when I do threading target sequence, and run the following command:
> $ROSETTA3/bin/partial_thread.default.linuxgccrelease -in:file:fasta 2_threading/1u19.fasta -in:file:alignment 1u19_2rh1.grishin -in:file:template_pdb 2rh1.pdb
I got the following result:
-bash: /bin/partial_thread.default.linuxgccrelease: No such file or directory
do I miss something?
It looks to me that the environment variable ROSETTA3 is not defined and pointing to your Rosetta installation. Try "echo $ROSETTA3" and I'd wager it returns a blank. Then, you can either set ROSETTA3 or just map directly to the location of the executable, which is what I usually do. The other item to check is that the os and compiler match with your build, e.g. linuxgccrelease or macosclangrelease. The easiest way to find this is information is to list the directory contents of the bin directory. You'll still want to use the executable that has ".default" in the name unless you want to use one of the "extras" like mpi.
Hope that helps
Thanks very much for your response.
You are right. I tried "echo $ROSETTA3" and it returned a blank.
"you can either set ROSETTA3 or just map directly to the location of the executable...". Could you give a bit details of commands I need to try?
Also "The other item to check is that the os and compiler match with your build...". Could you give a bit details?
I actually have the similar problem when I run RosettaCM hybridize:
-bash: /bin/rosetta_scripts.default.linuxgccrelease: No such file or directory
Thanks again so much!! I just started Rosetta and a lot to learn.
You'll first need to determine where Rosetta is installed on your system so you have the full path to the bin directory. Did you download pre-built binaries from the website? Then maybe Rosetta is in your Downloads folder still. Of if you've moved it, to where has it been relocated. If you're using an install on a shared system you might contact your system administrator to identify the install directory.
Once you have the full path to Rosetta (for example, /user/user_name/Rosetta), the bin directory will be in main/source. So, the full path to the executable is /user/user_name/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease. Remember that you need to match the suffix to your particular operating system and compiler. What operating system are you using?
With respect to environment variables, I personally find them to be ... not so useful. (I always forget to reset them or forget that I set them previously and now I have weird errors.) And, the commands for setting these are also different depending on your operating system (Mac or Linux). There are great tutorials for setting environment variables online, so I recommend googling for 'environment variables linux' or 'environment variables mac'. Or, you can skip the environment variable and just type the whole path, which is what I do -- with tab-complete it's really not that bad.
Thank you so much!!
The installation might have something wrong and I couldn't find bin folder anywhere, so I re-install the Rosetta and it is working well now.
Again thanks so much!