|
|
(7 intermediate revisions by 2 users not shown) |
Line 1: |
Line 1: |
| '''All existing articles and links are blue, whereas a red link corresponds to an article that does not yet exist - by clicking on the red link you start creating that article!''' | | '''This page is now obsolete since it was creating before too much of hierarchy structure. Use the Navigation Panel in the Side Bar instead.''' |
|
| |
|
| == Expression and Purification ==
| | --[[User:3ND03P|3ND03P]] 09:40, 5 March 2008 (CET) |
| * [[SLIC cloning]]
| |
| * [[Tags]]
| |
| * [[Expression systems]]
| |
| * [[Expression screening]]
| |
| * [[Purification]]
| |
| * [[Cleavage: wanted and unwanted]]
| |
| * [[DNA and DNA-binding proteins]]
| |
| * [[Expression and Purification: Tips and Tricks]]
| |
| | |
| == Crystals ==
| |
| | |
| === Crystal growth and manipulation ===
| |
| * [[Modifying the protein to crystallize better]]
| |
| * [[Crystallization screens and methods]]
| |
| * [[Robots for crystallization setup]]
| |
| * [[Biophysical methods]] for characterizing proteins and their crystals
| |
| * [[Visualization of crystal growth]]
| |
| * [[Robots for crystal mounting]]
| |
| * [[Crystal growth: Tips and Tricks]]
| |
| | |
| === Data collection ===
| |
| * [[Synchrotron beamlines]]
| |
| * [[Cryo]]
| |
| * [[Strategies]]
| |
| * [[Data quality]]
| |
| * [[Radiation damage]]
| |
| * [[Data collection: Tips and Tricks]]
| |
| | |
| == Crystallography ==
| |
| | |
| === Theory ===
| |
| * [[Basics of Crystallography]]
| |
| * [[Phase problem]], and [[Phasing]]
| |
| * [[R-factors]]
| |
| * [[References and links]]
| |
| | |
| === Programs ===
| |
| ==== by package ====
| |
| (large packages first)
| |
| * [[CCP4]]
| |
| * [[CNS]]
| |
| * [[PHENIX]]
| |
| * [[SHELX C/D/E/L]] (homepage at [http://shelx.uni-ac.gwdg.de/SHELX])
| |
| * moleman, lsqman, ... from [http://xray.bmc.uu.se/usf/ Uppsala Software Factory]
| |
| * XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds homepage] and [http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS XDSwiki]
| |
| * HKL [http://www.hkl-xray.com homepage]
| |
| * [[COOT]]
| |
| * [http://www.pymolwiki.org/index.php/Main_Page PyMol] wiki
| |
| * [[O]]
| |
| * [[ARP/wARP]]
| |
| * [[SHARP]] [http://www.globalphasing.com homepage]
| |
| * [http://www.solve.lanl.gov/index.html Solve/Resolve]
| |
| * ...
| |
| | |
| ==== by task ====
| |
| * [[Data reduction]]
| |
| * [[Molecular replacement]] (MR)
| |
| * [[Experimental phasing (SIR/MIR and SAD/MAD)]]
| |
| * [[Model building]]
| |
| * [[Refinement]]
| |
| * [[Model validation]]
| |
| * [[Solving a structure: Tips and Tricks]]
| |
| * [[Model building and refinement: Tricks and Tips]]
| |
| | |
| == Bioinformatics ==
| |
| * [[Servers and programs for sequence analysis]]
| |
| * [[Structure based sequence alignment]]
| |
| * [[Servers for structure analysis|Servers and programs for protein structure analysis]]
| |
| * [[Programs for nucleic acid structure analysis|Programs for nucleic acid structure analysis]]
| |
| * [[Servers for ligand topologies/parameters]]
| |
| * [[Prediction of structure from sequence: servers and programs]]
| |
| * [[Programs for visualization]] (see also [[Model building]])
| |
| * [[Links to Bioinformatics websites]]
| |
| | |
| == Hardware: computing and displaying ==
| |
| * [[Computer hardware]]
| |
| * [[Operating systems and Linux distributions]]
| |
| * [[Programming and programming languages]]
| |
| * [[Visualization: graphics cards and 3D|Graphics cards and 3D]]
| |
| | |
| == FAQ and troubleshooting ==
| |
| * [[Expression and Purification: Tips and Tricks|protein is not expressed or cannot be purified]]
| |
| * [[Crystal growth: Tips and Tricks|crystals don't grow]]
| |
| * [[Solving a structure: Tips and Tricks|phases too bad]]
| |
| * [[Model building and refinement: Tricks and Tips|model does not refine]]
| |