Fix external links in documentation.

GALigandDock-Preprocessing.md

@@ -66,7 +66,7 @@ Skip conformer generation! You don't need it anymore. Any single conformation is
 
 #### HOW TO MAKE A PROPER MOL2 FILE
 **1. If your input is in pdb or mol2 format**
-Requires installation of OpenBabel (http://openbabel.org/wiki/Main_Page). If it is pdb format, first strip ligand part in your pdb file as "ligand.pdb", then run:
+Requires installation of [OpenBabel](http://openbabel.org/). If it is pdb format, first strip ligand part in your pdb file as "ligand.pdb", then run:
 ```
 obabel -i pdb ligand.pdb -o mol2 -O ligand.mol2 
 ```
@@ -78,4 +78,4 @@ obabel -i mol2 ligand.mol2 -o mol2 -O ligandH.mol2 -p [pH of your interest; usua
 
 **2. If your input is in SMILES string**
 There are multiple ways of converting SMILES to mol2 file, you can use Openbable as well. We recommend online demo version of Corina:
-https://www.mn-am.com/online_demos/corina_demo
+https://www.mn-am.com/online_demos/corina_demo

Rosetta-Servers.md

@@ -1,7 +1,7 @@
 Rosetta servers
 ===============
 
-The [[RosettaCommons (external link)|https://www.rosettacommons.org/about]] (the group of labs that maintain Rosetta) maintains a number of [[servers for free public academic use (external link)|https://www.rosettacommons.org/software/servers]]. Servers for commercial use are also availible from an external provider.
+The [[RosettaCommons (external link)|https://www.rosettacommons.org/about]] (the group of labs that maintain Rosetta) maintains a number of [servers for free public academic use (external link)](https://rosettacommons.org/software/getting-started/). Servers for commercial use are also availible from an external provider.
 
 ###Public Servers
 
@@ -25,8 +25,6 @@ It also provides [[interface alanine scanning|interface analyzer]] and [[DNA int
 
 * The [PIPER-FlexPepDock server ](http://piperfpd.furmanlab.cs.huji.ac.il/) provides access to Rosetta's global docking of a peptide onto a receptor (where the binding pocket is unknown).
 
-* [RosettaDiagrams](http://www.rosettadiagrams.org/) provides a graphical interactive service to produce [[RosettaScripts]] XML files, with some ability to run the scripts as well.
-
 * [[FunHunt|http://funhunt.furmanlab.cs.huji.ac.il/]], short for funnel hunt, tries to distinguish correct protein-protein complex orientations from decoy orientations.
 It searches for [[energy landscape|Glossary#general-terms_energy-landscape]] funnels using Rosetta's docking code.
 

_Layout.html

@@ -44,7 +44,7 @@ <h1>{{ page.title }}</h1>
 					 class="action-home-page">Documentation home</a></li>
 				<li class="minibutton"><a href="https://www.rosettacommons.org/"
 					 class="action-home-page">RosettaCommons Website</a></li>
- 				<li class="minibutton"><a href="https://www.rosettacommons.org/docs/feedback?ref={{page.path}}"
+ 				<li class="minibutton"><a href="https://rosettacommons.org/contact/"
 					 class="action-home-page">Feedback</a></li>
 			</ul>
 		</div>

application_documentation/Application-Documentation.md

@@ -2,7 +2,7 @@
 
 Below is a list of the currently released applications containing developer documentation. Click on an application to
 see a more detailed description of the purpose and for detailed examples. If a released application is missing, please
-file a bug in our [issue tracker](http://bugs.rosettacommons.org).
+file a bug in our [issue tracker](https://github.com/RosettaCommons/rosetta/issues).
 
 If you are unsure which application best fits your biological problem, you may want to start [[here|Solving-a-Biological-Problem]].
 

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 "Integrative protein modeling in RosettaNMR from sparse paramagnetic restraints" 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 at [[Build-Documentation]] and [[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:
 
@@ -853,4 +853,4 @@ nmr:pcs:optimize_tensor                       Optimize the metal ion position an
 
 8. Schmitz, C. and A.M. Bonvin, _Protein-protein HADDocking using exclusively pseudocontact shifts._ J Biomol NMR, 2011. **50** (3): p. 263-6.
 
