how can we calculate Rosetta score on some decoy set?

Member Site Forums PyRosetta PyRosetta – General how can we calculate Rosetta score on some decoy set?

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    • #1617

        I need to calculate the Rosetta score(energy)on Rosetta All-atom Decoy Set and ITASSER Decoy set.

        I will be grateful,if you guide me how can I do it or are there any papers that contain the

        results of the Rosetta Program on ITASSER and Rosetta All-atom decoy sets?

        Thanks in audiences.

      • #8923

          Hi, you can use the score_jd2 application. Pass it a list of the paths to your decoy files (-in:file:l PDBList.txt) and it will score your decoys.

          You may also want to look at:


        • #8939

            I have not rosetta_source folder/directory.

            Do i need download any files?

          • #8944


              the files Rosetta source and Rosetta database were downloaded from

              and copy them to “C:Python27Scripts” and then run ./ bin mode=release in sygwin with path “/cygdrive/c/Python27/Scripts”
              with the error

              “scons: *** No SConstruct file found.
              File “”, line 905, in _main”

              Do i need any files?

            • #8945

                Why do you copy them into C:Python27Scripts?

                You should not need to do this. Just download the files, cd into source and run ./ bin mode=release. Python should already be setup, paths will be setup to use python, etc. ./ is the same as saying python Since it looks like you have already installed scons, you can, instead, call scons directly: scons bin mode=release. If none of this works, I would recommend installing ubuntu linux or virtualizing it within windows using virtualbox. It’ll make things much easier. Especially if you run into compile errors.

              • #8972


                  I tried using the command ./ bin mode=release in rosetta_source folder. but it give the following error.

                  scons: Reading SConscript files …
         reports this is a non-version-control release version of Rosetta
                  scons: done reading SConscript files.
                  scons: Building targets …
                  g++ -o build/src/release/cygwin/1.7/32/x86/gcc/4.5/default/protocols/wum/WorkUnitBase.os -c -isystem external/boost_1_46_1/ -pipe -ffor-scope -Wall -Wextra -pedantic -Wno-long-long -malign-double -march=pentium4 -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -DNDEBUG -Isrc -Iexternal/include -Isrc/platform/cygwin/32/gcc/4.5 -Isrc/platform/cygwin/32/gcc -Isrc/platform/cygwin/32 -Isrc/platform/cygwin -Iexternal/boost_1_46_1 -Iexternal/dbio -I/usr/include -I/usr/local/include src/protocols/wum/
                  src/protocols/wum/ In member function ‘void protocols::wum::WorkUnitBase::print(std::ostream&, bool) const’:
                  src/protocols/wum/ error: ‘max’ was not declared in this scope
                  src/protocols/wum/ In member function ‘void protocols::wum::WorkUnitBase::set_wu_type(const std::string&)’:
                  src/protocols/wum/ error: ‘min’ was not declared in this scope
                  src/protocols/wum/ In member function ‘void protocols::wum::WorkUnitBase::set_options(const std::string&)’:
                  src/protocols/wum/ error: ‘min’ was not declared in this scope
                  scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/4.5/default/protocols/wum/WorkUnitBase.os] Error 1
                  scons: building terminated because of errors.

                  what shall i do in this case?

                • #8925


                    Thank you,But how can I download score_jd2 application?
                    score_jd2 application is executable in windows platform?


                  • #8926

                      Please see the user guide:

                      You will need to download the source and compile. The program will be in /bin directory in source directory after compilation. Please see the guide for relevant flags and how to generally run Rosetta.

                    • #8933

                        Thank you

                        I Studied and followed
                        1. Platforms
                        2. Install SCons
                        3. Build Rosetta
                        I installed Scons as mentioned

                        and installed cygwin

                        how can I install Rosetta at windows platform?

                      • #8934

                          I have only compiled Rosetta on Linux + Mac machines. However, I would assume that if you installed a compiler (GCC), you should be good to go. I read that when you install cygwin it will ask you if you want to install additional packages, one of them being GCC compiler. After that, you should be able to follow the instructions in ‘Build Rosetta’

                        • #8937


                            I installed GCC compiler and then copy the cygwin terminal to path:”C:Python27Scripts”

                            while i am runing “scons.bat bin mode=release” in cygwin

                            i am getting error:
                            “scons: *** No SConstruct file found.
                            File “”, line 905, in _main”
                            what to do next?


                          • #8938

                              Not exactly sure, but try:

                              ./ bin mode=release

                              in the rosetta_source directory

                            • #8940

                                When you download Rosetta, you will need to download both the Rosetta source and Rosetta database compressed files. Unzip, and there you go. Or download everything as a bundle, which includes tools, demos, etc….

                              • #8974

                                  Hey Mirzaie, can you start a new thread on this in the build/install forum? I don’t know what to do, so maybe someone else will be able to help here.

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