diff --git a/GALigandDock-Preprocessing.md b/GALigandDock-Preprocessing.md index b85db59dd..25fb72794 100644 --- a/GALigandDock-Preprocessing.md +++ b/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 \ No newline at end of file +https://www.mn-am.com/online_demos/corina_demo diff --git a/Rosetta-Servers.md b/Rosetta-Servers.md index 7f095f269..1669c2cd9 100644 --- a/Rosetta-Servers.md +++ b/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. diff --git a/_Layout.html b/_Layout.html index 4bcae562b..6d9e55c0b 100644 --- a/_Layout.html +++ b/_Layout.html @@ -44,7 +44,7 @@

{{ page.title }}

class="action-home-page">Documentation home
  • RosettaCommons Website
    • -
  • Feedback
    • diff --git a/application_documentation/Application-Documentation.md b/application_documentation/Application-Documentation.md index 13ccce5f1..c7fa9c174 100644 --- a/application_documentation/Application-Documentation.md +++ b/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]]. diff --git a/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md b/application_documentation/RosettaNMR-with-Paramagnetic-Restraints.md index d8e6263fb..a4797a082 100644 --- 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 "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_ _1__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. \ No newline at end of file +9. Iwahara, J., C.D. Schwieters, and G.M. Clore, _Ensemble approach for NMR structure refinement against_ _1__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. diff --git a/application_documentation/antibody/CDR-Cluster-Identification.md b/application_documentation/antibody/CDR-Cluster-Identification.md index f31289526..44eb27377 100644 --- a/application_documentation/antibody/CDR-Cluster-Identification.md +++ b/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. diff --git a/application_documentation/docking/ligand-dock.md b/application_documentation/docking/ligand-dock.md index fbaef9278..995d81662 100644 --- a/application_documentation/docking/ligand-dock.md +++ b/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 diff --git a/application_documentation/rna/rna-design.md b/application_documentation/rna/rna-design.md index 346adf5d4..e6a7840b8 100644 --- a/application_documentation/rna/rna-design.md +++ b/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 .) 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 \ No newline at end of file +* [RiboKit](http://ribokit.github.io/): RNA modeling & analysis packages maintained by the Das Lab diff --git a/application_documentation/structure_prediction/abinitio-relax.md b/application_documentation/structure_prediction/abinitio-relax.md index b491ee9dd..773d77050 100644 --- a/application_documentation/structure_prediction/abinitio-relax.md +++ b/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 ( ) 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 ======= @@ -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 \ No newline at end of file +* [[Commands collection]]: A list of example command lines for running Rosetta executable files diff --git a/application_documentation/structure_prediction/backrub.md b/application_documentation/structure_prediction/backrub.md index 73069c91d..ff95dc56a 100644 --- a/application_documentation/structure_prediction/backrub.md +++ b/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 diff --git a/application_documentation/structure_prediction/minirosetta-comparative-modeling.md b/application_documentation/structure_prediction/minirosetta-comparative-modeling.md index 0d10c51ee..6e207d1fd 100644 --- a/application_documentation/structure_prediction/minirosetta-comparative-modeling.md +++ b/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 ( ) 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. diff --git a/application_documentation/structure_prediction/mr-protocols.md b/application_documentation/structure_prediction/mr-protocols.md index 1ab0b2e0d..2014bce62 100644 --- a/application_documentation/structure_prediction/mr-protocols.md +++ b/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 ( ). The fragment files should be built with the full-length sequence; rosetta handles remapping the fragments if not all gaps are rebuilt. Options ======= diff --git a/build_documentation/TACC.md b/build_documentation/TACC.md index 52bdd1ad4..58d0e7cb2 100644 --- a/build_documentation/TACC.md +++ b/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 \ No newline at end of file +* [[Analyzing Results]]: Tips for analyzing results generated using Rosetta diff --git a/coupled-moves.md b/coupled-moves.md index 2fd21ae37..84bc55e94 100644 --- a/coupled-moves.md +++ b/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 \ No newline at end of file +* [[I want to do x]]: Guide to choosing a mover diff --git a/development_documentation/Coding-Conventions.md b/development_documentation/Coding-Conventions.md index 8d71c2d17..a9fc57d53 100644 --- a/development_documentation/Coding-Conventions.md +++ b/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). diff --git a/development_documentation/Development-Documentation.md b/development_documentation/Development-Documentation.md index 9b6ba294b..08d7290bf 100644 --- a/development_documentation/Development-Documentation.md +++ b/development_documentation/Development-Documentation.md @@ -14,10 +14,7 @@ The documentation for the various libraries is a bit scattered. Here is a parti **Internal libraries:** -- Publicly available [Doxygen code documentation](https://www.rosettacommons.org/manuals/latest/main/) describing the interface to Rosetta objects and functions -- Historical version of the documentation, including both user manual and code documentation. - - The [Rosetta 3.5 user manual](https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/), with documentation for the core and protocols libraries; curiously, this lacks RosettaScripts documentation - - The [Rosetta 3.4 user manual](https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/), with documentation for the core and protocols libraries and on RosettaScripts (an older version, for historical reference only) +- Publicly available [Doxygen code documentation](https://docs.rosettacommons.org/manuals/latest/) describing the interface to Rosetta objects and functions For RosettaCommons developers, we have a version of the Doxygen documentation which also includes code. (Password protected access). diff --git a/development_documentation/code_structure/namespaces/namespace-core-io-pdb.md b/development_documentation/code_structure/namespaces/namespace-core-io-pdb.md index f1e4309eb..fb5cdad86 100644 --- a/development_documentation/code_structure/namespaces/namespace-core-io-pdb.md +++ b/development_documentation/code_structure/namespaces/namespace-core-io-pdb.md @@ -12,12 +12,8 @@ A PDB file is broken up into records, made up of one line each, and identified by a record name in the first six columns. The different kinds of records are described at: - http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/part_11.html + https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html -Each record is made up of fields belonging to one of sixteen different -types. The different kinds of fields are described at: - - http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/part_13.html The primary public interface is @c PDBReader, which turns a PDB file into a series of records. It behaves as an iterator through a @@ -65,4 +61,4 @@ An equivalent @c PDBWriter has not yet been written. * [[Glossary]]: Brief definitions of Rosetta terms * [[RosettaEncyclopedia]]: Detailed descriptions of additional concepts in Rosetta. * [[Rosetta overview]]: Overview of major concepts in Rosetta -* [[Development Documentation]]: The main development documentation page \ No newline at end of file +* [[Development Documentation]]: The main development documentation page diff --git a/development_documentation/tutorials/doxygen-tips.md b/development_documentation/tutorials/doxygen-tips.md index ae9d89bed..f50d59f3f 100644 --- a/development_documentation/tutorials/doxygen-tips.md +++ b/development_documentation/tutorials/doxygen-tips.md @@ -1,6 +1,6 @@ #Tips for writing doxygen documentation -The extensive Doxygen manual ( [http://www.stack.nl/\~dimitri/doxygen/manual.html,](http://www.stack.nl/~dimitri/doxygen/manual.html,) [http://www.stack.nl/\~dimitri/doxygen/commands.html](http://www.stack.nl/~dimitri/doxygen/commands.html) ) is well worth browsing. Doxygen provides a wide variety of options for documenting code and can be adapted for general documentation as well. This page well take you through some of the commonly used features in Rosetta3 documentation. +The extensive Doxygen manual ( ) is well worth browsing. Doxygen provides a wide variety of options for documenting code and can be adapted for general documentation as well. This page well take you through some of the commonly used features in Rosetta3 documentation. [[_TOC_]] diff --git a/getting_started/Comparing-Structures.md b/getting_started/Comparing-Structures.md index 518edf997..92935d670 100644 --- a/getting_started/Comparing-Structures.md +++ b/getting_started/Comparing-Structures.md @@ -42,7 +42,7 @@ significant than overlapping two proteins of length 100 to 7 angstroms resolution? There are a variety of ways to try to normalize these. Skolnick has some useful suggestions. Mammoth has it's own built in. But an extremely easy to grasp, quick and dirty measure is the RMS100 -([http://www.proteinscience.org/cgi/content/full/10/7/1470](http://www.proteinscience.org/cgi/content/full/10/7/1470)). +(). This renormalizes any RSMD to the the value it would have if the proteins were of length 100 and at the same level of statistical significance. I recommend using this before trying anything fancy. diff --git a/getting_started/FAQ.md b/getting_started/FAQ.md index caaf95d98..6a40cda7e 100644 --- a/getting_started/FAQ.md +++ b/getting_started/FAQ.md @@ -80,7 +80,7 @@ There have been a large number of Rosetta papers, so finding the appropriate one Generally, you want to cite the paper which presented the protocol which you are using in your paper. Often the relevant publications are listed on the documentation page for the application you used. -You can also take a look at the [[Rosetta canon]] for major papers, and for a somewhat comprehensive list of Rosetta related publications. +You can also take a look at the [[Rosetta canon]] for major papers. #### Where is Rosetta software documentation? @@ -116,7 +116,7 @@ Most Rosetta protocols, though, are intrinsically serial for each output structu #### How can I create a fragment file? -We highly recommend to use the Robetta server to create fragment file. It is possible to run fragment picking locally, but requires the installation of a number of dependencies and is non-trivial. +We highly recommend to use the Robetta server to create fragment file. It is possible to run fragment picking locally, but requires the installation of a number of dependencies and is non-trivial. #### What is an "unrecognized residue"? diff --git a/getting_started/Getting-Started.md b/getting_started/Getting-Started.md index 7e48e9979..9ffd2788c 100644 --- a/getting_started/Getting-Started.md +++ b/getting_started/Getting-Started.md @@ -74,12 +74,12 @@ Commercial Rosetta Servers Local installation and use of Rosetta -------------------------------------- -For academic or commercial users, you can [[request a license|http://c4c.uwc4c.com/express_license_technologies/rosetta]]. -These licenses are free for academic users. -Once you have a license, you can [[download the code here|https://www.rosettacommons.org/software/license-and-download]]. +Rosetta cam be downloaded from . +Academic and non-commercial users are automatically granted a non-commercial-use-only license with the download. +Commercial use requires a paid license obtainable from [UW CoMotion](https://els2.comotion.uw.edu/product/rosetta). + Note that the download comes as a [[tar archive|http://en.wikipedia.org/wiki/Tar_(computing)]]. -We don't distribute [[executables/binaries|http://en.wikipedia.org/wiki/Executable]] for most purposes, we distribute [[source code|http://en.wikipedia.org/wiki/Source_code]]. -As a consequence, you will need to [[compile|http://en.wikipedia.org/wiki/Compiler]] the code before use. +Pre-compiled executables are available for some platforms. [[Source code|http://en.wikipedia.org/wiki/Source_code]] is also availible, such that you can [[compile|http://en.wikipedia.org/wiki/Compiler]] on platforms where pre-compiled executables are not availible. Introductory Rosetta Tutorials ------------------------------ @@ -97,7 +97,7 @@ You may need administrative rights to install [[dependencies|Build-Documentation * Next, navigate to the `source` directory: `cd main/source`. -* Rosetta uses [[SCons|http://www.scons.org]] as a compile assistant. You will likely need to [[download| http://www.scons.org/download.php]] and install this first. +* Rosetta uses [[SCons|http://www.scons.org]] as a compile assistant. Rosetta comes with a copy of SCons, which should work for most systems. * The basic compilation command is `./scons.py -j mode=release bin`. Replace with a number one processor fewer than your computer has. diff --git a/getting_started/Resources-for-learning-biophysics-and-computational-modeling.md b/getting_started/Resources-for-learning-biophysics-and-computational-modeling.md index 216753f23..dccba6592 100644 --- a/getting_started/Resources-for-learning-biophysics-and-computational-modeling.md +++ b/getting_started/Resources-for-learning-biophysics-and-computational-modeling.md @@ -1,13 +1,13 @@ Using Rosetta requires some pre-existing understanding of biochemistry, biophysics, and molecular modeling. -Jeff Gray at Johns Hopkins teaches a course very relevant to understanding how to work with Rosetta, and that [[course page|http://graylab.jhu.edu/courses/540.414/]] is a fantastic (and often Rosetta-specific) resource. +Jeff Gray at Johns Hopkins teaches a course very relevant to understanding how to work with Rosetta, and that [course page](https://graylab.jhu.edu/resources.php/courses) is a fantastic (and often Rosetta-specific) resource. It even has videos of lectures. Some other education suggestions: * Fersht: Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding * Voet & Voet: Biochemistry * Brandon & Tooze: Introduction to Protein Structure -* [[Richardson: Anatomy and Taxonomy of Protein Structure|http://kinemage.biochem.duke.edu/teaching/anatax/]] +* [Richardson: Anatomy and Taxonomy of Protein Structure](http://kinemage.biochem.duke.edu/teaching/anatax) * Dill & Brumberg: Molecular Driving Forces; * Physical Biology of the Cell * http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/protein.htm diff --git a/getting_started/Rosetta-canon.md b/getting_started/Rosetta-canon.md index 29b2736a5..43ee94b6f 100644 --- a/getting_started/Rosetta-canon.md +++ b/getting_started/Rosetta-canon.md @@ -11,8 +11,6 @@ We distilled these references to a core canon: the papers we assume each other t These are organized by field in order of Rosetta entering the field, and chronological order within each group. -A more complete (but probably not 100% complete) list can be found [here](http://www.rosettacommons.org/about/pubs). - [[_TOC_]] Protein Structure Prediction diff --git a/internal_documentation/BundleGridSampler.md b/internal_documentation/BundleGridSampler.md index c3f95cb06..cd5f82d50 100644 --- a/internal_documentation/BundleGridSampler.md +++ b/internal_documentation/BundleGridSampler.md @@ -36,7 +36,7 @@ Generates a helical bundle, sampling user-specified ranges of parameters and out ``` -Default parameter values or parameter ranges are set in the BundleGridSampler tag, and overrides are set in the individual Helix tags. Refer to the MakeBundle mover for options that both movers have in common. Additional options include: +Default parameter values or parameter ranges are set in the BundleGridSampler tag, and overrides are set in the individual Helix tags. Refer to the [[MakeBundleMover]] for options that both movers have in common. Additional options include: - [parameter]\_min, [parameter]_max: Minimum and maximum parameter values for a range to be sampled. - [parameter]\_samples: The number of samples. Note that the total number of samples is the product of all individual samples, and this can get quite large very fast. - [parameter]\_copies\_helix: This option may only be specified in a Helix sub-tag. It indicates that a particular parameter for that helix is always set to the same value as that parameter from a previously-defined helix. See below for an example. @@ -68,4 +68,4 @@ In order to sample a range of parameters, keeping a parameter value for two diff ###See also * [[The Crick params file format|Crick-params-files]] * [[MakeBundle|MakeBundleMover]] mover -* [[PerturbBundle]] mover \ No newline at end of file +* [[PerturbBundle]] mover diff --git a/internal_documentation/FileIOOverview.md b/internal_documentation/FileIOOverview.md index d39fb111d..6f93723d8 100644 --- a/internal_documentation/FileIOOverview.md +++ b/internal_documentation/FileIOOverview.md @@ -4,7 +4,7 @@ Document created 31 January 2016 by Vikram K. Mulligan (vmullig@uw.edu) as part ## Supported molecular structure file formats in Rosetta -Rosetta currently supports Protein Data Bank format (PDB). Recently, support for the new macromolecular Crystallographic Information File (mmCIF) format has been added. A number of third-party applications exist for viewing and manipulating these formats. Examples include PyMOL, Chimera, and Swiss-PDB Viewer. +Rosetta currently supports Protein Data Bank format (PDB). Recently, support for the new macromolecular Crystallographic Information File (mmCIF) format has been added. A number of third-party applications exist for viewing and manipulating these formats. Examples include PyMOL, Chimera, and Swiss-PDB Viewer. Additionally, Rosetta has a proprietary structure file format called "silent" format. Rosetta's silent files have the advantage of being a compact means of storing multiple structures, with the full information needed to reconstruct a Rosetta pose, at full machine numerical precision. (Re-importing a structure that was exported to a third-party format, on the other hand, can lead to information