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Revision as of 17:38, 20 October 2020
Rosetta Guide
#Assuming you downloaded the Rosetta Source Code to the directory “Software” on your c drive on a linux subsystem for windows this would be your way of unpacking: >cd /mnt/c/Software >tar -xvzf rosetta[releasenumber].tar.gz >cd rosetta[releasenumber]/main/source #[releasenumber] can be simply replaced by the Rosetta version you downloadedWe recommend gcc as a compiler because it provides goof performance and can easily installed using apt-get. After you installed gcc you can continue to the main Rosetta installation.
#sudo gives superuser allowance, that is needed to install the program. You also need to enter your password before the installation begins. >sudo apt-get gccRosetta provides you a python script that is able to locate your installed compiler and automatically compile the program afterwards. Use the following command to change your current directory to the source folder of Rosetta.
#The -j flags defines the number of cores Rosetta can use to compile the source code. The more cores you pick the shorter the installation will take. Take in mind that a installation of Rosetta will take really long, if you are compiling on a single core it can take longer than 24h. > ./scons.py -jAfter the installation is finished the bin directory should be added to your source folder. You can check if the installation was successful by running one of Rosetta’s multiple in the bin folder. This is done by simply writing the name of the program in the command prompt. If you want extras added to your installation like MPI, which can be used for big modelling runs because it allows the execution of multiple Rosetta tasks on multiple cores you can add an additional flag in your scons command. You can see all options in the Rosetta documentation.mode=release bin
#Checking if the installation was successful: When the error thrown after running the application is thrown by Rosetta the installation succeeded. >$PATH_TO_ROSETTA$/main/source/bin/AbinitioRelax.default.linuxgccrelease ERROR: Error: can't read sequence! Use -in::file::fasta sequence.fasta or -in::file::native native.pdb! ERROR:: Exit from: src/protocols/abinitio/AbrelaxApplication.cc line: 372 [ ERROR ]: Caught exception: File: src/protocols/abinitio/AbrelaxApplication.cc:372 [ ERROR ] UtilityExitException ERROR: Error: can't read sequence! Use -in::file::fasta sequence.fasta or -in::file::native native.pdb! #The internal Rosetta error shows us that Rosetta is installed. #Rosetta wih MPI support can be added by adding the mpi flag to your scons command: >./scons.py extras=mpiNow you successfully installed Rosetta and can continue with the tutorials either on our Wiki page, the Meiler Lab page or the Rosetta Documentation itself.
## WP_063844486 2rad.pdb # scores_from_program: 0 0 ---------------------------------------MRFEEWVKDKHIPFKLNHPDDNYDDFKPLRKIIGDTRVVALGENSHFIKEFFLLRHTLLRFFIEDLGFTTFAFEFGFAEGQIINNWIHGQGTDDEIGRFLKHFYYPEELKTTFLWLREYNKAA--KEKITFLGIDIPRNGGSYLPNMEIVHDFFRTADKEALHIIDDAFNIAKKIDYFSTSQAALNLHELTDSEKCRLTSQLARVKVRLEAMAPIHIEKYGIDKYETILHYANGMIYLDYNIQAMSGFISG----GGMQG-DMGAKDKYMADSVLWHLKNPQSEQKVIVVAHNAHIQKTPILYDGFLSCLPMGQRLKNAIGDDYMSLGITSYSGHTAALYPEVDTKYGFRVDNFQLQEPNE-----GSVEK------AISGCGVTNSFVFFRNIPEDLQSIPNMIRFDSIYMKAELEKAFDGIFQIEKSSVSEVVYE------- 0 MKKKIIIAIVASAITMTHFVGNTYADSKTEVSVTAPYNTNQIAKWLEAHAKPLKTTNPTASLNDLKPLKNMVGSASIVGLGEATHGAHEVFTMKHRIVKYLVSEKGFTNLVLEEGWDRALELDRYVLTGK--GNPSQHLTPVFKTKEMLDLLDWIRQYNANPKHKSKVRVIGMDIQSVNENVYNN---IIEYIKANNSKLLPRVEEKIKG---LIPVTK--DMNTFESLTKEEKEKYVLDAKTISALLEENKS----------YLN--GKSKEFAWIKQNARIIEQFTTMLATPPDKPADFYLKHDIAMYENAKWTEEH--L-GKTIVWGHNGHVSKTNML--SFIYPKVAGQHLAEYYGKRYVSIGTSVYEGQYNVKNSDGEFG---PYGTLKSDDPNSYNYIFGQVKKDQFFIDLRKANGVTKTWLN—EQHPIFAGITTEGPDIPKTVDISLGKAFDILVQIQKVSPSQVHQLEHHHHHH #The first sequence is the target sequence, the second sequence the template sequence. Note that the sequences should both be written in one line and both start with a 0 and a space. Further information on the Grishin format can be found in the Rosetta Documentation.Now you can use the Rosetta partial thread applications to thread the target sequence on the structure of your template.
