# Modules available

This page provides a list of the modules available on the cluster. The list may differ from the modules currently installed on the **Merlin 7** cluster.

!!! tip "Finding the right module"
    If you need a specific software package or version, use `module avail` or `module spider` to check which versions are available before loading the module.

To load a module, run: `module load [module_name]`

## Electron Microscopy

| Software         | Module name        | CPU/A100 nodes  | GH nodes               | Run type               |
| -------------    | ----------------   | :-------------: | :-------------------:  | ---------------------- | 
| CryoSPARC        | -                  | ✓               | ✓                      | Batch job              |
| RELION           | `relion`           | ✓               | ✓ (IMOD not available) | Interactive, Batch job |
| LipIDens         | `lipidens`         | ✓               | ✓                      | Interactive            |
| ModelAngelo      | `model_angelo`     | ✓               | ✓                      | Batch job              |
| BindCraft        | `BindCraft`[^1]    | ✓               | ✓                      | Batch job              |
| CryoDECO         | `cryodeco`         | ✓               | -                      | Batch job              |
| CryoRanker       | `cryo_ief`         | ✓               | -                      | Batch job              |
| Cryo-IEF         | `cryo_ief`         | ✓               | -                      | Batch job              |
| CryoSamba        | `cryosamba`[^2]    | ✓               | -                      | Interactive            |
| crYOLO           | `crYOLO`           | ✓               | -                      | Interactive, Batch job |
| CryoDRGN         | `cryodrgn`         | ✓               | -                      | Batch job              |
| pyEM             | `pyem`             | ✓               | -                      | Batch job              |
| Phenix           | `phenix`[^3]       | ✓               | -                      | Interactive            |
| MotionCor3       | `MotionCor3`       | ✓               | ✓                      | Batch job              |
| AreTomo3         | `AreTomo3`         | ✓               | -                      | Batch job              |
| AreTomo2         | `AreTomo2`         | ✓               | ✓                      | Batch job              |
| spIsoNet         | `spIsoNet`         | ✓               | -                      | Batch job              |
| IsoNet           | `IsoNet`           | ✓               | -                      | Interactive, Batch job |
| IsoNet2          | `IsoNet2`          | ✓               | -                      | Batch job              |
| Warp             | `warp`             | ✓               | -                      | Interactive            |
| ctffind4         | `ctffind4`         | ✓               | ✓                      | Batch job              |
| ResMap           | `ResMap`           | ✓               | ✓                      | Interactive, Batch job |
| pytom-match-pick | `pytom-match-pick` | ✓               | ✓                      | Batch job              |
| topaz            | `topaz`            | ✓               | ✓                      | Batch job              |

## Protein Structure Prediction and Design

| Software          | Module name                          | CPU/A100 nodes  | GH nodes              | Run type               |
| ----------------- | ------------------------------------ | :-------------: | :-------------------: | ---------------------- |
| AlphaFold 3       | `alphafold3`                         | ✓               | ✓                     | Batch job              |
| AlphaFold 2       | `alphafold`[^4]                      | ✓               | -                     | Batch job              |
| dl_binder_design  | dl_binder_design_module.sh [^5],[^6] | ✓               | -                     | Batch job              |
| ROCKET            | rocket_module.sh [^7]                | ✓               | -                     | Batch job              |
| GRASP-JAX         | GRASP_module.sh [^8]                 | ✓               | -                     | Batch job              |
| Rosetta           | `Rosetta`[^9]                        | ✓               | ✓                     | Batch job              |
| Germinal          | germinal_module.sh[^10]              | ✓               | -                     | Batch job              |
| Chai-1            | `chai-1`                             | ✓               | ✓                     | Batch job              |
| Boltz-2           | `boltz`                              | ✓               | ✓                     | Batch job              |
| BoltzDesign1      | BoltzDesign1_module.sh[^11]          | ✓               | -                     | Interactive, Batch job |
| RFdiffusion       | `RFdiffusion`                        | ✓               | -                     | Batch job              |
| ProteinMPNN       | `ProteinMPNN`                        | ✓               | -                     | Batch job              |
| prosculpt         | prosculpt_module.sh[^12]             | ✓               | -                     | Interactive, Batch job |
| ColabFold         | `colabfold`                          | ✓               | -                     | Batch job              |
| AF3x              | `af3x`                               | ✓               | -                     | Batch job              |

