Table Of Contents

• emClarity binary
  • Description
  • Download links
• Compiling from source
• Matlab MCR
  • Description
  • Checking the install
• Third party
  • IMOD
  • Chimera

emClarity binary

Description

To make distribution of precompiled versions of emClarity easier, they are shared via google drive. The naming format of the binary and the run script are emClarity_1_X_X and emClarity_1_X_X_v19a. The latter specifies the required version of the MATLAB compiler runtim. This are in a zipped folder, in the bin directory, alongside all the same same tutorial, suggested parameters, and useful scripts in the docs folder. The source code is no longer included, but if you want to work on it, use the git repo.

Download links

• At the moment these are the same. Version 1.5.3 is now considered stable

Current stable version: vs 1.5.3.11

Working beta version: vs 1.5.3.11

Compiling from source

If you would like to compile emClarity from a particular commit, update your local repository to point to proper hash (I'm assuming if you are compiling, you know how to do this.)

Go into the folder emClarity/testScripts

Edit the compilation script, a sort of "make" if you will. The following can be whatever you'd like, but please set them to something other than what I use to prevent some confusion.

1. set the suffix for the binary | binaryOutName="1_0_0" --> binaryOutName="myCustomEMC"

2. set the suffix for the run script | scriptOutName=19a --> scriptOutName="myEMC"

3. set the path to the binary dependencies that emClarity requires for per-tilt ctf estimation, and in the future all IMOD based operations. (Please see the requirements page.)

You'll see the command called requires that matlab be on your path (and licensed obviously.)

>$ ./mCompile.sh emClarity.m

Matlab MCR

Description

The Mathworks(r) software is closed source, however, the do provide the Matlab Compiler Runtime.

Only MCR_2019a with CUDA 10 or newer is supported.

Matlab unpacks sloppy, so I tend to do the following

mkdir ${HOME}/matlab_install && cd ${HOME}/matlab_install
unzip /path/to/download/MATLAB_Runtime_R2020b_Update_3_glnxa64.zip
mkdir /path/to/local/install/matlab-2020b
./install -mode silent -agreeToLicense yes -destinationFolder /path/to/local/install/matlab-2019a

NOTE that you add the suggested LD_LIBRARY_PATH variables printed at the end of a successful MCR install directly to your emClarity_1_2_0_19a run script under the line "MCR_BASH." You also need to add the value for emClarity_ROOT as the directory where you installed.

Checking the install

After following the instructions provided by the Mathworks, you may test your install using the following

emClarity check

Third party

IMOD

The tomography community owes a large debt to the guys & gals over at UC boulder. We use a number of their programs, in particular for reconstruction of tomograms using local alignments and also for 3d visualization and editing of template matching results.

Imod just had a major new release, and I have not tested against this. Please install a local version of v 4.10.18 with CUDA for your appropriate system from [http://bio3d.colorado.edu/ftp/latestIMOD/ here]

Chimera

Not strictly essential, but recommended. This is used to perform a local alignment of the eve/odd half-sets prior to FSC calculation when the Fsc_withChimera flag is enabled in the parameter file. Other than this, I just use it for visualization. Tested agains version 11.1.2