loss.) However, silent files must be converted to a third-party format (e.g. PDB format) to view structures with third-party viewers (e.g.PyMOL). @@ -29,4 +29,4 @@ For file export, the process occurs in reverse: the Pose is converted to a Struc Overview of the third-party structure file import/export machinery in Rosetta. )>> -Conversion from Pose to other proprietary Rosetta formats (e.g. silent file format) is handled by other modules, and does not go through the StructFileRep object. The StructFileRep object is only intended for output to third-party formats, in which there might not be 1:1 correspondence between the way in which data are stored in the Pose and the way in which data are stored in the file. \ No newline at end of file +Conversion from Pose to other proprietary Rosetta formats (e.g. silent file format) is handled by other modules, and does not go through the StructFileRep object. The StructFileRep object is only intended for output to third-party formats, in which there might not be 1:1 correspondence between the way in which data are stored in the Pose and the way in which data are stored in the file. diff --git a/internal_documentation/RosettaAcademy.md b/internal_documentation/RosettaAcademy.md index a1356ccd5..07d4b7d52 100644 --- a/internal_documentation/RosettaAcademy.md +++ b/internal_documentation/RosettaAcademy.md @@ -12,10 +12,10 @@ Most people in the community are using PyMol (download from http://www.pymol.org * http://pymol.sourceforge.net/newman/userman.pdf * https://pymolwiki.org/index.php/Practical_Pymol_for_Beginners -Some people are using Chimera (http://www.cgl.ucsf.edu/chimera/), which seems to have some additional functionality for density maps if you are working with X-ray electron density maps or Cryo-EM maps. Tutorials can be found at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/frametut.html. +Some people are using Chimera (http://www.cgl.ucsf.edu/chimera/), which seems to have some additional functionality for density maps if you are working with X-ray electron density maps or Cryo-EM maps. Tutorials can be found at https://www.cgl.ucsf.edu/chimera/tutorials.html There is also the Discovery Studio Visualizer for Scientific Linux and Windows systems: -* http://accelrys.com/products/collaborative-science/biovia-discovery-studio/visualization-download.php +* https://discover.3ds.com/discovery-studio-visualizer-download ## Basic biochemistry To work in Rosetta, you need to know some basic biochemistry about amino acids and protein structure. You can learn this by picking up a biochemistry book (such as Voet & Voet: Biochemistry) or look at: @@ -25,10 +25,10 @@ To work in Rosetta, you need to know some basic biochemistry about amino acids a ## Foldit (developed by Center for Game Science at UW, Bakerlab, and UMass Dartmouth (Firas Khatib)) Foldit is a videogame created for the general public to solve real-life scientific puzzles involving protein structure and function. It is an excellent starting point to learn about protein structure as it does not require any previous knowledge. Once you download it, it will take you through tutorials where you are learning about all the moves and modifications you can do to a protein structure with a lot of fun along the way. Keep in mind that the terminology that Foldit uses is a bit different than what we are using in Rosetta (even though the code underneath Foldit is Rosetta code), but if you understand the concepts using Foldit, you can easily apply them in Rosetta. Also, the score in Foldit is opposite from Rosetta: in Foldit a higher score is better, in Rosetta, a lower energy is desired. -Download it at http://fold.it/portal/ +Download it at ## Eterna - for RNA (developed by Rhiju Das, Stanford) -A similar tool to FoldIt is available for RNA. It was developed by Rhiju Das' lab at Stanford (http://www.stanford.edu/~rhiju/). You can play and learn about it here: http://eterna.cmu.edu/web/ +A similar tool to FoldIt is available for RNA. It was developed by Rhiju Das' lab at Stanford (http://www.stanford.edu/~rhiju/). You can play and learn about it here: ## Introduction to Linux To know about how to navigate a terminal in Linux, you need to learn some basic commands. Learning some basic tricks with BASH coding often proves useful in expediting your workflow. There are plenty of resources available on the web: @@ -56,7 +56,7 @@ Here are some useful links that will help you understand terminology that is use * [[Glossary]] Some concepts are also explained in the PyRosetta tutorials: -* http://www.pyrosetta.org/tutorials +* http://www.pyrosetta.org/documentation/tutorials ## Documentation There is considerable documentation available within this wiki. Additional documentation is available here: https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/index.html. @@ -108,7 +108,7 @@ If you want to develop in Rosetta, you need to learn C++. If you have never scri * short online videos - Bucky's tutorials: http://www.youtube.com/watch?v=tvC1WCdV1XU&list=PLC6E50B89DA30C77A -* book: Sam's teach yourself C++ in 21 days: http://www.amazon.com/Sams-Teach-Yourself-Edition-ebook/dp/B0028CK0GW/ref=sr_1_1?ie=UTF8&qid=1375469877&sr=8-1&keywords=c%2B%2B+sams+5th+edition +* book: Sam's teach yourself C++ in 21 days: https://www.amazon.com/Sams-Teach-Yourself-Days-5th/dp/0672327112 ## ROSIE (set up by Sergey Lyskov, Jeff Gray's lab, Johns Hopkins) ROSIE is an abbreviation for "Rosetta Online Server that Includes Everyone". It is a server that runs several Rosetta applications without requiring the knowledge of Python, C++ or anything difficult. Perfect to use for the Newbie, however, only few applications are available and some of them are very specialized - more to come in the future. Check it out at https://rosie.rosettacommons.org/. Also, if you are a RosettaCommons developer and are planning on setting up a server on ROSIE for your own application, contact Sergey Lyskov at sergey.lyskov[at]gmail.com and he will give you instructions on how to do it. It should be pretty quick and easy with about two pages of code or less! @@ -131,7 +131,6 @@ If you are planning to develop in Rosetta and want to put together your own prot Extended information from the above intro is available here: [[GithubWorkflow]] but it is suggested to become intimately familiar with various git commands. Several online resources are available, among them: * nicely explained, not too long: http://gitref.org/ * shorter cheat sheet: https://www.kernel.org/pub/software/scm/git/docs/everyday.html -* short videos: http://www.youtube.com/GitHubGuides ## IDE: To write and develop code, it is much easier if you have an IDE (Integrated Development Environment) available. It is basically an editor and compiler, which also links to version control and has tons of nice little features like linking to functions somewhere else in the code, bracket completion, indentation, finding errors, etc. The two IDEs commonly used are @@ -183,7 +182,7 @@ There are plenty of useful links available that are connected with Rosetta, in a * RosettaDesign server - Kuhlman lab, University of Chapel Hill, NC: http://rosettadesign.med.unc.edu/ -* Rosetta@cloud - pay-per-use service for the experimental community: http://rosetta.insilicos.com/what/ +* Levitate - pay-per-use service for the experimental community: https://levitate.bio/ * Rosetta@home - donate computer time to solve scientific problems to RosettaCommons when you are not using your computer: http://boinc.bakerlab.org/rosetta/ diff --git a/internal_documentation/code_templates.md b/internal_documentation/code_templates.md index 203d56920..e550425c1 100644 --- a/internal_documentation/code_templates.md +++ b/internal_documentation/code_templates.md @@ -45,7 +45,7 @@ Here is an example of creating a new mover for carbohydrates: The README in the directory will help you get started. This page also has information on adding new src templates for new Rosetta classes. -https://github.com/RosettaCommons/main/blob/master/source/code_templates/README.md +https://github.com/RosettaCommons/rosetta/blob/main/source/code_templates/README.md #Etc diff --git a/meta/History-of-Rosetta-documentation.md b/meta/History-of-Rosetta-documentation.md index 4b3eecca4..dffbb73f0 100644 --- a/meta/History-of-Rosetta-documentation.md +++ b/meta/History-of-Rosetta-documentation.md @@ -13,7 +13,7 @@ Rosetta documentation has usually been focused on the needs of the moment, but n Early documentation =================== -The only surviving early documentation is that embedded in the literature, particularly in papers of the [[Rosetta Canon]] or others in our [publication list](http://www.rosettacommons.org/about/pubs). +The only surviving early documentation is that embedded in the literature, particularly in papers of the [[Rosetta Canon]] or others in our publication list. RosettaWiki =========== @@ -22,7 +22,7 @@ The (private) RosettaWiki was created around 2003. Originally, it held all sorts Doxygen days ============ By the [[early days|Rosetta timeline]] of "mini" (Rosetta3) development, Doxygen ([web link](http://www.doxygen.org) ([Wikipedia entry](http://en.wikipedia.org/wiki/Doxygen)) documentation