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| best results in EMAN2, and that is most easily accomplished in the workflow. | best results in EMAN2, and that is most easily accomplished in the workflow. It will take you all the way through a canonical reconstruction starting with data you've already processed in EMAN1 (or any other image processing package for that matter). This is written targeting primarily Linux/Mac users, but hopefully windows users will be able to follow along. |
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| We will call the directory where your eman1 data resides '/eman1' | For purposes of this tutorial will call the directory where your eman1 data resides 'eman1'. You should also make another directory where your EMAN2 project will reside. We will call this 'eman2', but you can use any name you like. 1. It is very important that you ''cd eman2'' before starting the EMAN2 GUI. Whatever directory you are in when you run e2workflow.py will become your project directory. 1. Run ''e2workflow.py''. Two GUI windows should appear. One will show the status of running background jobs. The other will contain a collapsible tree of workflow items. 1. In the workflow window, click on the ''Single Particle Reconstruction'' item. * Note that you are not expanding the list here, but clicking on the actual words. * This should pop up a window containing project parameters. * Fill in the first 4 parameters. Don't worry about the last 2. * Close the window. 1. Now, expand the ''Single Particle Reconstruction'' item so you can see the detailed workflow under it. 1. There are now 3 possibilities, for getting your data into EMAN2. You MUST reprocess the CTF in EMAN2, rather than use the already processed data from EMAN1 (unless you don't plan on doing any CTF correction), but on the bright side, this process is MUCH easier in EMAN2. So, the data we will import is the un phase-flipped data. It must also be completely unfiltered. Just the original, raw data. * If you have the original micrographs/CCD frames, and EMAN1 style ''.box'' files : 1. Select ''Filter Raw Data'' 1. Press the ''Browse to Add'' button 1. Browse to, and select your micrograph/CCD files, and click ok. 1. Select which options you need to use, then press ''OK'' * It is important to get ''Inversion'' right. The final particles MUST appear '''bold''' white on a darker background, so whether you check this box depends on whether you are using stain or in cryo, and how the data was digitized. You can double-click on one of the images in the list to display it an see if you need inversion. * ''Filter X-ray Pixels'' is important for CCD data, but not if you are using a phase-plate. * ''edgenorm, generate thumbnail'', and ''associate with project'' should all be checked * ''in-place processing'' should normally be unchecked. 1. Under ''Particles'', select ''Coordinate Import'' * If you don't have those, but do have individual particle stack files without CTF correction for each frame : * If you only have a ''start.hed'' file containing phase-flipped particles from EMAN1 : |
Porting an EMAN1 refinement project to EMAN2
A Quickstart Guide
This quickstart makes use of the workflow, as the goal here is presumably to get the best results in EMAN2, and that is most easily accomplished in the workflow. It will take you all the way through a canonical reconstruction starting with data you've already processed in EMAN1 (or any other image processing package for that matter). This is written targeting primarily Linux/Mac users, but hopefully windows users will be able to follow along.
For purposes of this tutorial will call the directory where your eman1 data resides 'eman1'. You should also make another directory where your EMAN2 project will reside. We will call this 'eman2', but you can use any name you like.
It is very important that you cd eman2 before starting the EMAN2 GUI. Whatever directory you are in when you run e2workflow.py will become your project directory.
Run e2workflow.py. Two GUI windows should appear. One will show the status of running background jobs. The other will contain a collapsible tree of workflow items.
In the workflow window, click on the Single Particle Reconstruction item.
- Note that you are not expanding the list here, but clicking on the actual words.
- This should pop up a window containing project parameters.
- Fill in the first 4 parameters. Don't worry about the last 2.
- Close the window.
Now, expand the Single Particle Reconstruction item so you can see the detailed workflow under it.
- There are now 3 possibilities, for getting your data into EMAN2. You MUST reprocess the CTF in EMAN2, rather than use the already processed data from EMAN1 (unless you don't plan on doing any CTF correction), but on the bright side, this process is MUCH easier in EMAN2. So, the data we will import is the un phase-flipped data. It must also be completely unfiltered. Just the original, raw data.
If you have the original micrographs/CCD frames, and EMAN1 style .box files :
Select Filter Raw Data
Press the Browse to Add button
- Browse to, and select your micrograph/CCD files, and click ok.
Select which options you need to use, then press OK
It is important to get Inversion right. The final particles MUST appear bold white on a darker background, so whether you check this box depends on whether you are using stain or in cryo, and how the data was digitized. You can double-click on one of the images in the list to display it an see if you need inversion.
Filter X-ray Pixels is important for CCD data, but not if you are using a phase-plate.
edgenorm, generate thumbnail, and associate with project should all be checked
in-place processing should normally be unchecked.
Under Particles, select Coordinate Import
- If you don't have those, but do have individual particle stack files without CTF correction for each frame :
If you only have a start.hed file containing phase-flipped particles from EMAN1 :