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cryolo_filament_import_relion [2018/12/18 11:57]
twagner
cryolo_filament_import_relion [2020/04/16 08:45]
twagner
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 ====== How to import crYOLO filament coordinates into Relion ====== ====== How to import crYOLO filament coordinates into Relion ======
 After the picking of filaments with crYOLO is done, one might want to import them into Relion. In this example I assume the following: After the picking of filaments with crYOLO is done, one might want to import them into Relion. In this example I assume the following:
-  * The folder ''micrographs'' containing your images. In this example the filenames are //Actin-ADP-BeFx_NUMBER.mrc//+  * The folder ''micrographs'' contains your images. In this example the filenames are //Actin-ADP-BeFx_NUMBER.mrc//
-  * Furthermore I assume you have a folder ''picked_boxes'' which contain your box files in helicon format. +  * The folder ''picked_boxes'' contains your box files in helicon format. 
  
 The following illustrates how you import the micrographs and box files into Relion: The following illustrates how you import the micrographs and box files into Relion:
  
-1. Move the box files from ''picked_boxes'' into the ''micrographs'' directory. The box-files and the micrographs should be in the same directory before importing them into Relion.+1. Move the box files from ''picked_boxes'' into the ''micrographs'' directory. The box files and the micrographs should be in the same directory before importing them into Relion.
  
 2. Start Relion 2. Start Relion
  
-3. We start with importing the box files. Select the import action. The //Node type// is //2D/3D particle coordinates//The //input files// pointing to your box files in the ''micrographs'' directory, where the running number is replaced by a *. Press //Run!// {{ ::01.png?500 |}} +3. We will start by importing the box files. Select the //Import// action. Under //Node type//, select //2D/3D particle coordinates//Under //input files//, point to your box files in the ''micrographs'' directory, where everything starting from the running number is replaced by a * (except the suffix (e.g. _autopick.box), if one exists). Press //Run!// {{ ::01.png?500 |}} 
  
-4. Now we import the corresponding mrc files. Select the //Import// action again. The //Node type// is //2D micrographs/tomogram//The //input files// pointing to your mrc files in the ''micrographs'' directory, where the running number is replaced by a *. Press //Run!// {{ ::02.png?500 |}} +4. Now we import the corresponding MRC files. Select the //Import// action again. Under //Node type//, enter //2D micrographs/tomogram//Under //input files//, point to your mrc files in the ''micrographs'' directory, where the running number is replaced by a *. Press //Run!// {{ ::02.png?500 |}} 
  
-5. Now we extract the particles. Select the //Particle extraction// action. Select the //micrographs.star// file for 'micrograph STAR file' and select the //coords_suffix.box// for //Input coordinates//{{ ::03.png?500 |}}+5. Now we will extract the particles. Select the //Particle extraction// action. For 'micrograph STAR file'select the //micrographs.star// file, and for //Input coordinates// select //coords_suffix.box//<note important> 
 +**micrographs.star**
  
-6. Select the //Helix// tab, set //Extract helical segments// to //Yes// and //Coordinates are start-end only// to //No//. Press //Run!//{{ ::03_b.png?500 |}}+ Use the micrographs.star file from your CTF estimation. It provides necessary information for further processing. 
 + 
 +Alternatively, you can set your pixelsize manually in the I/O tab of the particle extraction job. 
 +</note> {{ ::03.png?500 |}} 
 + 
 +6. Go to the extract tab and set your Particle box size. 
 + 
 +7. Select the //Helix// tab, and set //Extract helical segments// to //Yes// and //Coordinates are start-end only// to //No//. Also change your Tube diameter. Press //Run!//{{ ::03_b.png?500 |}}
  
 Now you have extracted your filament particles :-) Now you have extracted your filament particles :-)
cryolo_filament_import_relion.txt · Last modified: 2020/04/16 08:45 by twagner