## Molecular and Volumetric Visualization

| Software          | Module name         | CPU/A100 nodes  | GH nodes              | Run type               |
| ----------------- | ------------------- | :-------------: | :-------------------: | ---------------------- | 
| ChimeraX          | `chimerax`          | ✓               | -                     | Interactive            |
| IMOD              | `IMOD`              | ✓               | -                     | Interactive, Batch job |
| MemBrain          | `membrain`          | ✓               | -                     | Interactive, Batch job |
| PyMOL             | `pymol`             | ✓               | -                     | Interactive            |
| napari            | `napari`            | ✓               | -                     | Interactive            |
| napari-boxmanager | `napari-boxmanager` | ✓               | -                     | Interactive            |
| napari-tomoslice  | `napari-tomoslice`  | ✓               | -                     | Interactive            |

## Molecular Dynamics

| Software      | Module name         | CPU/A100 nodes  | GH nodes              | Run type               |
| ------------- | ------------------- | :-------------: | :-------------------: | ---------------------- | 
| DNet          | dnet_module.sh[^13] | ✓               | -                     | Interactive, Batch job |
| NAMD          | `NAMD`              | ✓               | ✓                     | Batch job              |
| VMD           | `vmd`               | ✓               | -                     | Interactive            |
| GROMACS       | `gromacs`           | ✓               | ✓                     | Batch job              |
| Amber26       | `amber`             | ✓               | ✓                     | Batch job              |
| AmberTools26  | `ambertools`        | ✓               | -                     | Batch job              |
| PLUMED        | `plumed`            | ✓               | ✓                     | Batch job              |
| LAMMPS        | `lammps`            | ✓               | ✓                     | Batch job              |
| SevenNet      | `sevennet`          | ✓               | ✓                     | Batch job              |
| dssp          | `dssp`              | ✓               | ✓                     | Batch job              |

## Bioinformatics

| Software      | Module name      | CPU/A100 nodes  | GH nodes              | Run type               |
| ------------- | ---------------- | :-------------: | :-------------------: | ---------------------- | 
| FastQC        | `fastqc`         | ✓               | -                     | Batch job              |
| SRA Toolkit   | `sratoolkit`     | ✓               | -                     | Batch job              |
| Entrez Direct | `edirect`        | ✓               | -                     | Batch job              |
| Cell Ranger   | `cellranger`     | ✓               | -                     | Batch job              |
| kalign        | `kalign`         | ✓               | ✓                     | Batch job              |
| Refgenie      | `refgenie`       | ✓               | ✓                     | Interactive            |
| Nextflow      | `nextflow`       | ✓               | ✓                     | Interactive, Batch job |
| nf-core       | `nf-core`        | ✓               | ✓                     | Interactive, Batch job |
| hh-suite      | `hhsuite`        | ✓               | ✓                     | Batch job              |
| hmmer         | `hmmer`          | ✓               | ✓                     | Batch job              |
| SeqKit        | `seqkit`         | ✓               | -                     | Batch job              |

[^1]: `module use Alps_A100; module load BindCraft` (A100 GPU nodes)
[^2]: `source /data/project/cls/shared/software/cryosamba/dev_2025_11/cryosamba_module.sh load`
[^3]: `module use MX; module load phenix/phenix-1.20-4459`
[^4]: `module use MX; module load alphafold`
[^5]: `source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh proteinmpnn_binder_design`
[^6]: `source /data/project/cls/shared/software/dl_binder_design/1.0.0/dl_binder_design_module.sh af2_binder_design`
[^7]: `source /data/project/cls/shared/software/rocket/0.2.0/rocket_module.sh load`
[^8]: `source /data/project/cls/shared/software/GRASP-JAX/dev_2025_11/GRASP_module.sh load`
[^9]: `module use MX; module load Rosetta`
[^10]: `source /data/project/cls/shared/software/germinal/dev_2025_10/germinal/germinal_module.sh load`
[^11]: `source /data/project/cls/shared/software/BoltzDesign1/dev_2025_07/BoltzDesign1_module.sh load`
[^12]: `source /data/project/cls/shared/software/prosculpt/1.1.4/prosculpt_module.sh load`
[^13]: `source /data/project/cls/shared/software/DNet/dnet_module.sh load`