Re: [phenixbb] Rosetta refinement and MR_Rosetta

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" 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#ins...

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 [[email protected]] Sent: Saturday, January 03, 2015 9:17 PM To: Terwilliger, Thomas Charles Cc: miyatake; [email protected] 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" 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#ins...

Let me know if that doesn't do it! All the best, Tom T

________________________________________ From: [email protected] [[email protected]] on behalf of miyatake [[email protected]] Sent: Saturday, January 03, 2015 7:34 AM To: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb