Wikiomics:Crystallography toolbox: Difference between revisions
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==Data integration== | ==Data integration== | ||
* | * [http://www.hkl-xray.com/ denzo]) (from HKL) | ||
* | * [http://www.ccp4.ac.uk/ mosflm] (from ccp4) | ||
* | * [http://www.csb.yale.edu/userguides/datamanip/dtrek/dtrek_descrip.html d*TREK ] | ||
* | * [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) | ||
* | * [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) | ||
* | * [http://www.msg.ucsf.edu/local/programs/epmr/epmr.html EPMR] | ||
* | * [http://www.mbg.duth.gr/~glykos/Qs.html Queen of Spades] | ||
* | * [http://journals.iucr.org/j/issues/2002/05/00/vi0166/vi0166bdy.html COMPANG] | ||
* | * [http://russel.bioc.aecom.yu.edu/server/NYSGRC.html BRUTEPTF ] (phased molecular replacement) | ||
===Heavy atom methods=== | ===Heavy atom methods=== | ||
====Patterson methods==== | ====Patterson methods==== | ||
* | * [http://www.solve.lanl.gov/ SOLVE] | ||
* fft (from ccp4) | * fft (from ccp4) | ||
* xHercules (from | * xHercules (from [http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html xtalview]) | ||
====Direct and dual-space methods==== | ====Direct and dual-space methods==== | ||
* SHELX-D [ | * SHELX-D from [http://shelx.uni-ac.gwdg.de/SHELX/ shelex ] | ||
* | * [http://www.hwi.buffalo.edu/SnB/ Shake and Bake (SnB)] | ||
* Rantan (from ccp4) | * Rantan (from ccp4) | ||
====Ab initio methods==== | ====Ab initio methods==== | ||
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===Phase refinement=== | ===Phase refinement=== | ||
* | * [http://www.globalphasing.com/sharp/ SHARP/autoSHARP] SHARP suite | ||
* Mlphare, Vecref (from ccp4) | * Mlphare, Vecref (from ccp4) | ||
* | * [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 | ||
** | **[http://xray.bmc.uu.se/~alwyn/ O ](from Uppsala Software Factory) | ||
** | **[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 | ||
** | **[http://www.afmb.univ-mrs.fr/-TURBO- Turbo Frodo] | ||
==Model refinement== | ==Model refinement== | ||
* | * [http://cns.csb.yale.edu/ CNS] | ||
* refmac (from ccp4) | * refmac (from ccp4) | ||
* | * [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] | ||
* | * [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] | ||
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{{stub}} | {{stub}} | ||
[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]] |
Latest revision as of 04:26, 27 February 2008
Crystallography toolbox
Data processing
Data integration
Scaling
Phasing
Molecular replacement
- MolRep (from ccp4)
- Beast (from ccp4)
- AMoRe (from ccp4)
- Phaser (from ccp4)
- EPMR
- Queen of Spades
- COMPANG
- BRUTEPTF (phased molecular replacement)
Heavy atom methods
Patterson methods
Direct and dual-space methods
- SHELX-D from shelex
- Shake and Bake (SnB)
- Rantan (from ccp4)
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
- Automated model building
- Resolve
- ARP/wARP (from ccp4) http://www.embl-hamburg.de/ARP/
- Fffear, ffjoin (from ccp4)
- Interactive model building
- O (from Uppsala Software Factory)
- coot
- Quanta [1]
- Xtalview
- Turbo Frodo
Model refinement
Structure validation
Utilities
Credits
- Tina Bakolitsa wrote this list
- Darek Kedra translated it into wiki and added links