was used to [[granular code documentation|development_documentation/tutorials/doxygen-tips]]. -This documentation has never been very complete but is still otherwise intact and used, and the generated documentation is available [here](http://www.rosettacommons.org/manuals/latest/main/). +This documentation has never been very complete but is still otherwise intact and used, and the generated documentation is available [here](https://docs.rosettacommons.org/manuals/latest/). When developers began to get serious about writing application documentation, they stuck with the Doxygen system in place and used it to build formatted webpages of just application documentation. diff --git a/meta/Rosetta-People.md b/meta/Rosetta-People.md index d4c9dfd92..97dabbc6c 100644 --- a/meta/Rosetta-People.md +++ b/meta/Rosetta-People.md @@ -1,29 +1,8 @@ #Rosetta people - -This page is the "Rosetta Glory", by analogy to the Rosetta [[Glossary]]: a list of important folks in the Rosetta community. This page is intentionally kept clear of pictures and contact info for privacy reasons - you will be able to find these people on the rosetta-devel [[email list|https://wiki.rosettacommons.org/index.php/Mailing_Lists]] if necessary. - -A comprehensive list of RosettaCommons PIs can be found [[here|http://www.rosettacommons.org/about]]. -The PIs are not otherwise documented on this page. (If there's no more text on this page for you, that's because it is blanked for the public version.) +A comprehensive list of RosettaCommons PIs can be found [[here|https://rosettacommons.org/about/labs/]]. - -####Andrew Leaver-Fay -Andrew is the [[benevolent dictator|http://en.wikipedia.org/wiki/Benevolent_dictator_for_life]] of the Rosetta codebase. -He is our most experienced computer scientist and software engineer, as well as having deep experience with almost all areas of Rosetta. -He is one of the few members of the community with the skills to optimize code. -He can answer almost any question, but as a consequence, is very busy. -Do feel free to ask for his help, but don't use him as your first resource. -You may see him as APL in in-code comments. - -####Sergey Lyskov -Sergey maintains our [[testing server]] resources, as well as ROSIE, one of our major [[Rosetta servers]]. -He is very responsive to requests for new features on either set of servers. -He is also a great person to talk to with questions about the testing architecture. - -####Yi Liu, Eran Kuchuk, Yuval Sadan, Oriel Goldstein -These fine folks (in this chronological order) have served as **Rosetta Manager**, serving as content administrators for the website and handling code releases. - - +Other people important in the Rosetta community are listed [[here|https://rosettacommons.org/about/team/]]. ##See Also @@ -31,4 +10,4 @@ These fine folks (in this chronological order) have served as **Rosetta Manager* * [[Rosetta overview]]: Overview of major concepts in Rosetta * [[RosettaEncyclopedia]]: Detailed descriptions of Rosetta terms * [[Glossary]]: Brief definitions of Rosetta terms -* [[Rosetta Timeline]]: Landmark Rosetta papers \ No newline at end of file +* [[Rosetta Timeline]]: Landmark Rosetta papers diff --git a/meta/Rosetta-Timeline.md b/meta/Rosetta-Timeline.md index 791992c9a..94367ecdd 100644 --- a/meta/Rosetta-Timeline.md +++ b/meta/Rosetta-Timeline.md @@ -33,8 +33,8 @@ As Rosetta grew, the Rosetta development world was no longer confined to just Da * Publication of Top7, the first design of a novel topology. [Kuhlman, et al.](http://www.sciencemag.org/content/302/5649/1364) * 2004-02 - * Publication of an alanine scanning protocol in Rosetta [Kortemme et al.](http://stke.sciencemag.org/cgi/content/full/sigtrans;2004/219/pl2) - * The [Robetta alanine scanning server](http://robetta.bakerlab.org/alascansubmit.jsp) goes online. + * Publication of an alanine scanning protocol in Rosetta [Kortemme et al.](https://doi.org/10.1126/stke.2192004pl2) + * The [Robetta alanine scanning server](http://old.robetta.org/) goes online. * 2005-06 * [Rosetta@Home](http://en.wikipedia.org/wiki/Rosetta@home) was launched. @@ -154,4 +154,4 @@ History History History History ----> \ No newline at end of file +---> diff --git a/rosetta_basics/Glossary/Glossary.md b/rosetta_basics/Glossary/Glossary.md index 531f73225..ff9980bbd 100644 --- a/rosetta_basics/Glossary/Glossary.md +++ b/rosetta_basics/Glossary/Glossary.md @@ -75,7 +75,7 @@ _Critical Assessment of PRediction of Interactions (CAPRI)_ | Protein-protein in _Critical Assessment of Techniques for Protein Structure Prediction (CASP)_ | [The Critical Assessment of protein Structure Prediction](http://predictioncenter.org/) (CASP) experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused. CASP has been held every two years starting in 1994. Rosetta has participated in several CASP experiments. _crystal neighbors_ | Is crystal structure a so called native structure? Crystal is composed of approximately 40\~70% of water molecules, which gives crystallographers confidence saying proteins in crystal lattice should be able to represent proteins in biological environments, especially when proteins in crystal lattice often times are able to undergo biological reactions they are capable of in cells. However, there is an inevitable artifact in crystal lattice - that is regions where proteins adjacent to each other, making so called crystal contacts. Conformations in regions where proteins have contacts somehow are altered to some extent. Rosetta sometimes is able to sample conformations where the RMSD are 3 or 4 A away from "native crystal structure" but have lower energies, which are the results from variations of a section of loop. And this loop region happens to locate at the spot where crystal contact occurs. Therefore, we now are thinking about our definition of "native structure", where native structure is supposed to be the conformation of the protein exists in cell. _crystallographic phasing_ | The critical step of solving a crystal structure is to get the phase either via molecular replacement or experimental methods. The technically easier way to get the phase is by the method of molecular replacement, where crystallographers utilize existing structures with high structural similarities to help guide the search of phase. However, in some hard cases, where there is no structurally similar structures exist, or structures have too low sequence identities (below 15\~20%), crystallographers then have to get the phase through experimental methods, which are much more tedious and difficult compared to molecular replacement method. Rosetta can generate or refine models using physically realistic full-atom force field, which sometimes can generate more accurate comparative models. For some of those hard cases, Rosetta therefore is able to provide better initial search models for molecular replace to find the solutions. ref: Qian et. al. High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259-264 (2007) -_CxxTest_ | This is the framework we use for [[unit tests]]. See also [[http://cxxtest.com]]. +_CxxTest_ | This is the framework we use for [[unit tests]]. See also . -------------------------- @@ -369,4 +369,4 @@ _XML_ | A hierachical data format, a custom version is used by RosettaScripts * [[Rosetta overview]]: Overview of major concepts in Rosetta * [[Resources for learning biophysics and computational modeling]] * [[Rosetta Timeline]]: History of Rosetta -* [[Units in Rosetta]]: Explains measurement units used in Rosetta \ No newline at end of file +* [[Units in Rosetta]]: Explains measurement units used in Rosetta diff --git a/rosetta_basics/PyMOL.md b/rosetta_basics/PyMOL.md index 28ba96bdb..2a96fe4d3 100644 --- a/rosetta_basics/PyMOL.md +++ b/rosetta_basics/PyMOL.md @@ -8,7 +8,7 @@ The [PyMOL Wiki](http://www.pymolwiki.org/index.php/Main_Page) contains documentation on the program methods and numerous examples. Beginners should start [with this tutorial](http://www.pymolwiki.org/index.php/Practical_Pymol_for_Beginners). -A simple [workshop](http://pyrosetta.org/tutorial.html) is part of the +A simple [workshop](https://www.pyrosetta.org/documentation/tutorials) is part of the [PyRosetta](/index.php/PyRosetta "PyRosetta") tutorials. If you are building PyMOL from source on Linux (this does not take long @@ -206,4 +206,4 @@ So long as you are using this freshly-built pymol, it will work with Rosetta nor * [[Comparing structures]]: Essay on comparing structures * [[Extending the PyMol Viewer]]: How to add new functionality to Rosetta's PyMOL Mover * [[PyRosetta Toolkit]]: Tutorials for using/modifying the PyRosetta Toolkit GUI -* [[PyRosetta Toolkit GUI]]: Information on the PyRosetta Toolkit user interface \ No newline at end of file +* [[PyRosetta Toolkit GUI]]: Information on the PyRosetta Toolkit user interface diff --git a/rosetta_basics/Rosetta-Basics.md b/rosetta_basics/Rosetta-Basics.md index 9252c6027..d16f31e0c 100644 --- a/rosetta_basics/Rosetta-Basics.md +++ b/rosetta_basics/Rosetta-Basics.md @@ -108,8 +108,9 @@ - [[Analyzing results]] ####Help -- [RosettaCommons Forums](http://rosettacommons.org/forum) -- [RosettaCommons Bug Tracker](http://bugs.rosettacommons.org) +- [Rosetta