cryolo_filament_import_relion

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cryolo_filament_import_relion [2018/12/18 11:57]
twagner
cryolo_filament_import_relion [2018/12/18 13:39]
shaikh
Line 1: Line 1:
 ====== 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 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. ​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//. {{ ::​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