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SPHIRE is a CryoEM software suite.


Loading the environment

SPHIRE is installed using Environment Modules.

To use it at CSSB/DESY call:

module load sphire/1.4

CSSB-specific Notes

Below are some CSSB specific path statements and tutorial add-ons.

CSSB/DESY cluster submission template

Use the maxwell cluster submission template with the full path or copy it to your project directory and modify it:

cp /beegfs/cssb/software/etc/em/sphire/1.4/ .
cp /beegfs/cssb/software/etc/em/sphire/1.4/ .

The GPU template should be used for crYOLO particle picking or Cinderella automatic 2D classification.

MPI settings

The amount of MPI processes set in the user interface will define how many nodes will be used.

So if you want to use 4 max-cssb nodes with each 48 cores you have to write 192 in the MPI processors field like in the settings above.

Most SPHIRE programs run fine up to 4 nodes.

Motion Correction

The unblur executable is at the location below. Please do not use the old unblur 1.0.2 for K3 movies.

Unblur cisTEM


Particle Coordinates

crYOLO training and prediction is recommended. More information on the config files and generic models are found on the crYOLO page. In SPHIRE use the following paths:


crYOLO needs a GPU to run. Please use the GPU template as mentioned above.

Automatic 2D classification

For Cinderella use the following path to the script and the generic model:


Continuing Jobs

When using the all partition the running jobs can be canceled before they are finished. Some SPHIRE programs like ISAC2 can autocontinue from previous steps by adding e.g. --restart=0 to the end of the ISAC2 commandline.

For specific numbers look in the Class2D folder for the highest main??? number and restart the job by adding e.g. --restart=17 (highest number -1) to the end of the ISAC2 commandline.

Known Issues

crYOLO Boxmanager

The user interface to start the crYOLO boxmanager sets by default the initial registered box size instead of the coordinate directory in the Advanced tab. If you follow the tutorial it should be an entry like: Coordinates/EMAN. The box size can be corrected later in the boxmanager's user interface.


The ISAC GPU version 2.3.2 was not compatible with this release at the time of testing and is therefore not installed with SPHIRE 1.4.

It can be used as follows:

module load sphire/1.3-mpi
module load cuda/10.1 'bdb:Particles#stack' 'Class2D_GPU' --radius=80 --CTF --gpu_devices=0
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