<div dir="ltr">Hi Dr Terwilliger<div><br></div><div>I have the pdb of the asymmetric unit and I am trying to fit it into my cryo-EM map of the whole structure( which has octahedral symmetry). Do I have so to do some-sort of pdb manipulation before the model_to_map operation ?</div><div><br></div><div>This is my command </div><div><br></div><div>phenix.map_to_model postprocess_test.mrc 2w0o_1chain.pdb resolution=4 d_min_ratio=0.89 seq_file=2w0o.fasta.txt >> model_to_map.log<br></div><div><br></div><div>the fasta sequence and the pdb file are both of a single unit </div><div><br></div><div>I hope my question makes sense this is my first time using phenix , </div><div><br></div><div>Sincerely</div><div>Joshua Lobo</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Aug 6, 2017 at 7:44 AM, Terwilliger, Thomas Charles <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p>Hi Joshua,<br>
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<p>I'm sorry for the slow reply. <span style="font-size:12pt">In phenix.map_to_model you normally do not need to specify any space group information. (For cryo-EM we use "P1" as the "space group" but you don't have to specify it).</span></p>
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<p>Let me know if that doesn't do it,<br>
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<p>All the best,<br>
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<p>Tom T<br>
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<div id="m_-5571834541326418413divRplyFwdMsg" 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-<wbr>online.org</a> <<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<wbr>online.org</a>> on behalf of Joshua Jude Lobo <<a href="mailto:jlobo@umn.edu" target="_blank">jlobo@umn.edu</a>><br>
<b>Sent:</b> Tuesday, August 1, 2017 12:50 PM<br>
<b>To:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] Appplying symmetry to a Cryo-EM map in phenix map_to _model</font>
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<div dir="ltr">Hi Phenix Group
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<div>I am very new to model building and using phenix . I am trying to use phenix.map_to_model to generate a model just using my cryo-EM map( mrc format) and a fasta sequence .My protein has octahedral symmetry . I found the use_space_group_symmetry argument
but am not sure what argument to give to impose the symmetry .</div>
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<div>Any inputs are appreciated</div>
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<div>Sincerely</div>
<div>Joshua Lobo</div>
<div>University of Minnesota Twin Cities </div>
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