Appion

Appion scripts interact with external packages in one of the two ways: Executing a shell command, or through python call. The name of the file in the call may not be the same as the standard installation as described by the package distributor.

If it is accessed from shell, you should either create soft link (preferred) or rename the file you downloaded (not best practice since you may get confused later. Test its accessibility from the environment you would run appion script.

For example, ctffin4 of whatever version would typically installed in /usr/local/bin. The executable file in there is called ctffind4.exe. You should do

cd /usr/local/bin
ln -s ctffind64.exe ctffind4

Next time, when you start a shell, try:

which ctffind4

It should be able to find the link and the actual executable file.ctffind64.exe

For files called through python, the file need to be in the environment variable PYTHONPATH You can test it in the appion environment with an import test.

python
python> import deProcessFrames

Program/module call alias name in Appion (myami-3.3, myami-beta branches, and trunk)¶

Package alias table¶

Those not mentioned here uses the original names in the call.

program package name	version	appion executable alias	Accessible
MotionCor2	1.0.2	motioncor2	shell
motioncorr v2.0 from Purdue	2.0	dosefgpu_driftcorr	shell
DE_process_frames.py	2.7.1	deProcessFrames.py	pythonpath
ctffind4	4.1.5	ctffind4	shell
Gctf	1.06	gctfCurrent	shell
ctftilt	1.5	ctftilt.exe	shell
FindEM	20/10/01	findem64.exe	shell
Gautomatch	0.53	gautomatch	shell
Spider	18.10	spider	shell
frealign	9.11	frealign_v9.exe and frealign_v9_mp.exe	shell
xmipp2 cl2d*	2.4	xmipp_mpi_class_averages	shell
xmipp3 cl2d*	3.1	xmipp_classify_CL2D	shell
EMAN1 proc2d	1.9	proc2d	shell

• default environment is xmipp2. All other xmipp functions wraps around xmipp2.
• xmipp3 conflict with xmipp2 is resolved in appion/bin/runXmipp3CL2D.py with a line of code
  

  csh -c 'modulecmd python load xmipp/3.1'
  

  
  Change it if desired.

Installation¶

External Package requirement of Appion scripts

Required for preprocessing pipeline up to stack making for Relion/CryoSparc¶

1. Configure .appion.cfg
2. Install External Packages
3. MotionCor2
4. Install Gctf
5. Install CtfFind. See Install Grigorieff lab software

Recommended for preprocessing pipelin particle picking¶

1. Compile FindEM

Required for 2D classification and other functions¶

1. Install EMAN (Only works for CentOS 6)
2. Install EMAN2
3. Install SPIDER
4. Install Xmipp (Xmipp2 Only works for CentOS 6)
5. Install UCSF Chimera
6. Install Ace2
7. Install Imod
8. Install Protomo2
9. Install EM Hole Finder

Older packages, install only if you still want to use them¶

1. MotionCorr (optional)
2. Install SIMPLE

Testing¶

1. Test Appion