Dear all:<br><br>I&#39;ve collected a data set for my crystal, which is a two-protein complex. However, normal molecular replacement method gives no solution and thus didn&#39;t work. Right now I&#39;m struglling with the phenix.mr_rosetta method. However, I&#39;ve got several problems when reviewing it, and thus looking forward to get some advice here.<br>
<br>1: <br>There are such words <b>&quot;<span style lang="EN-US">NOTE 2: If your structure contains more than one chain or requires more
than one homology model to represent the structure, then you need to use
mr_model_preparation and phenix.automr to place your model. Then you can start
phenix.mr_rosetta with already_placed=True</span></b><b>&quot;</b>  in phenix documentation page. My understanding for this sentences is: the solution derived from <b>automr</b> is treated as an original searching model for phenix.mr_rosetta, in which case,  we should add the command line <b>&quot;<span lang="EN-US">run_prerefine=True \</span><span style lang="EN-US"><span style>  </span>number_of_prerefine_models=1000</span>&quot;</b>. However, what is <b>mr_model_preparation</b> for? And if no solution is given by <b>automr</b>, what should I do? What&#39;s more important, why not endow the phenix.mr_rosetta program to be capable of dealing with data set from multi-chain protein complexes? Since I thought the idea of preliminary manipulation by the program <b>automr</b> would decrease the power of <b>phenix.mr_rosetta</b>. <br>
<br>2:<br>Two .hhr files are produced. But as displayed in the phenix.mr_rosetta documentation page, only one .hhr file like <b>&quot;hhr_files=bfr258e.hhr&quot;</b> are listed in the command line. Why? <br><br>Could somebody give me any advice on this, please?<br>
<br>Thank you and best regards<br>chen<br><br><br>-- <br>Cheng Chen, Ph.D. Candidate<br>Laboratory of Structural Biology<br>Life Science Building,Tsinghua University<br>Beijing 100084<br>China<br><br><br>-<br>