Discussions](https://github.com/RosettaCommons/rosetta/discussions) +- [Old RosettaCommons Forums (read only)](http://rosettacommons.org/forum) +- [Rosetta Issue Tracker](https://github.com/RosettaCommons/rosetta/issues) ##See Also diff --git a/rosetta_basics/RosettaEncyclopedia.md b/rosetta_basics/RosettaEncyclopedia.md index 755d984e5..27e2c6687 100644 --- a/rosetta_basics/RosettaEncyclopedia.md +++ b/rosetta_basics/RosettaEncyclopedia.md @@ -111,7 +111,7 @@ The low-resolution mode in Rosetta is often dubbed Centroid Mode, since the side #### Fullatom Model -In the all-atom representation of ROSETA every atom is explicitly represented. What is notable is that proton-names are quite different from what is used in the NMR community (http://www.bmrb.wisc.edu/referenc/nomenclature/). There are two main differences: a) if only 2 protons are present on an sp3 hybridized carbon Rosetta numbers them 1, 2 whereas the NMR community numbers them 2, 3. b) Rosetta puts the number that differentiates between protons bound to the same carbon in front of the atom name whereas the NMR community puts this number at the very end of the atom name. The reminder of the atom name is usually obtained by taking the name of the carbon and replacing C->H. CD1 –> nHD1, whereas n=1,2,3 is the id-number of the proton. +In the all-atom representation of ROSETA every atom is explicitly represented. What is notable is that proton-names are quite different from what is used in the NMR community (). There are two main differences: a) if only 2 protons are present on an sp3 hybridized carbon Rosetta numbers them 1, 2 whereas the NMR community numbers them 2, 3. b) Rosetta puts the number that differentiates between protons bound to the same carbon in front of the atom name whereas the NMR community puts this number at the very end of the atom name. The reminder of the atom name is usually obtained by taking the name of the carbon and replacing C->H. CD1 –> nHD1, whereas n=1,2,3 is the id-number of the proton. NMR Rosetta diff --git a/rosetta_basics/file_types/chemical-shift-file.md b/rosetta_basics/file_types/chemical-shift-file.md index 4435f5e07..26e866882 100644 --- a/rosetta_basics/file_types/chemical-shift-file.md +++ b/rosetta_basics/file_types/chemical-shift-file.md @@ -54,7 +54,6 @@ Chemical shift input : * [[File types list]]: List of file types used in Rosetta * [[CS-Rosetta wiki page|CS-Rosetta]] -* [[Official CS-Rosetta website (external link)|http://csrosetta.chemistry.ucsc.edu/]] * [[Additional CS-Rosetta information (external link)|http://spin.niddk.nih.gov/bax/software/CSROSETTA/]] * [[CS Rosetta RNA]]: RNA modeling application that uses chemical shift data * [[Rosetta Basics]]: The Rosetta Basics home page @@ -62,4 +61,4 @@ Chemical shift input : * [[Glossary]]: Brief definitions of Rosetta terms * [[RosettaEncyclopedia]]: Detailed descriptions of additional concepts in Rosetta. * [[Rosetta overview]]: Overview of major concepts in Rosetta -* [[Application Documentation]]: Links to documentation for a variety of Rosetta applications \ No newline at end of file +* [[Application Documentation]]: Links to documentation for a variety of Rosetta applications diff --git a/rosetta_basics/file_types/sql/Database-IO.md b/rosetta_basics/file_types/sql/Database-IO.md index dd8e56dba..5d92cd043 100644 --- a/rosetta_basics/file_types/sql/Database-IO.md +++ b/rosetta_basics/file_types/sql/Database-IO.md @@ -4,7 +4,7 @@ Database Drivers ---------------- -Rosetta has support for interacting with SQLite3, MySQL and PostgreSQL database backends. This page describes the backends, how to get started using them, and what has already been done. The SQLite3 backend is tested extensively in the *integration\_tests* with every commit, and the PostgreSQL and MySQL support is tested through the BuildBot framework ( [PostgreSQL](http://buildbot.graylab.jhu.edu:8010/builders/UNC.Mac.PostgreSQL.tests) , MySQL). +Rosetta has support for interacting with SQLite3, MySQL and PostgreSQL database backends. This page describes the backends, how to get started using them, and what has already been done. The SQLite3 backend is tested extensively in the *integration\_tests* with every commit, and the PostgreSQL and MySQL support is tested through the [Rosetta test server](https://benchmark.graylab.jhu.edu/). - **SQLite3** - [SQLite3](http://www.sqlite.org/) is a light-weight database engine that stores each database as a file in the filesystem, and is optimized for single connections to database stored on a local drive. diff --git a/rosetta_basics/fixing-errors.md b/rosetta_basics/fixing-errors.md index fc7a1bc7b..b25d9993b 100644 --- a/rosetta_basics/fixing-errors.md +++ b/rosetta_basics/fixing-errors.md @@ -80,11 +80,11 @@ Segmentation faults (segfaults) are one of the hardest errors to debug. They're Do check that all your inputs are correct and that there aren't any obvious errors in your configuration. Also, the extra error checking in debug mode (e.g. relax.linuxgccdebug) can often change a segfault into an assertion error. Often though, figuring out the cause of a segfault requires running Rosetta under a debugger and developer attention. -Take heart, though. Ideally, Rosetta should never result in a segfault. At the very least the developer should have done error checking and printed out an interpretable error message. If you encounter a segfault, please submit a bug report to either the Rosetta bug tracker or to the Rosetta forums . +Take heart, though. Ideally, Rosetta should never result in a segfault. At the very least the developer should have done error checking and printed out an interpretable error message. If you encounter a segfault, please submit a bug report to either the Rosetta issue tracker or to the Rosetta disscussion form . ##See Also * [[Running Rosetta with options]] * [[MPI]]: Information about running Rosetta in MPI mode -* [[Troubleshooting Rosetta development|Common errors]] \ No newline at end of file +* [[Troubleshooting Rosetta development|Common errors]] diff --git a/rosetta_basics/graphics-and-guis.md b/rosetta_basics/graphics-and-guis.md index 06399fec5..3b1aff6b0 100644 --- a/rosetta_basics/graphics-and-guis.md +++ b/rosetta_basics/graphics-and-guis.md @@ -30,7 +30,7 @@ which will prime your PyMol session to receive and display the coordinates sent [[See RosettaScripts Documentation | Movers-RosettaScripts#PyMolMover]] ####PyRosetta -[See PyRosetta Documentation](http://www.pyrosetta.org/tutorials#TOC-PyMOL_Mover) +[See PyRosetta/PyMOL Documentation](https://www.pyrosetta.org/documentation/pymol_mover-tutorial) ####Command Line diff --git a/rosetta_basics/scoring/MHCEpitopeEnergy.md b/rosetta_basics/scoring/MHCEpitopeEnergy.md index 45365ed55..dd4ceea5c 100644 --- a/rosetta_basics/scoring/MHCEpitopeEnergy.md +++ b/rosetta_basics/scoring/MHCEpitopeEnergy.md @@ -223,7 +223,7 @@ Once you have a PSSM (or other way of determining what sequences to look at), yo Note that you will probably want to use this in the "constraint" mode to look at the hotspot regions in your protein, as making a database to cover the entire protein sequence is likely prohibitively expensive. To cover non-hotspot regions, the Propred matrices are probably sufficient to ensure that the immunogenicity stays low. -Assuming you want to use NetMHCII as your predictor, you will first need to download and install NetMHCII (http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCII), and set the environment variable ```NMHOME``` to the location of the NetMHCII binary. +Assuming you want to use NetMHCII as your predictor, you will first need to download and install NetMHCII (https://services.healthtech.dtu.dk/services/NetMHCII-2.3/), and set the environment variable ```NMHOME``` to the location of the NetMHCII binary. Especially when using a PSSM, you need to be very careful to avoid a combinatorial explosion of peptides to process. Consider the following advice: @@ -339,4 +339,4 @@ custom_scorefxn.set_weight(pyrosetta.rosetta.core.scoring.score_type_from_name(" * [[Scoring explained]] * [[Score functions and score types |score-types]] * [[Adding a new energy method to Rosetta|new-energy-method]] -* [[Design-centric guidance terms|design-guidance-terms]] \ No newline at end of file +* [[Design-centric guidance terms|design-guidance-terms]] diff --git a/scripting_documentation/PyRosetta/PyRosetta-Toolkit-GUI.md b/scripting_documentation/PyRosetta/PyRosetta-Toolkit-GUI.md index d3dffc592..91b54f7e9 100644 --- a/scripting_documentation/PyRosetta/PyRosetta-Toolkit-GUI.md +++ b/scripting_documentation/PyRosetta/PyRosetta-Toolkit-GUI.md @@ -26,7 +26,7 @@ PyRosetta Setup: Optional PyMOL Integration Setup: -- See [http://www.pyrosetta.org/pymol\_mover-tutorial](http://www.pyrosetta.org/pymol_mover-tutorial) +- See Optional SCWRL Integration Setup: @@ -225,7 +225,6 @@ Tips - -Set default Scorefunction through the scorefunction window - Used by all protocols. - -Save and Load GUI Sessions using the file menu - -Advanced Users: To add personal windows and functions to the GUI, see developer html in pyrosetta\_toolkit/documentation directory. -- Please visit [http://bugs.rosettacommons.org](http://bugs.rosettacommons.org) for any Toolkit-specific bugs ### Bashrc Setup diff --git a/scripting_documentation/PyRosetta/PyRosetta-Toolkit.md b/scripting_documentation/PyRosetta/PyRosetta-Toolkit.md index 92efcccd7..c81ff8faf 100644 --- a/scripting_documentation/PyRosetta/PyRosetta-Toolkit.md +++ b/scripting_documentation/PyRosetta/PyRosetta-Toolkit.md @@ -25,7 +25,7 @@ Copy the code from pyrosetta/SetPyRosettaEnvironment.sh to your .bashrc (linux) **Setup PyMOL.