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Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations

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Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations


I installed rosetta_bin_linux_2021.07.61567 mode=debug and then ran Rosetta CM Hybridization. However, it gives the error messages as 'Could not open file /Rosetta/rosetta_bin_linux_2020.08.61146_bundle/main/database/citations/rosetta_citations'. I have deleted everthing with 'rosetta_bin_linux_2020.08.61146_bundle'. I do see this rosetta_citations file in my current 'rosetta_bin_linux_2021.07.61567_bundle/database/citation path. May I know why it looks for the citations file in my earlier old version? How to fix it?



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Wed, 2022-06-15 11:26

Rosetta finds the database location in several ways.

The first (and prefered) method is an autodetection one. Based on the installation directory, it will find the corresponding database directory and use that.

The second is the -database command line option. If you specify that, Rosetta will use that directory for the database.

The third is an environment variable. If you set ROSETTA3_DB, Rosetta can use the path set there to figure out where the database is.

The priorities of these three methods is to preferentially use the command line option. If the command line option isn't specified, it uses the environment variable. If neither the command line option or the environment variable are set, use the autodetection method.


My guess is that you have the ROSETTA3_DB environment variable set, and it's pointing to an older version of Rosetta. (You can check this by running `env | grep ROSETTA`) This only really works well if you have a single Rosetta version installed. Even then, it's only necessary if you're reorganizing the Rosetta directory. If you're running Rosetta out of the download directory, my suggestion is to remove the command which sets the ROSETTA3_DB environment variable (e..g in your bashrc/profile/etc. files)

If you can't see where the ROSETTA3_DB variable is being set, then my suggestion would be to explicitly specify the database path using the `-database` command line option.

Wed, 2022-06-15 11:40

Just Figured it out! Thank you.

Wed, 2022-06-15 13:46