-9. Iwahara, J., C.D. Schwieters, and G.M. Clore, _Ensemble approach for NMR structure refinement against_ <sup>_1_</sup>_H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule._ J Am Chem Soc, 2004. **126** (18): p. 5879-96.
+9. Iwahara, J., C.D. Schwieters, and G.M. Clore, _Ensemble approach for NMR structure refinement against_ <sup>_1_</sup>_H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule._ J Am Chem Soc, 2004. **126** (18): p. 5879-96.

application_documentation/antibody/CDR-Cluster-Identification.md

@@ -10,7 +10,7 @@ This application matches each CDR of an antibody to North/Dunbrack CDR clusters
 
 # References
 
-Adolf-Bryfogle J,  Xu Q,  North B, Lehmann A,  Roland L. Dunbrack Jr, [PyIgClassify: a database of antibody CDR structural classifications](http://nar.oxfordjournals.org/cgi/reprint/gku1106?ijkey=mLgOMi7GHwYPx77&keytype=ref) , Nucleic Acids Research 2014
+Adolf-Bryfogle J,  Xu Q,  North B, Lehmann A,  Roland L. Dunbrack Jr, [PyIgClassify: a database of antibody CDR structural classifications](https://doi.org/10.1093/nar/gku1106) , Nucleic Acids Research 2014
 
 North B, Lehmann A, Dunbrack R, [A new clustering of antibody CDR loop conformations](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065967/pdf/nihms-249534.pdf) (2011). JMB 406(2): 228-256.
 

application_documentation/docking/ligand-dock.md

@@ -114,7 +114,7 @@ Automatic RosettaLigand Setup (ARLS)
 -Deprecated- (still works, just generally not recommended any longer)
 Most of the steps to set up a RosettaLigand docking run have been automated by the `       arls.py      ` script (`rosetta/main/source/src/apps/public/ligand_docking/`, run with –help for brief instructions). For those who prefer a manual approach, the individual steps are detailed in the following sections.
 
