[phenixbb] Rosetta refinement and MR_Rosetta
Terwilliger, Thomas Charles
terwilliger at lanl.gov
Sun Jan 4 05:45:31 PST 2015
I notice that the Phenix web site I pointed you to at
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:
2. Then set your shell variables. The command depends on whether you are using csh or
For sh or bash shells you say:
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
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,
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
Thank you for your reply.
When I execute the command line,
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>
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?
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:
> You can see the full instructions for this at:
> 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,
> 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
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