RosettaCommons · NooraAz · May 2, 2024 · May 2, 2024 · roccomoretti · May 2, 2024
diff --git a/Release-Notes.md b/Release-Notes.md
@@ -785,7 +785,7 @@ A new Job Distributor, JD3, is ready for use.  This is mostly invisible to end u
 Although most improvements were in Rosetta3.7, we continue to improve the fraction of unmodified PDBs Rosetta can handle.  (Don't worry - we've always been able to handle canonical protein well - but we are doing an ever-improving job with strange stuff like the GFP fluorophore, chemically concatenated ligands, glycans, RNA, etc).
 
 ###Cxx11 builds
-Rosetta turned on Cxx11 features in its C++.  This deprecates the compatibility of a lot of older compilers. See <https://www.rosettacommons.org/docs/latest/build_documentation/Cxx11Support> for more information.
+Rosetta turned on Cxx11 features in its C++.  This deprecates the compatibility of a lot of older compilers. See <https://www.rosettacommons.org/docs/latest/Building_Rosetta/Cxx11Support> for more information.
 
 ###Executable naming
 We've tweaked the build system such that the built executables are named a little more simply.  The tripartite names (rosetta_scripts.default.linuxgccrelease) will work as before, but now the two-part names rosetta_scripts.linuxgccrelease) will always point towards the default build, instead of the most recent build.
@@ -951,7 +951,7 @@ Enzyme specificity re-design (using coupled_moves) ([http://www.ncbi.nlm.nih.gov
 * Multiple refactorings in the chemistry layers, allowing:
     * Poses with carbohydrates
     * Better support for ribonucleoprotein
-    * Support for all ligands in the PDB’s chemical dictionary (note you must [install that dictionary separately](build_documentation/Build-Documentation#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary))
+    * Support for all ligands in the PDB’s chemical dictionary (note you must [install that dictionary separately](Building_Rosetta/Building-Rosetta#setting-up-rosetta-3_obtaining-additional-files_pdb-chemical-components-dictionary))
     * Support for runtime manipulation of chemistry (adding/removing atoms)
     * Support for rotamer libraries with arbitrary numbers of backbone torsion dependencies
     * Automatic setup of bonds to [metal ions](rosetta_basics/non_protein_residues/Metals).  

diff --git a/_Sidebar.md b/_Sidebar.md
@@ -1,6 +1,6 @@
 [[Getting Started]]
 
-[[Build Documentation|build_documentation/Build-Documentation]]
+[[Building Rosetta|Building_Rosetta/Building-Rosetta]]
 
 [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]]
 

diff --git a/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md b/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md
@@ -8,7 +8,7 @@ The protocol capture is also available in the demos repository under `Rosetta/de
 
 This document is a protocol capture to the manuscript &quot;Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints&quot; by Kuenze G. et al. For following the steps in this protocol capture, it is recommended that the user downloads the weekly release version **v2019.02-dev60579** , which is available at [https://www.rosettacommons.org/software/license-and-download](https://www.rosettacommons.org/software/license-and-download).
 
-Instructions on how to install Rosetta, information on software dependencies and install times, and how to get started with the program can be found on the Rosetta Commons documentation webpages: [https://www.rosettacommons.org/docs/latest/build\_documentation/Build-Documentation](https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation) and [https://www.rosettacommons.org/docs/latest/getting\_started/Getting-Started](https://www.rosettacommons.org/docs/latest/getting_started/Getting-Started).
+Instructions on how to install Rosetta, information on software dependencies and install times, and how to get started with the program can be found on the Rosetta Commons documentation webpages: [https://www.rosettacommons.org/docs/latest/build\_documentation/Building-Rosetta](https://www.rosettacommons.org/docs/latest/Building_Rosetta/Building-Rosetta) and [https://www.rosettacommons.org/docs/latest/getting\_started/Getting-Started](https://www.rosettacommons.org/docs/latest/getting_started/Getting-Started).
 
