Hello Rosetta users,
I have a few questions with respect to antibody modelling in Rosetta.
The current version of Rosetta I'm using is a pre-compiled version 3.13 of Linux. I always get an error when I perform the first step of Antibody Modeling:
antibody.static.linuxgccrelease \ -fasta antibody_chains.fasta
I checked and found that the solution to this problem was to install a higher version of GCC.
But after I installed a higher version of GCC=11.2.0, this error persisted no matter how much I changed my environment variables.
And I see in the "ROSETTA_CRASH.log" file:
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-39)"
This means that my Compiler has never been successfully changed.
I would like to ask how can I change the compiler called by the Rosetta? Is there a config file to control the compiler version?
Scons throws away all the enviorment varibles by default.
You can edit `main/source/tools/build/site.settings` to add overides. If this file does not exist, type cp tools/build/user.settings.template tools/build/user.settings, then proceed to edit it.
or you can also import your enviorment
– Uncomment (i.e. remove the pound sign from) the import os line.
– Uncomment the program_path“ : os.environ[“PATH”].split(”:“), line.
– Uncomment the “ENV” : os.environ, line.
If the line “ENV” : os.environ, does not exist, add it to the “overrides” section:
More info here: https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation
Thank you so much for your help, Ajasja
I solved the problem in a different way.
I used a pre-compiled version of Rosetta when the C++ version problem occurred.
I downloaded the source code, compiled and installed it using a higher version of c++ (8.1.3), and the problem disappeared, even though the c++ version in my current environment is 4.8.5.
So, I think Rosetta may have built some C++ code into it when it was compiled, and it may execute independently of the C++ version in the environment.
Based on this information, I suspect that the pre-compiled version of "Rosetta 3.13 source + binaries for Linux" on the website may be problematic, at least for this step of antibody homology modeling not working properly.