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start [2021/02/02 12:09]
shaikh
start [2021/02/19 09:56]
twagner
Line 1: Line 1:
 ===== SPHIRE Wiki ===== ===== SPHIRE Wiki =====
-<WRAP group> 
  
-<WRAP left 10%> +If you want to dig deep into the SPHIRE pipeline then you are in the right place. This Wiki will provide you with information about the major programs within SPHIRE and how to use them. Of course, you will also find information about installation, additional utilities, frequently asked questions and known issues. In addition, you can find usage tutorials and SPHIRE's version history. Just follow the links in the sidebar. 
-{{ wiki:logo.png?nolink&72}} + 
-</WRAP> +Happy cryo-EM'ing!
-If you want to dig deep into the SPHIRE pipeline then you are in the right place. This Wiki will provide you with information about the major programs within SPHIRE and how to use them. Of course, you will also find information about installation, additional utilities, frequently asked questions and known issues. In addition, you can find usage tutorials and SPHIRE's version history. Just follow the links in the sidebar. Happy cryo-EM'ing! +
-<WRAP clear/> +
-</WRAP>+
  
 ===== Short application info ===== ===== Short application info =====
  
-<WRAP group> +\\ **Projects** \\  \\ Main project settings, such as name, pixel, and particles sizes.|{{  :icons:icon_settings_64.png?nolink&64x64}}| 
- +| \\ **Cter** \\  \\ CTF estimation and graphical evaluation tool.|{{  :icons:icon_ctf_64.png?nolink&64x64}}| 
-<WRAP left 10%> +| \\ **Window** \\  \\ Particle picking and extraction.|{{  :icons:icon_window_few_64.png?nolink&64x64}}| 
-[[:pipeline:project:start|{{ icons:icon_settings_64.png?72}}]] +| \\ **ISAC** \\  \\ Reproducible class average calculation.|{{  :icons:icon_isac_plus_few_64.png?nolink&64x64}}| 
-</WRAP> +| \\ **Viper** \\  \\ Reproducible //ab initio// model calculation.|{{  :icons:icon_viper6_darkerlines_64.png?nolink&64x64}}| 
-=== Project === +| \\ **Meridien** \\  \\ Automatic high-resolution 3D refinement.|{{  :icons:icon_meridien_darkerline_64.png?nolink&64x64}}| 
-Main project settings, such as name, pixel, and particles sizes. +| \\ **Sort3D** \\  \\ Reproducible 3D clustering.|{{  :icons:icon_sort3d_64.png?nolink&64x64}}| 
-<WRAP clear /> +| \\ **Subtract** \\  \\ Signal subtraction.|{{  :icon_subtract_64.png?nolink&64x64}}| 
-\\ +| \\ **LocalRes** \\  \\ Real-space local resolution calculation.|{{  :icons:icon_localres_64.png?nolink&64x64}}| 
- +| \\ **Movie** \\  \\ Movie frame alignment with [[http://grigoriefflab.janelia.org/unblur|Unblur]] and drift evaluation tools.|{{  :icons:icon_movie_64.png?nolink&64x64}}| 
-<WRAP left 10%> +\\ **Utilities** \\   \\ Tools and scripts to make your life easier. \\ |{{  :icons:icon_utilities2_64.png?nolink&64x64}}|
-[[:pipeline:cter:start|{{ icons:icon_ctf_64.png?72}}]] +
-</WRAP> +
-=== Cter === +
-CTF estimation and graphical evaluation tool. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:window:start|{{ icons:icon_window_few_64.png?72}}]] +
-</WRAP> +
-=== Window === +
-Particle picking and extraction. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:isac:start|{{ icons:icon_isac_plus_few_64.png?72}}]] +
-</WRAP> +
-=== Isac === +
-Reproducible class average calculation. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:viper:start|{{ icons:icon_viper6_darkerlines_64.png?72}}]] +
-</WRAP> +
-=== Viper === +
-Reproducible //ab initio// model calculation. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:meridien:start|{{ icons:icon_meridien_darkerline_64.png?72}}]] +
-</WRAP> +
-=== Meridien === +
-Automatic high-resolution 3D refinement. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:sort3d:start|{{ icons:icon_sort3D_64.png?72}}]] +
-</WRAP> +
-=== Sort3D === +
-Reproducible 3D clustering. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:subtract:start|{{ :icon_subtract_64.png?72}}]] +
-</WRAP> +
-=== Subtract === +
-Signal subtraction. +
-<WRAP clear /> +
-\\ +
- +
-<WRAP left 10%> +
-[[:pipeline:localres:start|{{ icons:icon_localres_64.png?72}}]] +
-</WRAP> +
-=== LocalRes === +
-Real-space local resolution calculation. +
-<WRAP clear /> +
-\\+
  
-<WRAP left 10%> +|
-[[:pipeline:movie:start|{{ icons:icon_movie_64.png?72}}]] +
-</WRAP> +
-=== Movie (Optional) === +
-Movie frame alignment with [[http://grigoriefflab.janelia.org/unblur|Unblur]] and drift evaluation tools. +
-<WRAP clear /> +
-\\+
  
-<WRAP left 10%> 
-[[:pipeline:utilities:start|{{ icons:icon_utilities2_64.png?72}}]] 
-</WRAP> 
-=== Utilities === 
-Tools and scripts to make your life easier. 
-<WRAP clear /> 
-\\ 
  
-</WRAP>  
start.txt · Last modified: 2021/02/19 10:26 by twagner