Hi,<br>I am trying to use phenix.mr_rosetta supplying a local.hhr file and using only the top alignment which is an NMR structure and the pre_refine option. It finishes the mr.model_preparation and writes out two pdbs  ( _sculpt and _chain that each have 10 ensembles) but then writes out a empty alignment.ali file (should be 100% identity between the template and the search model). Below is the error I get in the RUN_1.log file. <br>
<br>Wrote dummy alignment to /pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali<br><br>******************* ERROR ENDING ***************<br><br>Sorry, the alignment file [&#39;/pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali&#39;] <br>
does not have enough lines (6 required, 0 found):<br><br><br>Note: last line needs to be &#39;--&#39;<br><br><br>******************* ERROR ENDING ***************<br><br>Sorry, the alignment file [&#39;../pre_refine/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/alignment.ali&#39;] <br>
does not have enough lines (6 required, 0 found):<br><br>Note: last line needs to be &#39;--&#39;<br><br>Thanks,<br>JJ<br><br><div style="padding: 0px; overflow: hidden; visibility: hidden; left: -5000px; position: absolute; z-index: 9999; margin-left: 0px; margin-top: 0px; word-wrap: break-word; color: black; font-size: 10px; text-align: left; line-height: 130%;" id="avg_ls_inline_popup">
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