[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.

1:
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
*"run_prerefine=True
\  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*.

2:
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
chen


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


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