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We have placed each individual software package in PReSTO under version control. Every PReSTO release come with a specific default (D) version installed for each individual software package. We can then test new versions of installed software, without disturbing the already installed software version. Prior to version control, every new install overwrite the previous installation.
The PReSTO menu is connected to the default (D) version of the latest release.
Sometimes researchers want to use the very latest version of an individual software package. The very latest version might already be installed, however not yet released due to testing and configuring of many packages that made up a PReSTO release. To see what versions are installed and available of each software package, please e.g. use module avail CCP4 or module –ignore-cache avail CCP4 to get a list of CCP4 versions installed.
Today in June 2024, structural biology softwares at NSC Tetralith defaults (D) into versions that correspond to PReSTO 10.0 release and we track features and limitations. The minor releases are not tracked at this page and the latest installs can be found using module –ignore-cache avail software for instance module –ignore-cache avail CryoSPARC for CryoSPARC.
PReSTO users can get a list of all software available in PReSTO 10.0 by
| **module -t –redirect avail | fgrep PReSTO-10.0** |
however we list it here as well.
| PReSTO release: | PReSTO-10.0 | PReSTO-9.0 |
|---|---|---|
| adxv | 1.9.15 | 1.9.15 |
| ALBULA | 4.1.3 | 4.1.3 |
| AlphaFold | 2.2.0 | 2.2.0 |
| APBS | 1.5 | 1.5 |
| ATSAS | 3.2.1 | 3.0.5 |
| arcimboldo_lite in CCP4 8.0 | CCP4 8.0.17 | CCP48.0.13 |
| autoPROC | 20240123 | 20230726 |
| bitshuffle | 0.5.1 | 0.5.1 |
| BUSTER | 20240123 | 20220726 |
| CCP4 v7.0 | 7.0.078 | 7.0.078 |
| CCP4 v8.0 | 8.0.017 | 8.0.013 |
| CCPN | 3.0.4 | 3.0.4 |
| Cheetah | 0.2.1 | 0.2.1 |
| Chimera | 1.17.3 | 1.17 |
| ChimeraX | 1.6.1 | 1.6.1 |
| cisTEM | 1.0.0 | 1.0.0 |
| CNS | 1.3 | 1.3 |
| CoordgenLibs | 3.0.1 | 3.0.1§ |
| crYOLO | 1.8.2 | 1.8.2§ |
| cryoDRGN | 2.3.0 | 2.3.0 |
| CryoSPARC | 4.4.1 | 3.3.2 |
| CrystFEL | 0.10.2 | 0.10.2 |
| ctffind (with and without CUDA) | 4.1.14 | 4.1.14 |
| CUDA 8 | 8.0.61 | 8.0.61 |
| CUDA 10 | 10.1.243 | 10.1.243 |
| CUDA 11 | 11.3.1 | 11.3.1 |
| cuDNN | 7.6.4.38 | 7.6.4.38§ |
| DIALS standalone | 3.18.0 | 3.16.0 |
| Durin | 2019v1 | 2019v1 |
| EMAN2 | 2.91 | 2.91 |
| fastDiffractionImageProcessing | 20200121 | 20200121 |
| foss | 2021a | 2021a |
| fosscuda | 2019b | 2019b§ |
| Gautomatch | 0.56 | 0.56 |
| GCC | 10.3.0 | 10.3.0 |
| GCCcore | 10.3.0 | 10.3.0 |
| gcccuda | 2019b | 2019b§ |
| GConf | 3.2.6 | 3.2.6§ |
| Gctf-VPP | 1.18 | 1.18 |
| Gctf | 1.06 | 1.06 |
| generate_XDS.INP | 1.19 | 1.17 |
| gompi | 2021a | 2021a |
| gompic | 2019b | 2019b§ |
| h5py | 3.2.1 | 3.2.1 |
| H5ToXds | 1.1.0 | 1.1.0 |
| HDF5 | 1.10.7 | 1.10.7 |
| hkl2map | 0.4.e-beta | 0.4.e-beta |
| iMosflm | 7.4.0 | 7.4.0 |
| LigPlotPlus | 2.2.8 | 2.2.8 |
| maeparser | 1.3.0 | 1.3.0§ |
| MariaDB | 10.4.13 | 10.4.13§ |
| MddNMR | 2.7 | 2.7 |
| Mesa | 19.1.7 | 19.1.7§ |
| MolProbity | 4.02-528 | 4.02-528 |
| MotionCor2 | 1.6.4 | 1.6.4 |
| msgpack-c | 4.0.0 | 4.0.0§ |
| NanoPeakCell | 0bce0c6 | 0bce0c6 |
| NCCL | 2.10.3 | 2.10.3 |
| NMRpipe | 11.1 | 11.1 |
| nXDS | 20240119 | 20230320 |
| O | 14.1 | 14.1§ |
| pdb2ins | 20180111 | 20180111 |
| Phenix | 1.21-5207 | 1.20.1-4487 |
| pipedream part of BUSTER | 1.4.1 | 1.4.0 |
| pocl | 1.4 | 1.4§ |
| POV-Ray | 3.7.0.7 | 3.7.0.7 |
| PRESTO-EM | 10.0 | 9.0 |
| PRESTO-NMR | 10.0 | 9.0 |
| PRESTO | 10.0 | 9.0 |
| protobuf | 3.10.0 | 3.10.0§ |
| pyFAI | 0.21.3 | 0.21.3 |
| PyMOL | 2.5.0 | 2.5.0 |
| PyRosetta | 4-342 | 4-342 |
| python-hostlist | 1.21 | 1.21§ |
| Relion-CPU | 4.0.0 | 4.0.0 |
| Relion-GPU | 4.0.0 | 4.0.0 |
| rhofit part of BUSTER | 1.2.8 | 1.2.8 |
| Rosetta in Phenix 1.21-5207 | 3.10 | 3.10 |
| Scipion | 3.0.12 | 3.0.12 |
| SHARP | 2.8.12 | 2.8.12 |
| SHELX in CCP4 v 8.0 | CCP4 10.0 | CCP4 8.0 |
| ShelXle | 1615 | 1554 |
| silx | 0.13.2 | 0.13.2§ |
| SPOT2PDB | 20190621 | 20190621 |
| TensorFlow | 1.15.5 | 1.15.5§ |
| tqdm | 4.41.4 | 4.41.4§ |
| USF Uppsala Software Factory | 20110630 | 20110630 |
| XDS-Viewer | 0.7 | 0.7 |
| XDS | 20230630 | 20230630 |
| XDS_from_H5.py | 0.3.0 | 0.3.0§ |
| XDSAPP3 | 3.1.9 | 3.1.9 |
| XDSCC12 | 20201209 | 20201209 |
| XDSGUI | 20230505 | 20230505 |
| XDSSTAT | 20210827 | 20210827 |
| XGANDALF | 20210730 | 20210730 |
| Xia2 in standalone DIALS | 3.18.0 | 3.16.0 |
| Xmipp | 3.23.03 | 3.23.03 |
| XSCALE_ISOCLUSTER | 20200727 | 20200727 |
§ Not available in PReSTO-10.0 but in earlier releases such as PReSTO-8.0
$ All HDF5 versions are 1.10.7, 1.12.1, and 1.12.1-ts
User Area
Guides, documentation and FAQ.
Applying for projects and login accounts.
National Supercomputer Centre
Linköping University
581 83 LINKÖPING
SWEDEN
Org.nr: 202100-3096
VAT.nr: SE202100309601
