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
?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
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From: [email protected]
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 < [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] < [email protected]> on behalf of Vandna Kukshal < [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
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
participants (2)
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Terwilliger, Thomas Charles -
Vandna Kukshal