This depo describes the steps to download RASP [1], from the website: http://melolab.org/webrasp/download.php.
It builds a Dockerfile over the code to be run easily.
To run the RASP algorithm using docker, you can use :
make docker_start
that build and run the container.
You can also build it by hand:
docker build -t rasp .
And then run it:
docker run -it rasp <ARGS>
and then replace the <ARGS> by the arguments needed.
For building the package, run in your CLI:
make
If you want to optimize the final programme run:
make CFLAG=<optimization flag>
where could be: "-O", "-O2", "-O3". For example:
"CFLAG=-O3".
For re-building, do:
make clean
make
All executables will be created in a local subfolder named "bin".
Before executing the software for the first time, please read the section below.
Before executing for the first time, you should set the environment variable "RASP":
export RASP=/path/to/the/rasp-fd/folder (in bash or ksh)
setenv RASP /path/to/the/rasp-fd/folder (in csh or tcsh)
Set this variable in your shell configuration file, commonly a hidden file with the end "rc" located in your home folder (e.g: ".tcshrc"). After that do not forget to either launch a new terminal or to run:
source ~/.tcshrc (in case your file is ".tcshrc").
If this configuration file does not exist, you must create it. If you do not know how to do this, please ask your system administrator.
Execute the software without any parameters and their mode of usage will be displayed in the screen.
In order to test the building of the package, enter the folder "example" and run the following instructions:
../bin/rasp_fd -e all -p 1a9n.pdb
You should get on screen the results saved in the file "output_all.txt".
../bin/rasp_fd -e bbr -p 1a9n.pdb
You should get on screen the results saved in the file "output_bbr.txt". Note that the three last values may be different since there is a randomization process.
../bin/rasp_profile_fd -e all -r -p 1a9n.pdb
You should get on screen the results saved in the file "profile_all.txt". A file called "profile.scr" will also be created.
Run "rasmol" as follows so as to visualize the structure and the energies for each residue.
rasmol -script profile.scr 1a9n.pdb
For questions, please write to:
Tomas Norambuena A. tanoramb@puc.cl Molecular Bioinformatics Laboratory Pontificia Universidad Catolica de Chile
[1] Miao, Z., & Westhof, E. (2017). RNA Structure: Advances and Assessment of 3D Structure Prediction. Annual Review of Biophysics, 46(1), 483–503. https://doi.org/10.1146/annurev-biophys-070816-034125