#Threading of the template sequences. This step is performed for every structure used as a template. You need to provide the templates structure as a pdb file, the targets sequence as a fasta file, the structures’ alignment and the path to the Rosetta database. > $PATH_TO_ROSETTA$/main/source/bin/partial_thread.default.linuxgccrelease -database $PATH_TO_ROSETTA$/main/database/ -in:file:fasta “target_structure.fasta” -in:file:alignment “alignment.grishin” -in:file:template_pdb “template.pdb” -ignore_unrecognized_resTo enhance the model’s precision structure fragments can be generated using the old Robetta webserver. The main script for Rosetta is a so-called XML File. You can add all steps Rosetta should perform by simply adding them to the Script.
#This is the example XML script similar to the one provided on the Rosetta Documentation site. <ROSETTASCRIPTS> <TASKOPERATIONS> </TASKOPERATIONS> <SCOREFXNS> <ScoreFunction name="stage1" weights="score3" symmetric="0"> <Reweight scoretype="atom_pair_constraint" weight="0.5"/> </ScoreFunction> <ScoreFunction name="stage2" weights="score4_smooth_cart" symmetric="0"> <Reweight scoretype="atom_pair_constraint" weight="0.5"/> </ScoreFunction> <ScoreFunction name="fullatom" weights="talaris2013_cart" symmetric="0"> <Reweight scoretype="atom_pair_constraint" weight="0.5"/> </ScoreFunction> </SCOREFXNS> <FILTERS> </FILTERS> <MOVERS> <Hybridize name="hybridize" stage1_scorefxn="stage1" stage2_scorefxn="stage2" fa_scorefxn="fullatom" batch="1" stage1_increase_cycles="1.0" stage2_increase_cycles="1.0" linmin_only="1"> <Fragments three_mers="aat000_03_05.200_v1_3" nine_mers="aat000_09_05.200_v1_3"/> <Template pdb="2qgm.pdb.pdb" cst_file="AUTO" weight="1.000" /> <Template pdb="2rad.pdb.pdb" cst_file="AUTO" weight="1.000"/> <Template pdb="3b55.pdb.pdb" cst_file="AUTO" weight="1.000"/> </Hybridize> </MOVERS> <APPLY_TO_POSE> </APPLY_TO_POSE> <PROTOCOLS> <Add mover="hybridize"/> </PROTOCOLS> </ROSETTASCRIPTS>Additionally, you have to give Rosetta the instructions on where to find the XML file, the target sequence and other options for example for the final structure relaxation. You can pick whatever options are suited for your simulation and simply add them to a text file that you add in the command prompt when starting the Rosetta application.
#This is an example for an options file. You have to add the names of the structures behind the flags (start with a – and the description, e.g. -nstruct). You can also provide this information directly in the command prompt but it is easier to have a options file. Let’s assume we named our file “options” # i/o -in:file:fasta EreB.fasta -parser:protocol ereb_hybridization.xml -nstruct 1 -database /mnt/c/Software/rosetta_src_2020.08.61146_bundle/main/database #-seed_offset# seed offset if necessary # relax options -relax:minimize_bond_angles -relax:minimize_bond_lengths -relax:jump_move true -default_max_cycles 200 -relax:min_type lbfgs_armijo_nonmonotone -relax:jump_move true -hybridize:stage1_probability 1.0 -restore_talaris_behavior # reduce memory footprint -chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm #Now the main simulation can be started using the Rosetta Scripts application, that is able to read the XML file and execute the commands: >$PATH_TO_ROSETTA$/main/source/bin/rosetta_scripts.linuxgccrelease @options -database $PATH_TO_ROSETTA$/main/database
University
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Experts
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Former iGEMers
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