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Hi Kendall,<br>
<br>
<blockquote cite="mid:C95C72D0.F415%25knettles@scripps.edu"
type="cite">
<title>Autobuild: problems with modified amino ac</title>
<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;"><br>
</span></font>
<ol>
<li><font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">methionines are converted to MSE
</span></font></li>
<li><font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">I’d like to include a .cif file
for b-mercapto-ethanol adducted cysteines: CME. The .cif
file is one that works for phenix.refine (listed below). I
suspect I am not writing the .eff file correctly:<br>
</span></font></li>
</ol>
<font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;"><br>
refinement.pdb_interpretation.apply_cif_modification<br>
{<br>
data_mod = cme<br>
residue_selection = chain A and resid 530<br>
residue_selection = chain B and resid 381<br>
}</span></font><br>
</blockquote>
<font face="Calibri, Verdana, Helvetica, Arial"><br>
If the above set of parameters works with phenix.refine, then it
should work in AutoBuild too. Just save <br>
<br>
</font><font face="Calibri, Verdana, Helvetica, Arial"><span
style="font-size: 11pt;">refinement.pdb_interpretation.apply_cif_modification<br>
{<br>
data_mod = cme<br>
residue_selection = chain A and resid 530<br>
residue_selection = chain B and resid 381<br>
}<br>
<br>
in a file </span></font>
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refinement_params.eff and run AutoBuild for example like this:<br>
<br>
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
phenix.autobuild data=w1.sca
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
seq_file=seq.dat model=coords.pdb
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
rebuild_in_place=True refine_eff_file=refinement_params.eff<br>
<br>
Why you think it doesn't work correctly from within phenix.autobuild
?<br>
<br>
Pavel.<br>
<br>
<br>
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