use and for refinement in phenix refinement which MTZ file i should use . I tried doing refinement with .sca file it gave me increase Rfree afte single cycle of refinement .
thanks for your suggestions.
--
Vandna Kukshal
Postdoctral Research Associate
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110
--
Vandna Kukshal
Postdoctral Research Associate
Dept. Biochemistry and Molecular Biophysics
Washington University School of Medicine
660 S. Euclid, Campus Box 8231
St. Louis, MO 63110