 This protocol capture contains instructions for applying paramagnetic restraints in the RosettaNMR framework to four different modeling tasks: protein _de no_ structure prediction (_protocol 1_), modeling of symmetric proteins (_protocol 2_), protein-ligand docking (_protocol 3_) and protein-protein docking (_protocol 4_). All required input files for running those RosettaNMR calculations can be found in the directory accompanying this protocol capture. Copy the file **protocol\_capture\_rosettanmr\_inputfiles.tar.gz** to your desired location and extract and unpack the input file directory by running the command:
 

diff --git a/application_documentation/_Sidebar.md b/application_documentation/_Sidebar.md
@@ -1,6 +1,6 @@
 [[Getting Started]]
 
-[[Build Documentation|build_documentation/Build-Documentation]]
+[[Building Rosetta|Building_Rosetta/Building-Rosetta]]
 
 [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]]
 

diff --git a/application_documentation/rna/auto-drrafter.md b/application_documentation/rna/auto-drrafter.md
@@ -29,7 +29,7 @@ A demo of auto-DRRAFTER is available in `ROSETTA_HOME/main/demos/public/drrafter
 ##Setting up auto-DRRAFTER
 
 1. Download Rosetta here <https://www.rosettacommons.org/software/license-and-download>. You will need to get a license before downloading Rosetta (free for academic users). auto-DRRAFTER will be available starting in Rosetta weekly releases *after* 2019.47. **auto-DRRAFTER is NOT available in Rosetta 3.11 (it will be available in 3.12)**.  
-2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here] (https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation).  
+2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here] (https://www.rosettacommons.org/docs/latest/Building_Rosetta/Building-Rosetta).  
 3. Make sure you have python installed and install networkx and mrcfile. For example, type: `pip install networkx mrcfile`
 4. Install EMAN2 version 2.22 (https://blake.bcm.edu/emanwiki/EMAN2/Install). Confirm that `e2proc3d.py` and `e2segment3d.py` are installed by typing:   
 ```

diff --git a/application_documentation/rna/drrafter.md b/application_documentation/rna/drrafter.md
@@ -20,7 +20,7 @@ A demo of DRRAFTER is available in `ROSETTA_HOME/demos/public/drrafter/`. Instru
 
 ## Installing DRRAFTER
 1. Download Rosetta [here](https://www.rosettacommons.org/software/license-and-download). You will need to get a license before downloading Rosetta (free for academic users). DRRAFTER is available in the Rosetta weekly releases starting with 2018.12. **DRRAFTER is NOT available in Rosetta 3.9.** 
-2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here](https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation). 
+2. If you're not using the precompiled binaries (these are available for Mac and Linux and you can access them by downloading source+binaries in Step 1), install Rosetta following the instructions available [here](https://www.rosettacommons.org/docs/latest/Building_Rosetta/Building-Rosetta). 
 3. Make sure that you have python (v2.7) installed.
 4. Install Rosetta RNA tools. See instructions and documentation [here] (https://www.rosettacommons.org/docs/latest/application_documentation/rna/RNA-tools).
 5. Check that the ROSETTA environmental variable is set (you should have set this up during RNA tools installation). Type `echo $ROSETTA`. This should return the path to your Rosetta directory. If it does not return anything, go back to step 4 and make sure that you follow the steps for RNA tools setup.  

diff --git a/application_documentation/tools/Tools.md b/application_documentation/tools/Tools.md
@@ -1525,9 +1525,9 @@ tools/analysis/apps/sequence_tolerance.R
 
 ## Build scripts
 
-* See [[Build Documentation]] for more information.
+* See [[Building Rosetta]] for more information.
 
-main/source/[[scons.py|Build Documentation]]    
+main/source/[[scons.py|Building Rosetta]]    
 &#8195; - Main script for Rosetta compilation.
 
 main/source/ninja_build.py    

diff --git a/build_documentation/Build-Documentation.md → build_documentation/Building-Rosetta.md b/build_documentation/Build-Documentation.md → build_documentation/Building-Rosetta.md
diff --git a/build_documentation/Scons-Overview-and-Specifics.md b/build_documentation/Scons-Overview-and-Specifics.md
@@ -59,7 +59,7 @@ Platforms are initially setup by functions in the <code>main/source/tools/build/
 
 ##See Also
 
-* [[Build Documentation]]: Information on setting up Rosetta
