cisTEM
cisTEM
cisTEM [1] is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. It was developed by Tim Grant, Alexis Rohou and Nikolaus Grigorieff and comprises a number of tools to process image data including movies, micrographs and stacks of single-particle images, implementing a complete “pipeline” of processing steps to obtain high-resolution single-particle reconstructions.
Installed Versions
All the available versions of cisTEM for use can be viewed by issuing the following commands. This applies for other applications as well.
module avail cistem
output:
----------------------------------------------- /usr/local/share/modulefiles --------
cistem/1.0.0
The default module can be loaded as:
module load cistem
The other versions of cisTEM can be loaded as:
module load cistem/<version>
Running cisTEM in HPC
Note: Since the movie/image in .mrc format can be in GigaBytes (GB) or TeraBytes (TB), the sample example here uses the temporary /scratch space as the working directory to run the job. The /scratch space is valid only for 14 days and provides 1TB of storage (see HPC Storage & Quota).
Create a directory (e.g. your caseID) at /scratch/pbsjobs/ and cd to it
mkdir /scratch/pbsjobs/<caseID>
cd /scratch/pbsjobs/<caseID>
Download the apoferritin test dataset (consists of bunch of movie files in .mrc format) from https://cistem.org/documentation#tab-1-1 [2] and transfer it to your working directory
or copy the exisitng apoferritin_data.tar.gz file from /usr/local/doc/CISTEM to current directory.
cp /usr/local/doc/CISTEM /apoferritin_data.tar.gz .
Untar the zipped file
tar -xzvf apoferritin_data.tar.gz
Request more than one processors up to 25 in a node monitoring the performance scale-up. In this example 8 processors, 10gb of RAM and 2 hours of time are requested. Please refer to HPC resource view for details. Using --exclusive flag, you can reserve the whole node (all CPUs and memory).
srun -c 8 --mem=10gb --time=02:00:00 --pty bash
Load cisTEM module
module load cistem
Execute:
cisTEM &
It will open the GUI. Follow the tutorials at:
Tutorial [3]: https://cistem.org/system/tdf/uploads/cisTEM_tutorial.pdf?file=1&type=cistem_details&id=7&force=
For better GUI experience, please follow the guide at HPC visual access.
Monitor the multiple CPUs being used using top command
top
output:
20395 <caseID> 20 0 549208 342004 3052 S 52.3 0.7 0:03.45 unblur
20391 <caseID> 20 0 550504 342024 3048 S 45.4 0.7 0:03.33 unblur
...
References:
[1] cisTEM Home
[3] cisTEM Tutorial