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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 :-) | ||