+* [[Building Rosetta]]: Information on setting up Rosetta
 * [[Getting Started]]: A page for people new to Rosetta. New users start here.
 * [[TACC]]: Information for running Rosetta on the TACC/Stampede cluster.
 * [[Commands collection]]: A list of example command lines for running Rosetta executable files

diff --git a/build_documentation/_Sidebar.md b/build_documentation/_Sidebar.md
@@ -1,6 +1,6 @@
 [[Getting Started]]
 
-[[Build Documentation|build_documentation/Build-Documentation]]
+[[Building Rosetta|Building_Rosetta/Building-Rosetta]]
 
 * [[Supported platforms|platforms]]
 

diff --git a/build_documentation/platforms.md b/build_documentation/platforms.md
@@ -86,14 +86,14 @@ To assist in checking for compatibility, we have put together a small Python tes
 downloadable from <https://raw.githubusercontent.com/RosettaCommons/rosetta_clone_tools/master/rosetta_compiler_test.py>
 
 Note: Even if the default compiler is a version without support, often there will be an updated compiler available on the system.
-Talk to your system administrator for more details, and see [the build documentation](Build-Documentation#setting-up-rosetta-3_alternative-setup-for-individual-workstations_scons-mac-linux) 
+Talk to your system administrator for more details, and see [the Building Rosetta](Building-Rosetta#setting-up-rosetta-3_alternative-setup-for-individual-workstations_scons-mac-linux) 
 for compiling with a non-default compiler.
 In worse-case scenarios, the weekly releases of Rosetta 2015.39 and before may be compatible with older compilers.
 
 ##See Also
 
 * [[Getting Started]]: A page for people new to Rosetta
-* [[Build Documentation]]: Instructions for building Rosetta
+* [[Building Rosetta]]: Instructions for building Rosetta
 * [[Scons Overview and Specifics]]: Advanced details on the Scons build system
 * [[TACC]]: Information for running Rosetta on the TACC/Stampede cluster.
 * [[Rosetta Servers]]: Web-based servers for Rosetta applications

diff --git a/development_documentation/Common-Errors.md b/development_documentation/Common-Errors.md
@@ -97,6 +97,6 @@ PhenixInterface::setAlgorithm(
 ##See Also
 
 * [[Development Documentation]]
-* [[Build Documentation]]
+* [[Building Rosetta]]
 * [[Scons Overview and Specifics]]: Detailed information on the Scons compiling system
 * [[FAQ]]
diff --git a/development_documentation/Development-Documentation.md b/development_documentation/Development-Documentation.md
@@ -109,5 +109,5 @@ For RosettaCommons developers, we have a version of the Doxygen documentation wh
 * [[PyRosetta]]: Wiki page for PyRosetta, the independent Python interface to Rosetta
 * [[Rosetta Timeline]]: History of Rosetta
 * [[Getting Started]]: A page for people new to Rosetta
-* [[Build Documentation]]: Information on building Rosetta
+* [[Building Rosetta]]: Information on building Rosetta
 * [[Running Rosetta with options]]: Instructions for running Rosetta executables
diff --git a/development_documentation/_Sidebar.md b/development_documentation/_Sidebar.md
@@ -1,6 +1,6 @@
 [[Getting Started]]
 
-[[Build Documentation|build_documentation/Build-Documentation]]
+[[Building Rosetta|Building_Rosetta/Building-Rosetta]]
 
 [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]]
 

diff --git a/development_documentation/code_structure/rosetta-library-structure.md b/development_documentation/code_structure/rosetta-library-structure.md
@@ -4,11 +4,11 @@ The `rosetta/main/source` directory contains eight top level directories of whic
 
 -   `src/` The src directory contains all the source files for the rosetta library. See [[An overview page for the src directory of the Rosetta|src-index-page]] for more information.
 -   `test/` The test directory contains source files for rosetta's unit tests. The integration, and scientific tests now live in rosetta/main/tests. Together, these two sets of tests are used to verify that the rosetta library is functioning correctly. See [[A Guide to Running and Writing Tests for Rosetta|rosetta-tests]] for more information on Rosetta Tests.
--   `bin/` The bin directory contains soft links to all the rosetta applications. Currently separate softlinks are stored for each combination of operating system (linux, macos), compiler(gcc, icc), and build mode (debug, release, release_debug). See the [[build documentation]] page for further information of the build system.
