[phenixbb] Rosetta refinement and MR_Rosetta
Terwilliger, Thomas Charles
terwilliger at lanl.gov
Mon Jan 5 05:49:46 PST 2015
Hi Miyatake,
I think we are getting close. That error message means the directory (exactly as typed on the terminal) does not exist or could not be found somehow.
What do you get if you type:
ls /Applications/rosetta_2014.35.57232_bundle
If you get a directory listing, can you do this:
echo $PHENIX_ROSETTA_PATH
ls $PHENIX_ROSETTA_PATH
Does that give you a directory listing? If yes, then try:
rosetta.build_phenix_interface
again. If that fails, try:
rosetta.build_phenix_interface rosetta_path=$PHENIX_ROSETTA_PATH
If that still fails, then can you type:
env
and then can you send me the terminal output for all of this?
Thanks!
-Tom T
________________________________________
From: miyatake [miyatake at riken.jp]
Sent: Monday, January 05, 2015 12:21 AM
To: Terwilliger, Thomas Charles
Cc: miyatake; phenixbb at phenix-online.org; irees at lbl.gov; Paul Adams
Subject: 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" <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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