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cryolo_filament_import_relion [2018/12/18 13:34]
shaikh 		cryolo_filament_import_relion [2020/04/15 08:51]
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:
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 2. Start Relion 2. Start Relion
  
-3. We will start with 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 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 the running number is replaced by a *. Press //Run!// {{ ::01.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 |}}  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 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//. {{ ::03.png?500 |}}+5. Now we will extract the particles. Select the //Particle extraction// action. For 'micrograph STAR file', select the //micrographs.star// file (You can find it in your Import/job00X directory), and for //Input coordinates// select //coords_suffix.box//. {{ ::03.png?500 |}}
  
-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 |}}+6. Select the //Helix// tab, and set //Extract helical segments// to //Yes// and //Coordinates are start-end only// to //No//. 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

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