-The inputs to ARLS are *apo* protein structures (.pdb) and cofactor and ligand files (.mol, .sdf, or .mol2). I typically use PyMOL to edit the proteins, [Babel](http://openbabel.org/wiki/Main_Page) to convert PDB ligands to SDF, and [Avogadro](http://avogadro.openmolecules.net/wiki/Main_Page) to fix any mistakes in the SDF (all are free). You also need a file with one line per docking case, listing the protein name, cofactor name(s) if any, and ligand name (without file extensions). This file shows docking several compounds into an apo structure of farnesyl transferase, in most cases including a farnesyl pyrophosphate as a cofactor:
+The inputs to ARLS are *apo* protein structures (.pdb) and cofactor and ligand files (.mol, .sdf, or .mol2). I typically use PyMOL to edit the proteins, [OpenBabel](http://openbabel.org/) to convert PDB ligands to SDF, and [Avogadro](https://avogadro.cc/) to fix any mistakes in the SDF (all are free). You also need a file with one line per docking case, listing the protein name, cofactor name(s) if any, and ligand name (without file extensions). This file shows docking several compounds into an apo structure of farnesyl transferase, in most cases including a farnesyl pyrophosphate as a cofactor:
 
 ```
 1fpp 1mzc_FPP 1o5m
@@ -453,7 +453,7 @@ Program-specific Options:
 Estimating docking confidence (PRELIMINARY)
 ===========================================
 
-A confidence index can be calculated as the correlation between energy score and the distance (RMSD) from the lowest energy pose. This method assumes that there is one low energy binding mode. Further Reading: [Maria I. Zavodszky, Andrew W. Stumpff-Kane, David J. Lee, and Michael Feig. **Scoring confidence index: statistical evaluation of ligand binding mode predictions** , *Journal of computer aided design* 1999, **23** (5):289-299](http://www.springerlink.com/content/nr435h2q15366664)
+A confidence index can be calculated as the correlation between energy score and the distance (RMSD) from the lowest energy pose. This method assumes that there is one low energy binding mode. Further Reading: [Maria I. Zavodszky, Andrew W. Stumpff-Kane, David J. Lee, and Michael Feig. **Scoring confidence index: statistical evaluation of ligand binding mode predictions** , *Journal of computer aided design* 1999, **23** (5):289-299](https://doi.org/10.1007/s10822-008-9258-8)
 
 
 ##See Also

application_documentation/rna/rna-design.md

@@ -25,7 +25,7 @@ References
 
 Das, R., Karanicolas, J., and Baker, D. (2010), "Atomic accuracy in predicting and designing noncanonical RNA structure". Nature Methods 7:291-294. [Paper.](http://www.stanford.edu/~rhiju/DasKaranicolasBaker2010ALL.pdf) [Link.](http://www.nature.com/nmeth/journal/v7/n4/abs/nmeth.1433.html)
 
-(Reprint available at [http://daslab.stanford.edu/pubs.html](http://daslab.stanford.edu/pubs.html) ).
+(Reprint available at <https://daslab.stanford.edu/publications/>.)
 
 Purpose
 ===========================================
@@ -134,4 +134,4 @@ chunk001_uucg_RNA.pack.out:                      Scores (with breakdown by score
 * [[Analyzing Results]]: Tips for analyzing results generated using Rosetta
 * [[Solving a Biological Problem]]: Guide to approaching biological problems using Rosetta
 * [[Commands collection]]: A list of example command lines for running Rosetta executable files
-* [RiboKit](http://ribokit.github.io/): RNA modeling & analysis packages maintained by the Das Lab
+* [RiboKit](http://ribokit.github.io/): RNA modeling & analysis packages maintained by the Das Lab

application_documentation/structure_prediction/abinitio-relax.md

@@ -48,12 +48,12 @@ Input Files
 
 -   Fasta file. Contains the amino acid protein sequence in fasta format. Example: `        rosetta_demos/abinitio/input_files/1elwA.fasta       ` .
 
--   Fragments files. Generate structural fragment libraries using either the publicly available webserver ( [http://robetta.bakerlab.org/fragmentsubmit.jsp](http://robetta.bakerlab.org/fragmentsubmit.jsp) ) or a local installation of the rosetta\_fragments package. Example: `        rosetta_demos/abinitio/input_files/aa1elwA03_05.200_v1_3       ` and `        rosetta_demos/abinitio/input_files/aa1elwA09_05.200_v1_3       ` .
+-   Fragments files. Generate structural fragment libraries using either the publicly available webserver ( <http://old.robetta.org/> ) or a local installation of the rosetta\_fragments package. Example: `        rosetta_demos/abinitio/input_files/aa1elwA03_05.200_v1_3       ` and `        rosetta_demos/abinitio/input_files/aa1elwA09_05.200_v1_3       ` .
 
 -   Native structure (optional). The native PDB structure may be used for benchmarking. When used, the RMSD to native is calculated for each model and provided as an extra column in the score line. Example: `        rosetta_demos/abinitio/input_files/1elw.pdb       `
 
 -   Psipred secondary structure prediction psipred\_ss2 file (optional). The Psipred secondary structure prediction file is necessary when the -use\_filters and -kill\_hairpins options are used (see below). Note: the fragment webserver runs Psipred and provides the psipred\_ss2 output file. Example: `        rosetta_demos/abinitio/input_files/1elwA.psipred_ss2. `
-Please note that the file format for these options has changed between Rosetta3.4 and 3.5 (the demo is also out of date).  Please see  [this](https://www.rosettacommons.org/content/killhairpin-error) post for more information.
+Please note that the file format for these options has changed between Rosetta3.4 and 3.5 (the demo is also out of date).  Please see  [this](https://forum.rosettacommons.org/content/killhairpin-error) post for more information.
 
 Options <a name="Options" />
 =======
@@ -223,4 +223,4 @@ Lowest scoring models that are in a cluster and that have a topology represented
 * [[Comparing structures]]: Essay on comparing structures
 * [[Analyzing Results]]: Tips for analyzing results generated using Rosetta
 * [[Solving a Biological Problem]]: Guide to approaching biological problems using Rosetta
-* [[Commands collection]]: A list of example command lines for running Rosetta executable files