--   `build/` The build directory is where all the object files and shared libraries for build configuration are stored. The directory structure is automatically created by the scons build system. See the [[build documentation]] page for further information of the build system.
+-   `bin/` The bin directory contains soft links to all the rosetta applications. Currently separate softlinks are stored for each combination of operating system (linux, macos), compiler(gcc, icc), and build mode (debug, release, release_debug). See the [[Building Rosetta]] page for further information of the build system.
+-   `build/` The build directory is where all the object files and shared libraries for build configuration are stored. The directory structure is automatically created by the scons build system. See the [[Building Rosetta]] page for further information of the build system.
 -   `scripts/` The scripts directory is the recommended location for all RosettaScripts XML files (in the rosetta_scripts subdirectory) and Python scripts for scientific purposes (in the python subdirectory). Private PyRosetta applications are also placed in this directory.
 -   `doc/` The doc directory [[once contained|History-of-Rosetta-documentation]] all the stand alone doxygen pages. Those pages are now this wiki (the documentation repository). It still holds an autogenerated page of option system information.
--   `tools/` The tools directory contains the files for the custom SCons Builder for the rosetta library. See the [[build documentation]] page for further information of the build system.
+-   `tools/` The tools directory contains the files for the custom SCons Builder for the rosetta library. See the [[Building Rosetta]] page for further information of the build system.
 -   `demo/` The demo directory once contained demos (now the demos repository).
 ##See Also
 

diff --git a/development_documentation/test/Running-Tests-on-the-Test-Server.md b/development_documentation/test/Running-Tests-on-the-Test-Server.md
@@ -75,7 +75,7 @@ If you happen to work on a project for which this seems appropriate—for exampl
 
 * [[Testing server]]: Information on the testing server
 * [[Integration tests]]: General information on Rosetta's integration tests
-* [[Build Documentation]]: Find instructions for building Rosetta mpi executables here
+* [[Building Rosetta]]: Find instructions for building Rosetta mpi executables here
 * [[Testing server]]: Server that can be used to run Rosetta integration tests automatically
   * [[Running Tests on the Test Server]]: Instructions for using the testing server
 * [[Testing home page|rosetta-tests]]

diff --git a/development_documentation/test/Writing-MPI-Integration-Tests.md b/development_documentation/test/Writing-MPI-Integration-Tests.md
@@ -26,7 +26,7 @@ Only those tests that have a `command.mpi` file will run in this mode.
 
 * [[Integration tests]]: General information on Rosetta's integration tests
 * [[Running Rosetta in MPI mode|running-rosetta-with-options#mpi]]
-* [[Build Documentation]]: Find instructions for building Rosetta mpi executables here
+* [[Building Rosetta]]: Find instructions for building Rosetta mpi executables here
 * [[Testing server]]: Server that can be used to run Rosetta integration tests automatically
   * [[Running Tests on the Test Server]]: Instructions for using the testing server
 * [[Testing home page|rosetta-tests]]

diff --git a/development_documentation/tutorials/devel-tutorials.md b/development_documentation/tutorials/devel-tutorials.md
@@ -35,5 +35,5 @@ The following is a list of guides for using specific Rosetta features or perform
 * [[PyRosetta]]: Wiki page for PyRosetta, the independent Python interface to Rosetta
 * [[Rosetta Timeline]]: History of Rosetta
 * [[Getting Started]]: A page for people new to Rosetta
-* [[Build Documentation]]: Information on building Rosetta
+* [[Building Rosetta]]: Information on building Rosetta
 * [[Running Rosetta with options]]: Instructions for running Rosetta executables
diff --git a/development_documentation/tutorials/writing-an-app.md b/development_documentation/tutorials/writing-an-app.md
@@ -23,5 +23,5 @@ This guide is under construction.  Clearly a "Writing a 'Writing a Rosetta Appli
 * [[RosettaEncyclopedia]]: Detailed descriptions of concepts in Rosetta.
 * [[RosettaScripts]]: Instructions for writing RosettaScripts, the Rosetta XML interface
 * [[PyRosetta]]: Wiki page for PyRosetta, the independent Python interface to Rosetta
-* [[Build Documentation]]: Information on building Rosetta
+* [[Building Rosetta]]: Information on building Rosetta