** -There is an awesome file you can put in your $HOME directory called .pymolrc . There is a file: [PyMOLPyRosettaServer.py](http://www.pyrosetta.org/pymol_mover-tutorial) . Add this command to your .pymolrc 'run path\_to\_pyrosetta/PyMOLPyRosettaServer.py' This enables the connection to run every time you open PyMOL, and the GUI is heavily integrated to use this awesome PyRosetta feature. +There is an awesome file you can put in your $HOME directory called .pymolrc . There is a file: [PyMOLPyRosettaServer.py](http://www.pyrosetta.org/documentation/pymol_mover-tutorial) . Add this command to your .pymolrc 'run path\_to\_pyrosetta/PyMOLPyRosettaServer.py' This enables the connection to run every time you open PyMOL, and the GUI is heavily integrated to use this awesome PyRosetta feature. **Run the GUI.** @@ -290,4 +290,4 @@ Adding to the code * [[PyMOL]]: More information on PyMOL * [[Extending the PyMol Viewer]]: How to add new functionality to Rosetta's PyMOL Mover * [[PyRosetta website (external)|http://www.pyrosetta.org]] -* [[Graphics and GUIs]]: Home page for graphical interfaces with Rosetta \ No newline at end of file +* [[Graphics and GUIs]]: Home page for graphical interfaces with Rosetta diff --git a/scripting_documentation/PyRosetta/PyRosetta.md b/scripting_documentation/PyRosetta/PyRosetta.md index 7408597a4..7de4d0e37 100644 --- a/scripting_documentation/PyRosetta/PyRosetta.md +++ b/scripting_documentation/PyRosetta/PyRosetta.md @@ -87,10 +87,10 @@ Rosetta developers creating new PyRosetta applications should place any public a More extensive PyRosetta-specific documentation is available: * - The main PyRosetta documentation page (thorough, but not too helpful for beginners) * - Frequently asked questions about PyRosetta -* - Tutorials on how to use PyRosetta (**best to dive in here**) -* - Example scripts using PyRosetta (somewhat useful) +* - Tutorials on how to use PyRosetta (**best to dive in here**) +* - Example scripts using PyRosetta (somewhat useful) * - Brief, general overview of PyRosetta -* - Link to download PyRosetta, installation instructions at the bottom of page. +* - Link to download PyRosetta, installation instructions at the bottom of page. A general overview of the general Rosetta object structure and organization can be found here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083816/ @@ -106,4 +106,4 @@ Note that currently, the PyRosetta Toolkit and other published apps are only dis * [[PyRosetta Toolkit Tutorial | PyRosetta Toolkit]]: Tutorials for using/modifying the PyRosetta Toolkit GUI * [[PyMOL]]: More information on PyMOL * [[Extending the PyMol Viewer]]: How to add new functionality to Rosetta's PyMOL Mover -* [[PyRosetta website (external)|http://www.pyrosetta.org]] \ No newline at end of file +* [[PyRosetta website (external)|http://www.pyrosetta.org]] diff --git a/scripting_documentation/PyRosetta/PyTXMS.md b/scripting_documentation/PyRosetta/PyTXMS.md index e72e0bdf0..3accfad38 100644 --- a/scripting_documentation/PyRosetta/PyTXMS.md +++ b/scripting_documentation/PyRosetta/PyTXMS.md @@ -55,7 +55,7 @@ To convert data between different MS versions (RAW to mzML or mzML to mgf), tool * OpenMS -http://www.openms.de/downloads/ +http://www.openms.de/ * Dinosaur and Taxlink @@ -133,4 +133,4 @@ Here is the list of expected outputs. Clearly, some of them are not produced acc * List of all selected XLs in a .txt file. ## Post Processing -Selected XLs can be validated one more step with DIA analysis approach -provided in the reference TX-MS main protocol- and be used again for modeling purpose. However, it is only necessary if few information is obtained and selected spectra would not be reliable. \ No newline at end of file +Selected XLs can be validated one more step with DIA analysis approach -provided in the reference TX-MS main protocol- and be used again for modeling purpose. However, it is only necessary if few information is obtained and selected spectra would not be reliable. diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/FeaturesDatabaseSchema.md b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/FeaturesDatabaseSchema.md index 836468aa3..e60f1785d 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/FeaturesDatabaseSchema.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/FeaturesDatabaseSchema.md @@ -165,7 +165,7 @@ GeometricSolvationFeatures HBondFeatures ------------- -The HBondFeatures (rosetta/main/source/src/protocols/features/HBondFeatures.hh) measures the geometry of hydrogen bonds. The most current reference is [Tanja Kortemme, Alexandre V. Morozov, David Baker, An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes, (JMB 2003)](http://www.sciencedirect.com/science/article/B6WK7-47WBSCV-T/2/d7c673dd51017848231e7b9e8c05fbca) . +The HBondFeatures (rosetta/main/source/src/protocols/features/HBondFeatures.hh) measures the geometry of hydrogen bonds. The most current reference is [Tanja Kortemme, Alexandre V. Morozov, David Baker, An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes, (JMB 2003)](https://doi.org/10.1016/s0022-2836(03)00021-4) . The features associated with hydrogen bonding include @@ -897,7 +897,7 @@ A protocol is represented as all the information necessary to reproduce the resu RadiusOfGyrationFeatures ------------------------ -Measure the radius of gyration for each structure. The radius of gyration measure of how compact a structure is in O(n). It is the expected displacement of mass from the center of mass. The Wikipedia page is has some [information](http://en.wikipedia.org/wiki/Radius_of_gyration) . Also see, Lobanov MY, Bogatyreva NS, Galzitskaya OV. [Radius of gyration as an indicator of protein structure compactness](http://www.springerlink.com/content/v01q1r143528u261/) . Molecular Biology. 2008;42(4):623-628. +Measure the radius of gyration for each structure. The radius of gyration measure of how compact a structure is in O(n). It is the expected displacement of mass from the center of mass. The Wikipedia page is has some [information](http://en.wikipedia.org/wiki/Radius_of_gyration) . Also see, Lobanov MY, Bogatyreva NS, Galzitskaya OV. [Radius of gyration as an indicator of protein structure compactness](https://doi.org/10.1134/S0026893308040195) . Molecular Biology. 2008;42(4):623-628. - **radius\_of\_gyration** : - *radius\_of\_gyration* : Let *C* be the center of mass and *ri* be the position of residue *i'* th of *n* residues, then the radius of gyration is defined to be *Rg = SQRT{SUM\_{ri}(ri-C)\^2/(n-1)}* . Note: the normalizing factor is *n-1* to be consistent with r++. Atoms with variant type "REPLONLY" are ignored. diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/MultiBodyFeaturesReporters.md b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/MultiBodyFeaturesReporters.md index 8c3be177f..113b27fa2 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/MultiBodyFeaturesReporters.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/MultiBodyFeaturesReporters.md @@ -140,9 +140,9 @@ Part of the RosettaAntibody and RosettaAntibodyDesign (RAbD) Framework **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. +North B, Lehmann A, Dunbrack R, [A new clustering of antibody CDR loop conformations](https://pmc.ncbi.nlm.nih.gov/articles/PMC3065967/) (2011). JMB 406(2): 228-256. **Overview** @@ -491,7 +491,7 @@ The PoseConformationFeatures reporter measures the conformation level informatio **Overview** -Measure the radius of gyration for each structure. The radius of gyration measure of how compact a structure is in O(n). It is the expected displacement of mass from the center of mass. The Wikipedia page is has some [information](http://en.wikipedia.org/wiki/Radius_of_gyration) . Also see, Lobanov MY, Bogatyreva NS, Galzitskaya OV. [Radius of gyration as an indicator of protein structure compactness](http://www.springerlink.com/content/v01q1r143528u261/) . Molecular Biology. 2008;42(4):623-628. +Measure the radius of gyration for each structure. The radius of gyration measure of how compact a structure is in O(n). It is the expected displacement of mass from the center of mass. The Wikipedia page is has some [information](http://en.wikipedia.org/wiki/Radius_of_gyration) . Also see, Lobanov MY, Bogatyreva NS, Galzitskaya OV. [Radius of gyration as an indicator of protein structure compactness](https://doi.org/10.1134/S0026893308040195) . Molecular Biology. 