[phenixbb] phenix autosol

Terwilliger, Thomas Charles terwilliger at lanl.gov
Sun Mar 13 08:23:13 PDT 2016


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 <vanxray at gmail.com>
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 <terwilliger at lanl.gov<mailto:terwilliger at lanl.gov>> 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: phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org> <phenixbb-bounces at phenix-online.org<mailto:phenixbb-bounces at phenix-online.org>> on behalf of Vandna Kukshal <vanxray at gmail.com<mailto:vanxray at gmail.com>>
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
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