cryolo_filament_import_relion

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cryolo_filament_import_relion [2018/12/18 13:34]
shaikh
cryolo_filament_import_relion [2018/12/18 13:39]
shaikh
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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 |}} 
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 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, 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