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<p>Hi Vandna,<br>
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<p><br>
</p>
<p>Almost...<br>
</p>
<p><br>
</p>
<p>Yes you should use <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);"><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">overall_best_refine_data.mtz</span></span>
for refinement. You don't need <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">exptl_fobs_phases_freeR_flag.mtz</span> as it is identical to <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">overall_best_refine_data.mtz</span>.<br>
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<p><br>
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<p>Yes you can provide autobuild or Coot with overall_best_denmod_map_coeffs.mtz as information for calculating a map. </p>
<p><br>
</p>
<p>Note that you provide this to autobuild with "input_map_file=<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">overall_best_denmod_map_coeffs.mtz</span>" and you also need to provide
autobuild with "data=<span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);">overall_best_refine_data.mtz</span>​".<br>
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<p><br>
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<p>All the best,<br>
</p>
<p>Tom T<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Vandna Kukshal <vanxray@gmail.com><br>
<b>Sent:</b> Sunday, March 13, 2016 8:28 AM<br>
<b>To:</b> Terwilliger, Thomas Charles<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] phenix autosol</font>
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<div>
<div dir="ltr">thank you very much for your reply.
<div> so as i understand that for further refinement I have to use <span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">overall_best_refine_data.mtz as well as exptl_fobs_phases_free R_flag.mtz file (which include
exptl phases with Free R ).</span></div>
<div><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">and in auto build i have to give </span><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">overall_best_denmod_map_</span><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px">coeffs.mtz
as well as in coot i have to use same. </span></div>
<div>After solving fromSAD i have trouble understanding all these files. </div>
<div>let me know if i understood correctly.</div>
<div>thanks for your valuable reply. </div>
<div><span style="color:rgb(0,0,0); font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px"><br>
</span></div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Mar 11, 2016 at 10:48 PM, Terwilliger, Thomas Charles
<span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br>
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<p>​Hi Vandna,<br>
</p>
<p><br>
</p>
<p>I'm sorry there are so many files from autosol...I know it is not obvious what to use.<br>
</p>
<p><br>
</p>
<p>You want to use:<br>
</p>
<p><br>
</p>
<p> overall_best.pdb as your best working model<br>
</p>
<p><br>
</p>
<p> overall_best_refine_data.mtz as your refinement data and </p>
<p> experimental phase information also used in refinement<br>
</p>
<p><br>
</p>
<p> overall_best_denmod_map_coeffs.mtz as your best working map coefficients.<br>
</p>
<p><br>
</p>
<p>Let me know if that doesn't do it!<br>
</p>
<p>All the best,<br>
</p>
<p>Tom T<br>
</p>
<p><br>
</p>
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<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b>
<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>> on behalf of Vandna Kukshal <<a href="mailto:vanxray@gmail.com" target="_blank">vanxray@gmail.com</a>><br>
<b>Sent:</b> Friday, March 11, 2016 5:52 PM<br>
<b>To:</b> PHENIX user mailing list<br>
<b>Subject:</b> [phenixbb] phenix autosol</font>
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<div>Hi , <br>
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I am solving a structure using selenium SAD using autosol. Autosol gave me nice solution but many loop and side chain density is missing. <br>
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<div style="font-size:12.8px">autosol gave me many different output MTZ files . <br>
</div>
<div style="font-size:12.8px">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 . <br>
</div>
<div style="font-size:12.8px">thanks for your suggestions.</div>
<div><br>
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-- <br>
<div><font face="verdana, sans-serif" size="1" style="font-family:verdana,sans-serif">Vandna Kukshal<br>
Postdoctral Research Associate</font><br>
Dept. Biochemistry and Molecular Biophysics<br>
Washington University School of Medicine<br>
660 S. Euclid, Campus Box 8231<br>
St. Louis, MO 63110</div>
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-- <br>
<div class="gmail_signature"><font face="verdana, sans-serif" size="1" style="font-family:verdana,sans-serif">Vandna Kukshal<br>
Postdoctral Research Associate</font><br>
Dept. Biochemistry and Molecular Biophysics<br>
Washington University School of Medicine<br>
660 S. Euclid, Campus Box 8231<br>
St. Louis, MO 63110</div>
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