[[https://csrosetta.chemistry.ucsc.edu | CS rosetta Home]] 
====== Tutorial ======
  *[[https://csrosetta.chemistry.ucsc.edu/node/1242 |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. 
    *[[https://www.rosettacommons.org/docs/latest/Home |Download]]
    *[[https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build |cs-Rosetta install toturial]]
        *Unpack<code>tar -xzf *.tgz</code>
        *Install openmpi<code>sudo apt-get install openmpi libopenmpi-dev </code><WRAP center round tip>
**<fc #ff0000>Error!</fc>**
If you get an error like 
<code>/usr/bin/ld: cannot find -lz</code>
SCons may be looking for 32 bit libraries on a 64 bit machine. Look up how to install the missing dependency; in this case<code>sudo apt-get install lib32z1-dev</code></WRAP> 
        *Compile<code>cd rosetta_src_2017.08.59291_bundle/main/source
ls bin</code>If not compiled, bin dir should be empty<code>$nohup ./scons.py -j 4 mode=release bin extras=mpi &</code>Building Rosetta,it might take hours<WRAP center round tip>
**<fc #ff0000>Tips!</fc>**
you might come across many mistakes, if you don't know how to handle ,the page following may helps
[[https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation|Help Documentation]]
</WRAP>	
  *Download and compile [[https://csrosetta.chemistry.ucsc.edu/downloads/toolbox| CS-Rosetta Toolbox]]
        *Download
        *Unpack<code>tar -xvzf csrosetta_toolbox_ver3.3.tgz</code>
        *Installation<WRAP center round tip>
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.
</WRAP><code>cd csrosetta3
nohup python install.py &</code><WRAP center round tip>
**<fc #ff0000>Error!</fc>**:cannot find rosetta binaries and rosetta database
We can specify the rosetta and rosetta databse with <code>./install.py -rosetta ***/rosetta/main/source/bin/ -rosetta_database ***/rosetta/main/database/</code></WRAP>
        *Update profile<code>#add the following into ~/.cshrc or ~/.bashrc
        #loading CS-Rosetta toolbox
        source $HOME/csrosetta3/com/init</code>
        *Test<code>pick_fragments -cs tutorials/inputs/SgR145.tab</code><WRAP center round tip>	
        "**<fc #ff0000>Error!</fc>**: 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>