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cryolo_filament_import_relion

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cryolo_filament_import_relion [2018/12/18 13:39]
shaikh 		cryolo_filament_import_relion [2020/04/16 08:45] (current)
twagner
Line 10: Line 10:
 2. Start Relion 2. Start Relion
  
-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 |}} +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. 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, and for //Input coordinates// select //coords_suffix.box//. <note important> 
 +**micrographs.star**
  
-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 |}}+ 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.1545136780.txt.gz · Last modified: 2018/12/18 13:39 by shaikh

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