Problem with running turtorial of rna denovo

It looks like you’re using the executables from Rosetta 3.5  There’s been a *lot* of improvements to the RNA code since Rosetta 3.5 was released 4 years ago, so I’d highly recommend updating to a more recent version, if possible.

While you’re using the executables from Rosetta 3.5, it looks like your database (specified with the ROSETTA3_DB environment variable) is *not* for Rosetta 3.5. The version mismatch issue is also probably why you’re having troubles – different versions have slightly different layouts and contents in the database directory. You should always use the version of the database which comes with the version of the code you’re using.

Most recent versions of Rosetta can autodetermine the location of the database if you don’t move the binaries and database from where they are in the download hierarchy. As such, you can forgo passing the -database option, or setting the ROSETTA3_DB environment variable, and not have to worry about database version mismatches.  — The one trick is that Rosetta will obey the ROSETTA3_DB environment variable if set, so you might have to delete/disable that, if it’s pointing to the wrong version (this looks like it’s the case for you).

It looks like you’re using the executables from Rosetta 3.5  There’s been a *lot* of improvements to the RNA code since Rosetta 3.5 was released 4 years ago, so I’d highly recommend updating to a more recent version, if possible.

While you’re using the executables from Rosetta 3.5, it looks like your database (specified with the ROSETTA3_DB environment variable) is *not* for Rosetta 3.5. The version mismatch issue is also probably why you’re having troubles – different versions have slightly different layouts and contents in the database directory. You should always use the version of the database which comes with the version of the code you’re using.

Most recent versions of Rosetta can autodetermine the location of the database if you don’t move the binaries and database from where they are in the download hierarchy. As such, you can forgo passing the -database option, or setting the ROSETTA3_DB environment variable, and not have to worry about database version mismatches.  — The one trick is that Rosetta will obey the ROSETTA3_DB environment variable if set, so you might have to delete/disable that, if it’s pointing to the wrong version (this looks like it’s the case for you).

It looks like you’re using the executables from Rosetta 3.5  There’s been a *lot* of improvements to the RNA code since Rosetta 3.5 was released 4 years ago, so I’d highly recommend updating to a more recent version, if possible.

While you’re using the executables from Rosetta 3.5, it looks like your database (specified with the ROSETTA3_DB environment variable) is *not* for Rosetta 3.5. The version mismatch issue is also probably why you’re having troubles – different versions have slightly different layouts and contents in the database directory. You should always use the version of the database which comes with the version of the code you’re using.

Most recent versions of Rosetta can autodetermine the location of the database if you don’t move the binaries and database from where they are in the download hierarchy. As such, you can forgo passing the -database option, or setting the ROSETTA3_DB environment variable, and not have to worry about database version mismatches.  — The one trick is that Rosetta will obey the ROSETTA3_DB environment variable if set, so you might have to delete/disable that, if it’s pointing to the wrong version (this looks like it’s the case for you).

Note that if IT is being slow or hesitant about it, you don’t *need* to get them to install things centrally.  Rosetta is set up such that you should be able to download and compile it in a user directory, without any sort of administrator privileges. (Well, aside from any privileges needed to compile C++ programs, which most users should be able to do on most Unix-like computer systems, assuming a usable compiler is installed.) So you should be able to install whatever version of Rosetta you like to your home directory, and then run it from there.

Note that if IT is being slow or hesitant about it, you don’t *need* to get them to install things centrally.  Rosetta is set up such that you should be able to download and compile it in a user directory, without any sort of administrator privileges. (Well, aside from any privileges needed to compile C++ programs, which most users should be able to do on most Unix-like computer systems, assuming a usable compiler is installed.) So you should be able to install whatever version of Rosetta you like to your home directory, and then run it from there.

Note that if IT is being slow or hesitant about it, you don’t *need* to get them to install things centrally.  Rosetta is set up such that you should be able to download and compile it in a user directory, without any sort of administrator privileges. (Well, aside from any privileges needed to compile C++ programs, which most users should be able to do on most Unix-like computer systems, assuming a usable compiler is installed.) So you should be able to install whatever version of Rosetta you like to your home directory, and then run it from there.