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ValueError("Path %s does not exist!" % path_name) for

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ValueError("Path %s does not exist!" % path_name) for

Hi everyone,

I want to model helices with but I get an error that rna_helix.linuxgccrelease isn't in the path where python script is looking for it:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/", line 27, in <module>

cmdline = rosetta_exe('rna_helix', rosetta_folder=args.rosetta_folder, extension=args.extension)

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/", line 35, in rosetta_exe


File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/", line 55, in check_path_exist

raise ValueError("Path %s does not exist!" % path_name)

ValueError: Path /home/software/rosetta_bin_linux_2021.16.61629_bundle/main/rna_helix.macosclangrelease


This ValueError regarding a MacOS version is due to the following line from but also appears for the Linux Version by deleting the MacOS extensions:

name_extensions = ['', ".linuxgccrelease", ".linuxclangrelease", ".macosgccrelease", ".macosclangrelease"]


I found that rna_helix.linuxgccrelease is located in Path /home/software/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin 

when it should be in /home/software/rosetta_bin_linux_2021.16.61629_bundle/main


By using rna_helix.linuxgccrelease instead of in bash it works and models a helix.

By running python in bash I get:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/", line 22, in <module>


PermissionError: [Errno 13] Permission denied: './bin/'

Feels like there's a problem with pathes in python script and/or in the symbolic links in


Hopefully I was able to explain everything traceably and you can shed some light on this situation. Big thanks in advance!


Kind regards


Post Situation: 
Wed, 2023-08-16 00:39

You should be able to specify the path to Rosetta with the -rosetta_folder option of -- Note that this is the path without the main folder present. (So /home/software/rosetta_bin_linux_2021.16.61629_bundle/ in your case.) Alternatively, this can also be the full bin path. (/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin)

If you don't give the -rosetta_folder option, it will try to use the $ROSETTA environment variable as if you had passed it to -rosetta_folder. Failing that, it will try to look for the Rosetta executables in your executable path.

You don't specify the full command line you used with, but I'm suspecting you used the -rosetta_folder option with the "main" designated. If so, try reruning without the "main" component in the path.


Wed, 2023-08-16 08:23

Thank you for your response!

You were absolutely right. By adding the -rosetta_folder tag with /home/software/rosetta_bin_linux_2021.16.61629_bundle/ as well as /home/software/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin it works out. Also by deleting "main" in .bashrc

But I am wondering if there will be trouble with the RNA_TOOLS path. Shoudn't it be like this now:

export RNA_TOOLS=$ROSETTA/main/tools/rna_tools

I tried this and also the original version RNA_TOOLS=$ROSETTA/tools/rna_tools  and no path errors were occuring for both... ?





Wed, 2023-09-13 02:16