Porting an EMAN1 refinement project to EMAN2

Note : This page is for those who hate to read, the tutorials provide a much better way of learning EMAN2. This will get you started if you just want to rapidly switch a project from EMAN1, though. Just remember if you find yourself asking 'but what does THAT mean' when you read this, you're reading the wrong page :^)

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.

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.

2. 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.

3. 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.

4. Now, expand the Single Particle Reconstruction item so you can see the detailed workflow under it.

5. 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. Pick only one of the following 3 sections in bold:

   • preferred option -> If you have the original micrographs/CCD frames, and EMAN1 style .box files :

     1. Select Filter Raw Data

     2. Press the Browse to Add button

     3. Browse to, and select your micrograph/CCD files, and click ok.

     4. 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.

     5. Under Particles, select Coordinate Import and Browse to Add again. Browse to and select your .box files, then press OK in both windows. Assuming your particle and box filenames match, everything should work well.

     6. You could actually go to the interactive particle picker and check/update the boxes at this point if you like, but we will just assume they are correct, and use Generate Output under Particles. Again, there are some options:

        • Box size is the most important one. In EMAN2, it is VERY important, if you want to obtain optimal results, to use a box size that is 1.5-2x the size of the maximum dimension of your particle. If you are dealing with a huge virus particle, you may need to skimp a bit on this, to avoid having a, say, 1500 box size, but some padding is essential for CTF correction to work well, and to avoid artifacts. See this list of good sizes to use. If you decide to change the box size later, it generally requires starting a new project from scratch, so consider this point very carefully.

        • You should select Write box image files, normalize.edgemean and bdb.

        • Only select invert here if you made a mistake at the earlier step, and your micrographs are still dark particles on a light background.

   • If you don't have those, but do have individual particle stack files without CTF correction for each frame :

     1. Double check to make sure your particle stacks have light particles on a darker background. If they have inverted contrast, you will need to invert them before proceeding. You can do this with e2proc2d.py <file> <file> --mult=-1 --inplace or any other method you like. Having this correct is CRITICAL to getting good results in EMAN2. Some of the algorithms require this.

     2. Select Particle Import under Particles, Browse to Add, and select all of your particle files. Press OK on both windows.

   • If you only have a start.hed file containing phase-flipped particles from EMAN1 :

     • Sorry, this section not complete yet

6. Now that your particles have been imported into the EMAN2 project, you can begin with CTF correction. It is important to note at this point that CTF correction in EMAN2 entails a lot more than just CTF correction. It also makes an SSNR evaluation for each micrograph, which is used to perform weighting and other tasks. So, even if you do not feel you need to do CTF correction (neg stain or phase plates for example), we STRONGLY encourage you to go through this process anyway. You are always free to disable the CTF amplitude correction at a later stage, but you will still be able to take advantage of the other computed image properties.