Difference between revisions of "Topics"

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'''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 ==
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--[[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 ===
 
* [[X-ray generators and detectors]] (experiences)
 
* [[Synchrotron beamlines]]
 
* [[Cryo]]
 
* [[Strategies]]
 
* [[Data quality]]
 
* [[Radiation damage]]
 
* [[Data collection: Tips and Tricks]]
 
 
 
== Crystallography ==
 
 
 
=== Theory ===
 
* [[Basics of Crystallography]]
 
* [[Phase problem]], and [[Phasing]]
 
* [[Twinning]]
 
* [[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]]
 
 
 
== See also ==
 
* [[Teaching crystallography]]
 
* [[Other crystallography links, or collections of links]]
 
* [[Other crystallography wikis]]
 

Latest revision as of 08:41, 5 March 2008

This page is now obsolete since it was creating before too much of hierarchy structure. Use the Navigation Panel in the Side Bar instead.

--3ND03P 09:40, 5 March 2008 (CET)