+* [[Commands collection]]: A list of example command lines for running Rosetta executable files

application_documentation/structure_prediction/backrub.md

@@ -226,7 +226,6 @@ New Features in Rosetta 3.2
 
 * [[Fasta file]]: Fasta file format
 * [[Fragment file]]: Fragment file format (required for abinitio structure prediction)
-* [[Backrub Server (external link)|https://kortemmelab.ucsf.edu/backrub/cgi-bin/rosettaweb.py?query=index]]: Web-based server that provides backrub ensembles for academic users
 * [[BackrubMover]]: The RosettaScripts backrub mover
 * [[Structure prediction applications]]: A list of other applications to be used for structure prediction
   * [[Abinitio relax]]: Application for predicting protein structures from sequences

application_documentation/structure_prediction/minirosetta-comparative-modeling.md

@@ -49,7 +49,7 @@ Input Files
 
 -   Fasta file. Contains the amino acid protein sequence in fasta format.
 
--   Fragment files. Generate structural fragment libraries using either the publicly available webserver ( [http://robetta.bakerlab.org/fragmentsubmit.jsp](http://robetta.bakerlab.org/fragmentsubmit.jsp) ) or a local installation of the rosetta\_fragments package.
+-   Fragment files. Generate structural fragment libraries using either the publicly available webserver ( <http://old.robetta.org/> ) or a local installation of the rosetta\_fragments package.
 
 -   Native structure (optional). The native PDB structure may be used for benchmarking. When used, the RMSD to native is calculated for each model and provided as an extra column in the score line.
 

application_documentation/structure_prediction/mr-protocols.md

@@ -46,7 +46,7 @@ scores_from_program: 0 1.00
 
 While multiple pairs of template alignment files are accepted, it is generally recommended to run just a single template/alignment with each job.
 
-In addition, a [[fragment file|fragment file]] may also be required, depending on the options selected. Rebuilding of gaps is done by fragment insertion (as in Rosetta ab initio); thus two backbone fragment files (3-mers and 9-mers) must be given. The [[application for building these|app-fragment-picker]] is included with rosetta but requires some external tools/databases. The easiest way to generate fragments is to use the Robetta server ( [http://robetta.bakerlab.org/fragmentsubmit.jsp](http://robetta.bakerlab.org/fragmentsubmit.jsp) ). The fragment files should be built with the full-length sequence; rosetta handles remapping the fragments if not all gaps are rebuilt.
+In addition, a [[fragment file|fragment file]] may also be required, depending on the options selected. Rebuilding of gaps is done by fragment insertion (as in Rosetta ab initio); thus two backbone fragment files (3-mers and 9-mers) must be given. The [[application for building these|app-fragment-picker]] is included with rosetta but requires some external tools/databases. The easiest way to generate fragments is to use the Robetta server ( <http://old.robetta.org/> ). The fragment files should be built with the full-length sequence; rosetta handles remapping the fragments if not all gaps are rebuilt.
 
 Options
 =======

build_documentation/TACC.md

@@ -1,6 +1,8 @@
 Using Rosetta and PyRosetta on TACC/Stampede
 ============================================
 
+*NOTE: The XSEDE project is no longer running. TACC still exists and may be providing access to Rosetta, but the information below may be out of date.*
+
 TACC/Stampede
 -------------
 
@@ -230,4 +232,4 @@ def MPIJobDistributor(njobs, fun):
 * [[Commands collection]]: Example command lines for Rosetta applications
 * [[Application documentation]]: Descriptions of Rosetta apps
 * [[Rosetta on different scales]]: Guidelines for how to scale your Rosetta runs
-* [[Analyzing Results]]: Tips for analyzing results generated using Rosetta
+* [[Analyzing Results]]: Tips for analyzing results generated using Rosetta

coupled-moves.md

@@ -81,7 +81,7 @@ For each position, look at all side chains modeled by CoupledMoves. Calculate th
 
 ## [5.3] Resfile preparation
 
-This section assumes familiarity with the resfile [documentation](https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles) and [manual](https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d1/d97/resfiles.html). 
+This section assumes familiarity with the resfile [documentation](https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles).
 
 Manually define packable residues: To achieve adequate sampling in a limited number of trials, set all residues to NATRO except target designable residues, e.g. a ligand binding pocket's first shell residues, motif residues, or individual secondary structure elements. Consider setting second-shell residues to NATAA to allow rotamer sampling.
 
@@ -508,4 +508,4 @@ To be added - contact Amanda for immediate questions
 
 # [12] See Also
 
-* [[I want to do x]]: Guide to choosing a mover
+* [[I want to do x]]: Guide to choosing a mover

development_documentation/Coding-Conventions.md

@@ -438,7 +438,7 @@ void fold_protein( std::string const & sequence );
 ####Doxygen Notes (See Doxygen Tips)
 * Doxygen reads in [[configuration parameters|http://www.stack.nl/~dimitri/doxygen/config.html]] from a "Doxyfile". (Called Doxyfile in the Rosetta++ CVS).
 * The index.html page is generated from comments in doxygen.h
-* Graphs are generated with the dot program from the [[graphiz|http://www.graphviz.org/]] package. (The path of which is specified in the Doxyfile.) The line and box colors are described [[here|http://www.stack.nl/~dimitri/doxygen/diagrams.html]].
+* Graphs are generated with the dot program from the [[graphiz|http://www.graphviz.org/]] package. (The path of which is specified in the Doxyfile.) The line and box colors are described [here](https://www.doxygen.nl/manual/diagrams.html).
 
 ###Debugging Output Guidelines
 * Use [[basic::Tracer|tracer]] for your main debug IO. Tracer output is buffered and because of that it is required to explicitly instruct Tracer object to flush output. To do that call Tracer::flush() member function or end your message with std::endl (it will call flush() function after new line symbols is send).