Dear all, I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit. However phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log& fails with the following error in log: End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it. To me it seems things are defined correctly: andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@ andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease Any idea of what's wrong would be greatly appreciated. Andreas -- Andreas Förster X-ray Crystallography Facility Manager Centre for Structural Biology Imperial College London
On Wed, Nov 26, 2014 at 8:18 AM, Andreas Förster
I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit.
First bit of advice: don't use Rosetta 3.5, Frank has fixed a bunch of bugs since then. You'll need one of the recent weekly releases.
However
phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log&
fails with the following error in log:
End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it.
This was a poorly written error message - that environment variable doesn't actually have the desired effect here. (It's fixed in the current code but we're overdue for a new nightly build.) The correct approach is to set the variable PHENIX_ROSETTA_PATH, which will point to the top level of the Rosetta distribution - in their newer directory layout this will have a sub-directory named "main", so if you don't see that, you're in the wrong place. -Nat
I got the same errors running rosetta in Phneix. It took me lots of time to make it run. I had to change the version of Phénix. I hope it helped. Ivan On 2014-11-26 17:18, Andreas Förster wrote:
Dear all,
I'm trying to get phenix.rosetta_refine to run. I think it's all set up properly, with Rosetta 3.5 and Phenix 1810 on RHEL 6.3 64bit.
However
phenix.rosetta_refine model.pdb data.mtz nproc=48 protocol=full > log&
fails with the following error in log:
End of input processing Sorry: The RosettaScripts executable could not be located. Please add the appropriate directory to your PATH environment variable, or set the variable ROSETTA_BIN to point to it.
To me it seems things are defined correctly:
andreas@csbstereo in phenix: echo $ROSETTA_BIN /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin
andreas@csbstereo in phenix: ls $ROSETTA_BIN | grep scripts rosetta_scripts.linuxgccrelease@ rosetta_scripts.default.linuxgccrelease@
andreas@csbstereo in phenix: ll $ROSETTA_BIN/rosetta_scripts.linuxgccrelease lrwxrwxrwx 1 csbadmin csb 93 Oct 9 2013 /csb/soft/Linux64/share/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -> ../build/src/release/linux/2.6/64/x86/gcc/4.4/default/rosetta_scripts.default.linuxgccrelease
Any idea of what's wrong would be greatly appreciated.
Andreas
participants (3)
-
Andreas Förster -
Ivan IVANOV -
Nathaniel Echols