Appion

h1. Upload Refinement

h2. How to upload a refinement that has been carried out in an external package, i.e. outside of Appion

# create a directory tree in the "recon" folder titled "Your_Refinement_Procedure/external_refinement_results", as for example: /ami/data17/appion/11jan11a/recon/external_package_test/external_package_results

# define a timestamp, e.g. "11jun03a" or "my_favorite_refinement_procedure_june03" or whatever you want.

# AT LEAST 2 files are needed per iteration per reference number for the refinement (the latter being the number of output models / references produced)

## 3D mrc file titled "recon_'timestamp'_it#_vol#.mrc (it# and vol# have 3 integers), as for example "recon_11jul18z_it001_vol001.mrc"

## particle data file titled "particle_data_'timestamp'_it#_vol#.txt" (it# and vol# have 3 integers), as for example "particle_data_11jul18z_it001_vol001.txt". This file MUST contain the following columns:

### particle number - *!!! PARTICLE NUMBERING STARTS WITH 1 !!!*

### phi Euler angle - rotation Euler angle around Z, in degrees

### theta Euler angle - rotation Euler angle around new Y, in degrees

### omega Euler angle - rotation Euler angle around new Z (in-plane rotation), in degrees

### shiftx - in pixels

### shifty - in pixels

### mirror - specify 1 if particle is mirrored, 0 otherwise. If mirrors are NOT handled in the package, and are represented by different Euler angles, leave as 0

### 3D reference # - 1, 2, 3, etc. Use 1 for single-model refinement case

### 2D class # - the number of the class to which the particle belongs. Leave as 0 if these are not defined

### quality factor - leave as 0 if not defined 

### kept particle - specifies whether or not the particle was discarded during the reconstruction routine. If it was KEPT, specify 1, if it was DISCARDED, specify 0. If all particles are kept, all should have a 1. 

### post Refine kept particle (optional) - in most cases just leave as 1 for all particles