Difference between revisions of "Wikiomics:Crystallography toolbox"

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==Data integration==
 
==Data integration==
* denzo (from HKL [http://www.hkl-xray.com/])  
+
* [http://www.hkl-xray.com/ denzo]) (from HKL)
* mosflm (from ccp4 [http://www.ccp4.ac.uk/])  
+
* [http://www.ccp4.ac.uk/ mosflm] (from ccp4)  
* d*TREK [http://www.csb.yale.edu/userguides/datamanip/dtrek/dtrek_descrip.html]
+
* [http://www.csb.yale.edu/userguides/datamanip/dtrek/dtrek_descrip.html d*TREK ]
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/]
+
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ XDS]
  
 
===Scaling===
 
===Scaling===
 
* scalepack (from HKL)  
 
* scalepack (from HKL)  
* scala (from ccp4)  
+
* [http://www.ccp4.ac.uk/ scala] (from ccp4)  
 
* xprep (from xprep/Bruker)  
 
* xprep (from xprep/Bruker)  
* XSCALE [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html]
+
* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE]
  
 
==Phasing==
 
==Phasing==
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* AMoRe (from ccp4)  
 
* AMoRe (from ccp4)  
 
* Phaser (from ccp4)  
 
* Phaser (from ccp4)  
* EPMR [http://www.msg.ucsf.edu/local/programs/epmr/epmr.html]
+
* [http://www.msg.ucsf.edu/local/programs/epmr/epmr.html EPMR]
* Queen of Spades [http://www.mbg.duth.gr/~glykos/Qs.html]
+
* [http://www.mbg.duth.gr/~glykos/Qs.html Queen of Spades]
* COMPANG [http://journals.iucr.org/j/issues/2002/05/00/vi0166/vi0166bdy.html]
+
* [http://journals.iucr.org/j/issues/2002/05/00/vi0166/vi0166bdy.html COMPANG]
* BRUTEPTF (phased molecular replacement, http://russel.bioc.aecom.yu.edu/server/NYSGRC.html)  
+
* [http://russel.bioc.aecom.yu.edu/server/NYSGRC.html BRUTEPTF ] (phased molecular replacement)
  
 
===Heavy atom methods===
 
===Heavy atom methods===
 
====Patterson methods====  
 
====Patterson methods====  
* SOLVE [http://www.solve.lanl.gov/]
+
* [http://www.solve.lanl.gov/ SOLVE]
 
* fft (from ccp4)  
 
* fft (from ccp4)  
* xHercules (from xtalview [http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html])  
+
* xHercules (from [http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html xtalview])  
  
 
====Direct and dual-space methods====  
 
====Direct and dual-space methods====  
* SHELX-D [from shelex http://shelx.uni-ac.gwdg.de/SHELX/]
+
* SHELX-D [from shelex http://shelx.uni-ac.gwdg.de/SHELX/ shelex ]
* Shake and Bake (SnB) [http://www.hwi.buffalo.edu/SnB/]
+
* [http://www.hwi.buffalo.edu/SnB/ Shake and Bake (SnB)]
 
* Rantan (from ccp4)  
 
* Rantan (from ccp4)  
  
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===Phase refinement===
 
===Phase refinement===
* SHARP/autoSHARP (SHARP suite [http://www.globalphasing.com/sharp/])
+
* [http://www.globalphasing.com/sharp/ SHARP/autoSHARP] SHARP suite
 
* Mlphare, Vecref (from ccp4)  
 
* Mlphare, Vecref (from ccp4)  
* Resolve http://www.solve.lanl.gov/
+
* [http://www.solve.lanl.gov/ Resolve]
 
* SHELX-E  
 
* SHELX-E  
 
* DM (from ccp4)  
 
* DM (from ccp4)  
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**Fffear, ffjoin (from ccp4)  
 
**Fffear, ffjoin (from ccp4)  
 
* Interactive model building  
 
* Interactive model building  
**O (from Uppsala Software Factory) [http://xray.bmc.uu.se/~alwyn/]
+
**[http://xray.bmc.uu.se/~alwyn/ O ](from Uppsala Software Factory)
** coot [http://www.ysbl.york.ac.uk/~emsley/coot/
+
**[http://www.ysbl.york.ac.uk/~emsley/coot/ coot]
 
**Quanta [http://www.accelrys.com/products/quanta/]
 
**Quanta [http://www.accelrys.com/products/quanta/]
 
**Xtalview  
 
**Xtalview  
**Turbo Frodo [http://www.afmb.univ-mrs.fr/-TURBO-]
+
**[http://www.afmb.univ-mrs.fr/-TURBO- Turbo Frodo]
  
 
==Model refinement==
 
==Model refinement==
* CNS [http://cns.csb.yale.edu/]
+
* [http://cns.csb.yale.edu/ CNS]
 
* refmac (from ccp4)  
 
* refmac (from ccp4)  
* TNT [http://www.uoxray.uoregon.edu/tnt/]
+
* [http://www.uoxray.uoregon.edu/tnt/ TNT]
 
   
 
   
 
==Structure validation==
 
==Structure validation==
* Procheck [http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html]
+
* Procheck [http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html Procheck]
* WhatIf [http://www.sander.ebi.ac.uk/whatif/]
+
* [http://www.sander.ebi.ac.uk/whatif/ WhatIf]
  
 
==Utilities==
 
==Utilities==
 
* Uppsala Software Factory (USF) [http://alpha2.bmc.uu.se/usf/]
 
* Uppsala Software Factory (USF) [http://alpha2.bmc.uu.se/usf/]
* ccp4
+
* [http://www.ccp4.ac.uk/ ccp4]
  
  

Revision as of 12:32, 17 January 2008

Crystallography toolbox

Data processing

Data integration

Scaling

  • scalepack (from HKL)
  • scala (from ccp4)
  • xprep (from xprep/Bruker)
  • XSCALE

Phasing

Molecular replacement

Heavy atom methods

Patterson methods

Direct and dual-space methods

Ab initio methods

  • Acorn (from ccp4)
  • Oasis (from ccp4)

Phase refinement

  • SHARP/autoSHARP SHARP suite
  • Mlphare, Vecref (from ccp4)
  • Resolve
  • SHELX-E
  • DM (from ccp4)
  • Dmmulti (from ccp4)
  • SOLOMON (from ccp4)

Model building

Model refinement

Structure validation

Utilities

  • Uppsala Software Factory (USF) [2]
  • ccp4


Credits

Template:Credits

  • Tina Bakolitsa wrote this list
  • Darek Kedra translated it into wiki and added links