2008;42(4):623-628. - **radius\_of\_gyration** : - *radius\_of\_gyration* : Let *C* be the center of mass and *ri* be the position of residue *i'* th of *n* residues, then the radius of gyration is defined to be *Rg = SQRT{SUM\_{ri}(ri-C)\^2/(n-1)}* . Note: the normalizing factor is *n-1* to be consistent with r++. Atoms with variant type "REPLONLY" are ignored. @@ -529,7 +529,7 @@ Report continuous segments of secondary structure. DSSP is used to define second **Overview** -Record a set of geometric parameters defined by two pieces of adjacent secondary structure. More information can be found here: [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000750](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000750) +Record a set of geometric parameters defined by two pieces of adjacent secondary structure. More information can be found here: **Tables** @@ -572,4 +572,4 @@ A structure is a group of spatially organized residues. The definition correspon protocol_id INTEGER, tag TEXT, UNIQUE (protocol_id, tag), - FOREIGN KEY (protocol_id) REFERENCES protocols (protocol_id) DEFERRABLE INITIALLY DEFERRED); \ No newline at end of file + FOREIGN KEY (protocol_id) REFERENCES protocols (protocol_id) DEFERRABLE INITIALLY DEFERRED); diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/TwoBodyFeaturesReporters.md b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/TwoBodyFeaturesReporters.md index aaa5916fa..a5762b9c8 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/TwoBodyFeaturesReporters.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/features_reporters/TwoBodyFeaturesReporters.md @@ -104,7 +104,7 @@ The ProteinBackboneAtomAtomPairFeatures reporter measures all the atom pair dist HBondFeatures ------------- -The HBondFeatures reporter measures the geometry of hydrogen bonds. The most current reference is [Tanja Kortemme, Alexandre V. Morozov, David Baker, An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes, (JMB 2003)](http://www.sciencedirect.com/science/article/B6WK7-47WBSCV-T/2/d7c673dd51017848231e7b9e8c05fbca) . +The HBondFeatures reporter measures the geometry of hydrogen bonds. The most current reference is [Tanja Kortemme, Alexandre V. Morozov, David Baker, An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes, (JMB 2003)](https://doi.org/10.1016/s0022-2836(03)00021-4) . The HBondFeatures feature reporter takes the following options: diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/FeaturesSettingUpR.md b/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/FeaturesSettingUpR.md index 2ca4761d2..153d88142 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/FeaturesSettingUpR.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/rscripts/FeaturesSettingUpR.md @@ -7,7 +7,7 @@ The Features Scientific Benchmark requires R version 2.11 or higher. > install.packages("package_name") - Alternatively to install everything from source see below. For more information see the [R Installation and Administration](http://cran.r-project.org/doc/manuals/R-admin.html) page or the [Comprehensive R Archive Network](http://cran.fhcrc.org/) . + Alternatively to install everything from source see below. For more information see the [R Installation and Administration](http://cran.r-project.org/doc/manuals/R-admin.html) page or the [Comprehensive R Archive Network](https://cran.r-project.org/) . cd /tmp wget http://mirrors.ibiblio.org/pub/mirrors/CRAN/src/base/R-2/R-2.12.1.tar.gz @@ -91,4 +91,4 @@ I have been enjoying using [RStudio](http://www.rstudio.org/) to do data analysi * [[Rosetta Database Output Tutorial]] * [[SQLite3 Interface]]: Specific information on using SQLite3 with Rosetta * [[Database support]]: Advanced details on Rosetta's interface with databases -* [[Database options]]: Database-related command line options \ No newline at end of file +* [[Database options]]: Database-related command line options diff --git a/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md b/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md index 120d4fb0a..4748463d1 100644 --- a/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md +++ b/scripting_documentation/RosettaScripts/FeaturesReporter/tutorials/FeaturesTutorialRunSciBench.md @@ -228,7 +228,7 @@ The features scientific benchmark can be run locally or on a MPI-based cluster. - **Feature Extraction** : Computational cost and space requirements for extracting features depends upon which *FeaturesReporters* are used. The default features for the *top8000* sample source use \~1Mb per structure. - **Feature Analysis** : Each feature analysis script makes a database query and then preforms the analysis. depending on how efficiently the database can be accessed and the complexity of the feature analysis and plot generation, each analysis usually takes between a minute or two to tens of minutes. -- **Batch Generation** : Prediction protocols to generate batches of structures are usually very computationally intensive, ranging from hundreds to thousands of CPU hours. Das and Baker have a nice [review](http://depts.washington.edu/bakerpg/drupal/system/files/das08A_0.pdf) of the Rosetta prediction protocols. Consult the documentation for specific protocol for more information. +- **Batch Generation** : Prediction protocols to generate batches of structures are usually very computationally intensive, ranging from hundreds to thousands of CPU hours. Das and Baker have a nice [review](https://doi.org/10.1146/annurev.biochem.77.062906.171838) of the Rosetta prediction protocols. Consult the documentation for specific protocol for more information. Batch Requirements @@ -263,4 +263,4 @@ The features scientific benchmark supports **single-threaded** , **MPI** and **C * [[Rosetta Database Output Tutorial]] * [[Database support]]: Advanced details on Rosetta's interface with databases * [[Database options]]: Database-related command line options -* [[I want to do x]]: Guide to choosing a mover \ No newline at end of file +* [[I want to do x]]: Guide to choosing a mover diff --git a/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubDDMover.md b/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubDDMover.md index 4d5944cdf..66b451061 100644 --- a/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubDDMover.md +++ b/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubDDMover.md @@ -25,5 +25,4 @@ Note: As of June 29, 2011, this mover was renamed from "Backrub" to "BackrubDD". * [[BackrubMover]]: Backrub-style backbone movements * [[Backrub]]: The backrub application -* [[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 * [[I want to do x]]: Guide to choosing a mover diff --git a/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubMover.md b/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubMover.md index 808d514d2..aef22bfa1 100644 --- a/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubMover.md +++ b/scripting_documentation/RosettaScripts/Movers/movers_pages/BackrubMover.md @@ -25,5 +25,4 @@ Purely local moves using rotations around axes defined by two backbone atoms. * [[BackrubDDMover]]: Backrub-style backbone and sidechain sampling * [[Backrub]]: The backrub application -* [[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 * [[I want to do x]]: Guide to choosing a mover diff --git a/scripting_documentation/RosettaScripts/Movers/movers_pages/DockingInitialPerturbationMover.md b/scripting_documentation/RosettaScripts/Movers/movers_pages/DockingInitialPerturbationMover.md index 9dcfea26e..822a6c8c7 100644 --- a/scripting_documentation/RosettaScripts/Movers/movers_pages/DockingInitialPerturbationMover.md +++ b/scripting_documentation/RosettaScripts/Movers/movers_pages/DockingInitialPerturbationMover.md @@ -7,8 +7,6 @@ This contains the functions that create initial positions for docking. You can either randomize partner 1 or partner 2, spin partner 2, or perform a simple perturbation. -Most of these options are also described [[here|https://www.rosettacommons.org/manuals/rosetta3.1_user_guide/opt_docking.html]]. - ```xml ``` @@ -34,4 +32,4 @@ Most of these options are also described [[here|https://www.rosettacommons.org/m * [[FlexPepDockMover]] * [[HighResDockerMover]] * [[Docking applications]]: Command line applications for docking -* [[I want to do x]]: Choosing a mover \ No newline at end of file +* [[I want to do x]]: Choosing a mover diff --git a/scripting_documentation/RosettaScripts/Movers/movers_pages/SetupPoissonBoltzmannPotentialMover.md b/scripting_documentation/RosettaScripts/Movers/movers_pages/SetupPoissonBoltzmannPotentialMover.md index bb96f46f0..055965231 100644 --- a/scripting_documentation/RosettaScripts/Movers/movers_pages/SetupPoissonBoltzmannPotentialMover.md +++ b/scripting_documentation/RosettaScripts/Movers/movers_pages/SetupPoissonBoltzmannPotentialMover.md @@ -8,7 +8,7 @@ Currently the feature is only supported by the **ddG** mover and filter. **[ Prerequisites ]** -- Build the customized version of [APBS](http://www.poissonboltzmann.org/apbs) and [iAPBS](http://mccammon.ucsd.edu/iapbs) , according to the instructions found in /path/to/rosetta/rosetta\_source/external/apbs/apbs-1.4-rosetta/README. +- Build the customized version of [APBS](http://www.poissonboltzmann.org) and [iAPBS](http://mccammon.ucsd.edu/iapbs) , according to the instructions found in /path/to/rosetta/rosetta\_source/external/apbs/apbs-1.4-rosetta/README. @@ -85,4 +85,4 @@ The default values are "bound" and "unbound", respectively. ##See Also * [[ddGMover]]: Supports the Poisson-Boltzmann