Phenix: Difference between revisions

268 bytes removed ,  22 May 2017
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[http://www.phenix-online.org/documentation/reference/rosetta_refine.html phenix.rosetta_refine] (and [http://www.phenix-online.org/documentation/reference/mr_rosetta.html phenix.mr_rosetta]) requires a working Rosetta installation. The easiest way is to download one of the weekly binary+source Rosetta bundles (to be found following this [https://www.rosettacommons.org/software/license-and-download link]). The tar-file only has to be unpacked; binaries and libraries are pre-compiled. Your .bashrc has to be modified to have e.g.
[http://www.phenix-online.org/documentation/reference/rosetta_refine.html phenix.rosetta_refine] (and [http://www.phenix-online.org/documentation/reference/mr_rosetta.html phenix.mr_rosetta]) requires a working Rosetta installation. The easiest way is to download one of the weekly binary+source Rosetta bundles (to be found following this [https://www.rosettacommons.org/software/license-and-download link]). The tar-file only has to be unpacked; binaries and libraries are pre-compiled. Your .bashrc has to be modified to have e.g.
  export PHENIX_ROSETTA_PATH=/usr/local/src/rosetta_bin_linux_2015.09.57646_bundle
  export PHENIX_ROSETTA_PATH=/usr/local/src/rosetta_src_2017.08.59291_bundle
export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database
(or similarly for .cshrc) and
(or similarly for .cshrc) and
  rosetta.build_phenix_interface
  rosetta.build_phenix_interface
needs to be run. (For MR_rosetta, installation is described at [http://www.phenix-online.org/documentation/reference/mr_rosetta.html#id17].)
needs to be run; the latter step takes hours.


If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation:
If this fails (for example, compiler error messages), then one must re-compile Phenix and/or Rosetta. Try to re-compile only Phenix first (and after that, try rosetta.build_phenix_interface again); Rosetta re-compilation may take hours. There are several issues associated with re-compilation:
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* to re-compile Rosetta: go to the main/source directory and issue:  
* to re-compile Rosetta: go to the main/source directory and issue:  
  ./scons.py -j8 mode=release bin
  ./scons.py -j8 mode=release bin
(The -j8 should be used if your machine has 8 or more cores.) I was able to re-compile Rosetta on CentOS7 whereas re-compilation stopped with an error on Ubuntu 12.04.5 LTS.
(The -j8 should be used if your machine has 8 or more cores.)


== See also ==
== See also ==
1,330

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