Tutorial

tutorials

Installation

Get the academic license for Rosetta at https://els.comotion.uw.edu/express_license_technologies/rosetta
Immediately, you will get the download link from Rosetta Commons by email.
Download and compile Rosetta.
- Download
- cs-Rosetta install toturial
  - Unpack
```
tar -xzf *.tgz
```
  - Install openmpi
```
sudo apt-get install openmpi libopenmpi-dev 
```
    Error! If you get an error like
    
    /usr/bin/ld: cannot find -lz
    
    SCons may be looking for 32 bit libraries on a 64 bit machine. Look up how to install the missing dependency; in this case
    
    sudo apt-get install lib32z1-dev
  - Compile
```
cd rosetta_src_2017.08.59291_bundle/main/source
ls bin
```
    If not compiled, bin dir should be empty
```
$nohup ./scons.py -j 4 mode=release bin extras=mpi &
```
    Building Rosetta,it might take hours
    
    Tips! you might come across many mistakes, if you don't know how to handle ,the page following may helps Help Documentation

Download
Unpack
```
tar -xvzf csrosetta_toolbox_ver3.3.tgz
```

Installation

The installation script is in the top-level toolbox directory and has to be run at least once for each installation.The installation script will perform several tasks:

	>>generate init script: csrosetta3/com/init 
	>>integrate ROSETTA 
	>>integrate existing TALOS+ or download from http://spin.niddk.nih.gov/NMRPipe 
	>>download chemical shift VALL from www.csrosetta.org 
	>>download BLAST executable from ftp.ncbi.nlm.nih.gov/blast/ 
	>>download genome/nr database from ftp.ncbi.nlm.nih.gov/blast/

The script is able to resume broken downloads and can also be rerun at a later time to check for any updates.

cd csrosetta3
nohup python install.py &

Error!:cannot find rosetta binaries and rosetta database We can specify the rosetta and rosetta databse with

./install.py -rosetta ***/rosetta/main/source/bin/ -rosetta_database ***/rosetta/main/database/

Update profile

#add the following into ~/.cshrc or ~/.bashrc
        #loading CS-Rosetta toolbox
        source $HOME/csrosetta3/com/init

Test

pick_fragments -cs tutorials/inputs/SgR145.tab

“Error!: Can't identify secondary structure file type (needs vertical psipred_ss2 or talos+ pred.ss):[target_name].fasta.talos/predSS.tab”

proceed as follows:

  1) Open the predSS.tab file that has been created in the folder [target_name].fasta.talos/predSS.tab
  2) Insert a line at the very top that says "REMARK TALOS-N"
  3) Resubmit your pick_fragments command on the command line. The fragment picker will pick up where it left off.</WRAP>