 * [[Running Rosetta with options]]: Instructions for running Rosetta executables
diff --git a/getting_started/FAQ.md b/getting_started/FAQ.md
@@ -29,7 +29,7 @@ Most modern processors should be suitable. The one limitation you may run into i
 
 #### How do I compile Rosetta?
 
-Please see the page [[Build Documentation]] or the [Installation tutorial](https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build) for instructions on how to compile and install Rosetta.
+Please see the page [[Building Rosetta]] or the [Installation tutorial](https://www.rosettacommons.org/demos/latest/tutorials/install_build/install_build) for instructions on how to compile and install Rosetta.
 
 #### Where can I learn how to use Rosetta?
 

diff --git a/getting_started/Getting-Started.md b/getting_started/Getting-Started.md
@@ -91,7 +91,7 @@ After downloading Rosetta, go through [these detailed tutorials](https://www.ros
 Local installation implies that one will be using Rosetta through a [[command line interface (or terminal)|http://en.wikipedia.org/wiki/Command-line_interface]].
 For local users, you are unlikely to want to install Rosetta to the entire system.
 Rosetta is quite happy to be compiled and installed by regular users without administrative rights — this is how the developers use it.
-You may need administrative rights to install [[dependencies|Build-Documentation#dependencies]].
+You may need administrative rights to install [[dependencies|Building-Rosetta#dependencies]].
 
 * First untar/uncompress your downloaded copy of the code (`tar -xvzf Rosetta[releasenumber].tar.gz`).
 
@@ -103,7 +103,7 @@ You may need administrative rights to install [[dependencies|Build-Documentation
 Replace <number_of_processors_to_use> with a number one processor fewer than your computer has.
 Expect compilation to take a while (hours on one processor).
 
-See our extensive [[build documentation|Build-Documentation#compiling-rosetta-3]] for further instructions and troubleshooting.
+See our extensive [[Building Rosetta|Building-Rosetta#compiling-rosetta-3]] for further instructions and troubleshooting.
 
 ###Windows
 Unfortunately, we are not currently able to support the whole of Rosetta on Windows.
@@ -136,7 +136,7 @@ Developers can update these doc pages through our [interactive wiki](https://www
 
 * [Introductory Rosetta Tutorials](https://www.rosettacommons.org/demos/latest/Home#tutorials)
 * [[Resources for learning biophysics and computational modeling]]
-* [[Build Documentation]]: Information on setting up Rosetta
+* [[Building Rosetta]]: Information on setting up Rosetta
 * [[I want to do x]]: Guides to specific types of structural perturbations using RosettaScripts
 * [[Application Documentation]]: Links to documentation for a variety of Rosetta applications
 * [[Analyzing Results]]: Tips for analyzing results generated using Rosetta

diff --git a/getting_started/_Sidebar.md b/getting_started/_Sidebar.md
@@ -14,7 +14,7 @@
 
 * [[Rosetta canon]]
 
-[[Build Documentation|build_documentation/Build-Documentation]]
+[[Building Rosetta|Building_Rosetta/Building-Rosetta]]
 
 [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]]
 

diff --git a/internal_documentation/GithubWorkflow.md b/internal_documentation/GithubWorkflow.md
@@ -48,7 +48,7 @@ Branching and merging is the preferred development pattern in git, and because t
     * You will need to pre-accept GitHub's RSA key fingerprint by following [[the last step of the SSH instructions|https://help.github.com/articles/generating-ssh-keys]].
 * People contributing code will need to sign either the [developer agreement]() (for members of a RosettaCommons member lab) or the [Contributor Licensing Agreement](insert link) before their PRs can be accepted.
     * Members of RosettaCommons labs should consult the internal wiki for more details on getting set up as a RosettaCommons member. (Ask other lab members for the website and login info.)
-* You will need some of the standard [[Rosetta external dependencies|Build-Documentation]] like a compiler, etc.
+* You will need some of the standard [[Rosetta external dependencies|Building-Rosetta]] like a compiler, etc.
 
 ####Obtaining Rosetta.
 

diff --git a/internal_documentation/_Sidebar.md b/internal_documentation/_Sidebar.md
@@ -1,6 +1,6 @@
 [[Getting Started]]
 
-[[Build Documentation|build_documentation/Build-Documentation]]
+[[Building Rosetta|Building_Rosetta/Building-Rosetta]]
 
 [[Rosetta Tutorials| https://www.rosettacommons.org/demos/latest/Home#tutorials ]]