[phenixbb] two problems about phenix.mr_rosetta

chen c chench06 at gmail.com
Wed Aug 8 01:50:39 PDT 2012

Dear all:

I'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't work. Right now I'm struglling with the phenix.mr_rosetta method.
However, I've got several problems when reviewing it, and thus looking
forward to get some advice here.

There are such words *"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**"* in phenix documentation page. My understanding
for this sentences is: the
solution derived from *automr* is treated as an original searching model
for phenix.mr_rosetta, in which case,  we should add the command line
\  number_of_prerefine_models=1000"*. However, what is *mr_model_preparation
* for? And if no solution is given by *automr*, what should I do? What'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 *automr* would
decrease the power of *phenix.mr_rosetta*.

Two .hhr files are produced. But as displayed in the phenix.mr_rosetta
documentation page, only one .hhr file like *"hhr_files=bfr258e.hhr"* are
listed in the command line. Why?

Could somebody give me any advice on this, please?

Thank you and best regards

Cheng Chen, Ph.D. Candidate
Laboratory of Structural Biology
Life Science Building,Tsinghua University
Beijing 100084

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