energy method -* [[I want to do x]]: Guide to choosing a mover \ No newline at end of file +* [[I want to do x]]: Guide to choosing a mover diff --git a/scripting_documentation/RosettaScripts/RosettaScripts-Conventions.md b/scripting_documentation/RosettaScripts/RosettaScripts-Conventions.md index c3c85797b..6621f210e 100644 --- a/scripting_documentation/RosettaScripts/RosettaScripts-Conventions.md +++ b/scripting_documentation/RosettaScripts/RosettaScripts-Conventions.md @@ -70,7 +70,6 @@ OR ##See Also -* [[RosettaDiagrams (external link)|http://www.rosettadiagrams.org/]]: Provides a graphical interactive service to produce RosettaScripts XML files, with some ability to run the scripts as well. * [[RosettaScripts]]: The RosettaScripts home page * [[RosettaScripts Movers|Movers-RosettaScripts]] * [[RosettaScripts Filters|Filters-RosettaScripts]] @@ -78,4 +77,4 @@ OR * [[I want to do x]]: Guide for making specific structural perturbations using RosettaScripts * [[Scripting Documentation]]: The Scripting Documentation home page * [[Solving a Biological Problem]]: Guide to approaching biological problems using Rosetta -* [[Getting Started]]: A page for people new to Rosetta \ No newline at end of file +* [[Getting Started]]: A page for people new to Rosetta diff --git a/scripting_documentation/RosettaScripts/RosettaScripts-database-connection-options.md b/scripting_documentation/RosettaScripts/RosettaScripts-database-connection-options.md index aa4b6afc5..51e59be69 100644 --- a/scripting_documentation/RosettaScripts/RosettaScripts-database-connection-options.md +++ b/scripting_documentation/RosettaScripts/RosettaScripts-database-connection-options.md @@ -24,7 +24,7 @@ Sqlite3 Specific Options ------------------------ - **database\_name** : The path and filename of the sqlite3 database. Usually it has a *.db3* extension. -- **database\_separate\_db\_per\_mpi\_process** : Append to the end of the database filename *\_\* . This is useful, for example in writing out separate database in parallel and then merging them together afterwards [(See main/tests/features/sample\_sources/merge.sh)](https://github.com/RosettaCommons/main/blob/master/tests/features/sample_sources/merge.sh) . +- **database\_separate\_db\_per\_mpi\_process** : Append to the end of the database filename *\_\* . This is useful, for example in writing out separate database in parallel and then merging them together afterwards [(See main/tests/features/sample\_sources/merge.sh)](https://github.com/RosettaCommons/rosetta/blob/main/tests/features/sample_sources/merge.sh) . - **database\_readonly** : Open the database file so it cannot be modified. PostgreSQL Specific Options diff --git a/scripting_documentation/RosettaScripts/RosettaScripts.md b/scripting_documentation/RosettaScripts/RosettaScripts.md index 8162b50ea..7a028857b 100644 --- a/scripting_documentation/RosettaScripts/RosettaScripts.md +++ b/scripting_documentation/RosettaScripts/RosettaScripts.md @@ -898,7 +898,6 @@ Another good troubleshooting tool is to simplify your XML. Try creating a stripp * [Introductory RosettaScripting Tutorial](https://www.rosettacommons.org/demos/latest/tutorials/scripting_with_rosettascripts/scripting_with_rosettascripts) * [Advanced RosettaScripting Tutorial](https://www.rosettacommons.org/demos/latest/tutorials/advanced_scripting_with_rosettascripts/advanced_scripting_with_rosettascripts) -* [[RosettaDiagrams (external link)|http://www.rosettadiagrams.org/]]: Provides a graphical interactive service to produce RosettaScripts XML files, with some ability to run the scripts as well. * [[I want to do x]]: Guide for making specific structural perturbations using RosettaScripts * [[Scripting Documentation]]: The Scripting Documentation home page * [[Solving a Biological Problem]]: Guide to approaching biological problems using Rosetta @@ -910,4 +909,4 @@ Another good troubleshooting tool is to simplify your XML. Try creating a stripp \ No newline at end of file +--> diff --git a/scripting_documentation/RosettaScripts/composite_protocols/fold_from_loops/FunFolDes.md b/scripting_documentation/RosettaScripts/composite_protocols/fold_from_loops/FunFolDes.md index 2e578eba6..e1d272a38 100644 --- a/scripting_documentation/RosettaScripts/composite_protocols/fold_from_loops/FunFolDes.md +++ b/scripting_documentation/RosettaScripts/composite_protocols/fold_from_loops/FunFolDes.md @@ -60,7 +60,7 @@ The **FunFolDes** protocol adds several remarks to the silent file output in ord # Main Components -* **[[NubInitioMover]]:** _[nub](https://en.oxforddictionaries.com/definition/nub) inito_ refers to the _ab initio_ process around a central point of a protein; in this case, the **motif**. This process is the key differentiating element of the **FunFolDes** protocol, and this mover is its main component. The Mover is assigned with the tasks of (a) obtaining the **motif** from the structure source, (b) unfolding the **template** and attach it to the **motif**'s edges, (c) fold the new structure and (d) evaluate the viability of the obtained folded protein to move forward through the process. +* **[[NubInitioMover]]:** _[nub](https://en.wiktionary.org/wiki/nub) inito_ refers to the _ab initio_ process around a central point of a protein; in this case, the **motif**. This process is the key differentiating element of the **FunFolDes** protocol, and this mover is its main component. The Mover is assigned with the tasks of (a) obtaining the **motif** from the structure source, (b) unfolding the **template** and attach it to the **motif**'s edges, (c) fold the new structure and (d) evaluate the viability of the obtained folded protein to move forward through the process. * **[[NubInitioLoopClosureMover]]:** When working with multi-segment **motif**s, this mover is able to ensure a final closed structure without affecting residues from the **motif** in any unexpected way. Ideally, this should be the last mover to call before the evaluation part of the _script_. Closing the cutpoints in the structure before any backbone movement will most likely result in changes between the correlative positions of the different segments of the **motif**. The mover is "smart" enough to evaluate if it is needed. Thus, it is highly recommended to always add it and let it decide whether or not it has to try to close any chain break. # Pipelines @@ -69,4 +69,4 @@ The **FunFolDes** protocol adds several remarks to the silent file output in ord * [[Reloading FunFolDes runs to further design/analyse|ReloadingFunFolDes]] # Documentation history: -* Written by Jaume Bonet. **March 2018**. \ No newline at end of file +* Written by Jaume Bonet. **March 2018**. diff --git a/scripting_documentation/RosettaScripts/composite_protocols/sewing/Segment-File-Generation.md b/scripting_documentation/RosettaScripts/composite_protocols/sewing/Segment-File-Generation.md index ca3bbad8c..98d59f490 100644 --- a/scripting_documentation/RosettaScripts/composite_protocols/sewing/Segment-File-Generation.md +++ b/scripting_documentation/RosettaScripts/composite_protocols/sewing/Segment-File-Generation.md @@ -14,7 +14,7 @@ The following DSSP codes are allowed: ```H``` (helix), ```L``` (loop), ```E``` ( ---------------------- ###Using the segment_file_generator app -The segment_file_generator app requires two command line arguments: ```motif_file```(see above) and ```pdb_list_file```. The ```pdb_list_file``` is a text file listing the paths to pdb files, separated by a newline character. Structure files can be queried from the RCSB protein database, or from sources such as the Richardson Lab's [Top 8000 Database](http://kinemage.biochem.duke.edu/databases/top8000.php) or the Dunbrack Lab's [PISCES Server](http://dunbrack.fccc.edu/PISCES.php). +The segment_file_generator app requires two command line arguments: ```motif_file```(see above) and ```pdb_list_file```. The ```pdb_list_file``` is a text file listing the paths to pdb files, separated by a newline character. Structure files can be queried from the RCSB protein database, or from sources such as the Richardson Lab's [Top 8000 Database](http://kinemage.biochem.duke.edu/research/top8000/) or the Dunbrack Lab's [PISCES Server](http://dunbrack.fccc.edu/PISCES.php). The application also takes one optional argument, ```strict_dssp_changes``` (default true). **NOTE 07/26/2018: There is currently a bug in the application that causes it to fail unless this flag is set to false.** When ```strict_dssp_changes``` is true, single-residue secondary structure elements are not recognized, allowing (for example) kinked helices to be treated as a single element rather than multiple elements. @@ -38,4 +38,4 @@ cp smotifs_H_1_100_L_1_100_H_1_100.segments HLH_HLELH_combined_segment_file.segm ##See Also * [[SEWING]] The SEWING home page * [[SEWING Dictionary]] -* [[Model comparison with geometric hashing]] \ No newline at end of file +* [[Model comparison with geometric hashing]] diff --git a/static-wiki-templates/page.mustache b/static-wiki-templates/page.mustache index 550a3d26c..07368c712 100644 --- a/static-wiki-templates/page.mustache +++ b/static-wiki-templates/page.mustache @@ -7,7 +7,7 @@
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