[phenixbb] Set up phenix and rosetta for phenix.rosetta_refine

Nigel Moriarty nwmoriarty at lbl.gov
Thu Mar 17 15:31:57 PDT 2016


I forgot to mention that the documentation for each nightly is available
via a link on the download page.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Mar 17, 2016 at 3:15 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Youglin
>
> I'm a little confused about what is going wrong here. However, I should
> point out that the requirement for two Rosetta installs has changed. The
> documentation on the website is for the major release 1.10.1. You can check
> the documentation for the nightly you are using by typing
>
> phenix.doc
>
> Look for the updated Rosetta install docs. Unfortunately,  you will have
> to get dev-2341 for this feature.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>
> On Tue, Mar 15, 2016 at 10:41 PM, Yonglin Hu <yonglinhu at gmail.com> wrote:
>
>> Hello List,
>>
>> I would like to perform phenix.rosetta_refine on a structure.  I
>> understand that to use this program, I need to set up phenix and rosetta
>> installations separated from those used in MR_Rosetta. I installed the most
>> recent phenix and rosetta and followed the online documents, but when I
>> tried to run "rosetta.build_phenix_interface", the program failed
>> immediately with the following error messages:
>>
>> False
>> scons: Reading SConscript files ...
>> Running versioning script ... fatal: Not a git repository (or any of the
>> parent directories): .git
>> Done. (0.0 seconds)
>> Could not find platform independent libraries <prefix>
>> Could not find platform dependent libraries <exec_prefix>
>> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
>> ImportError: No module named site
>> CalledProcessError: Command '['./update_options.sh']' returned non-zero
>> exit status 1:
>>   File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line
>> 172:
>>     main()
>>   File "/usr/local/rosetta-refine/rosetta/main/source/SConstruct", line
>> 163:
>>     SConscript("SConscript", "build")
>>   File
>> "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py",
>> line 614:
>>     return method(*args, **kw)
>>   File
>> "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py",
>> line 551:
>>     return _SConscript(self.fs, *files, **subst_kw)
>>   File
>> "/usr/local/rosetta-refine/rosetta/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py",
>> line 260:
>>     exec _file_ in call_stack[-1].globals
>>   File "/usr/local/rosetta-refine/rosetta/main/source/SConscript", line
>> 28:
>>     subprocess.check_call(["./update_options.sh"])
>>   File
>> "/usr/local/rosetta-refine/phenix-dev-2328/base/lib/python2.7/subprocess.py",
>> line 540:
>>     raise CalledProcessError(retcode, cmd)
>>
>> These messages are not very informative and I don't know what to do next.
>>
>> Any help will be greatly appreciated.
>>
>> Yonglin Hu
>> _______________________________________________
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>>
>
>
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