[phenixbb] Rosetta refinement and MR_Rosetta

miyatake miyatake at riken.jp
Sun Jan 4 23:21:41 PST 2015


Dear Tom,

Thank you so much for your help.

However, I still see the error message below:



[HM-MacBook-Pro:/Applications/ccp4-6.5] miyatake% rosetta.build_phenix_interface
Traceback (most recent call last):
  File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
    run(sys.argv[1:])
  File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 51, in run
    raise RuntimeError("Rosetta path invalid:\n%s" % rosetta_path)
RuntimeError: Rosetta path invalid:
/Applications/rosetta_2014.35.57232_bundle
[HM-MacBook-Pro:/Applications/ccp4-6.5] miyatake% rosetta.build_phenix_interface
Traceback (most recent call last):
  File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
    run(sys.argv[1:])
  File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 51, in run
    raise RuntimeError("Rosetta path invalid:\n%s" % rosetta_path)
RuntimeError: Rosetta path invalid:
/Applications/rosetta_2014.35.57232_bundle
[HM-MacBook-Pro:/Applications/ccp4-6.5] miyatake% rosetta.build_phenix_interface nproc=8
Traceback (most recent call last):
  File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
    run(sys.argv[1:])
  File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 51, in run
    raise RuntimeError("Rosetta path invalid:\n%s" % rosetta_path)
RuntimeError: Rosetta path invalid:
/Applications/rosetta_2014.35.57232_bundle















On Sun, 4 Jan 2015 13:45:31 +0000
"Terwilliger, Thomas Charles" <terwilliger at lanl.gov> wrote:

> Hi Miyatake,
> 
> I notice that the Phenix web site I pointed you to at 
> 
>    http://www.phenix-online.org/documentation/reference/rosetta_refine.html#installation
> 
> has a typo and says setenv PHENOX_ROSETTA_PATH; perhaps that was what the problem was!  We have fixed the typo for future releases.
> 
> So in case that wasn't the problem, here is how to set the shell variable PHENIX_ROSETTA_PATH:
> 
> 1. Notice the location of your Rosetta installation.  For example it might be at:
> 
>   /usr/local/rosetta_2014.16.56682_bundle
> 
> 2.  Then set your shell variables.  The command depends on whether you are using csh or 
> 
> For sh or bash shells you say:
>  
> export PHENIX_ROSETTA_PATH=/usr/local/rosetta_2014.16.56682_bundle
> export ROSETTA3_DB=/usr/local/rosetta_2014.16.56682_bundle/main/database
> 
> or for csh/tcsh shells:
> 
> setenv PHENIX_ROSETTA_PATH "/usr/local/rosetta_2014.16.56682_bundle"
> setenv ROSETTA3_DB "/usr/local/rosetta_2014.16.56682_bundle/main/database"
> 
> You can check that it worked by saying
> 
>   echo $PHENIX_ROSETTA_PATH
>   echo $ROSETTA3_DB
> 
> and you should get back the paths that you defined. Then your rosetta.build_phenix_interface command should work.
> 
> Let me know if that doesn't do it!
> All the best,
> Tom T
> 
> ________________________________________
> From: miyatake [miyatake at riken.jp]
> Sent: Saturday, January 03, 2015 9:17 PM
> To: Terwilliger, Thomas Charles
> Cc: miyatake; phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Rosetta refinement and MR_Rosetta
> 
> Dear Tom,
> 
> Thank you for your reply.
> 
> When I execute the command line,
> 
>    rosetta.build_phenix_interface nproc=8
> 
> I see the error message below;
> 
> 
> Traceback (most recent call last):
>   File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 106, in <module>
>     run(sys.argv[1:])
>   File "/Applications/Phenix-dev-1894/Contents/phenix-dev-1894/build/../modules/phenix/phenix/command_line/rosetta_build_phenix_interface.py", line 49, in run
>     or set environment variable PHENIX_ROSETTA_PATH.""")
> RuntimeError: Path to Rosetta not found.  Please specify rosetta_path=PATH on command line,
> or set environment variable PHENIX_ROSETTA_PATH.
> 
> 
> 
> 
> Why did it happen?
> 
> Best regards,
> 
>     H. Miyatake
> 
> 
> 
> 
> 
> On Sat, 3 Jan 2015 17:29:58 +0000
> "Terwilliger, Thomas Charles" <terwilliger at lanl.gov> wrote:
> 
> > Hi Miyatake,
> >
> > Can you possibly make sure that you have 2 installations of Rosetta, one for mr_rosetta and one separately configured for rosetta_refine...The second one you set up with:
> >
> >   rosetta.build_phenix_interface
> >
> > You can see the full instructions for this at:
> >
> >     http://www.phenix-online.org/documentation/reference/rosetta_refine.html#installation
> >
> > Let me know if that doesn't do it!
> > All the best,
> > Tom T
> >
> > ________________________________________
> > From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of miyatake [miyatake at riken.jp]
> > Sent: Saturday, January 03, 2015 7:34 AM
> > To: phenixbb at phenix-online.org
> > Subject: [phenixbb] Rosetta refinement and MR_Rosetta
> >
> > Dear Phenix users,
> >
> > Hello,
> >
> > I run MR_Rosetta without any problems.
> >
> > When I run, however, Rosetta refinement, it stopped with
> > a message "can't find rosetta_bin".
> >
> > Why did it happen?
> >
> >     H. Miyatake
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> 



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