Table of Contents
Update packages
The tarballs linked to this page are for use with CCP4 updater (ccp4um) in off-line mode. Normally these are not needed: ccp4um integrated in ccp4i, ccp4i2 and ccp4cloud checks for new updates in the background, and, in active mode, downloads and installs them.
Follow instructions below if you do intend to use the CCP4 updater in off-line mode.
Linux, Mac OS X
1. Download and unzip:
2. Start Update Manager from the terminal as in this example:
ccp4um -d ~/Downloads/ccp4-9-macosx-x86_64Windows
1. Download and unzip:
2. Double-click on CCP4-Console icon on the Desktop
3. Start Update Manager from CCP4-Console as in the example below.
Example
The full path to downloaded and unzipped update directory:
C:\Users\Andrey\Downloads\ccp4-9-updates-win64The command to run on CCP4-Console:
ccp4um -d C:\Users\Andrey\Downloads\ccp4-9-updates-win64An issue with double occurrence of ccp4-9-updates-win64 in the folder path.
There are several ways of performing step (1). One of them is to download the zip-archive, right mouse click on the archive icon and select Extract All… from the menu. The Extract window opens with the default destination path ending with ccp4-9-updates-win64. With such a default, the path to update folder will have two occurrences of ccp4-9-updates-win64 in it, for example:
C:\Users\Andrey\Downloads\ccp4-9-updates-win64\ccp4-9-updates-win64Correct URI in (3) accordingly in such a case or move the internal folder to a more convenient location.
Known issues with Update Manager
-
Issue: CCP4 Cloud does not start on macOS Big Sur
Solution: apply CCP4 Update 010 or higher -
Issue: Screen Time (macOS Catalina or above) has been found to block the installation and updates of CCP4 in various ways. It may block all files from CCP4 websites while displaying a warning page, or it may block individual files and you will see CCP4 Setup Manager or Update Manager complain of a checksum mismatch.
Solution: we recommend switching Screen Time off completely during the CCP4 installation and update processes.
Reporting bugs
All bugs should be reported to ccp4@ccp4.ac.uk.
Update summaries
Update 9.0.001
Date: 16.07.24
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| crank2 | updated to version 2.0.346 | yes | yes | yes | yes |
| Moorhen | updated to version 0.9.3 | yes | yes | yes | yes |
| Coot | updated to version 0.9.8.95 | yes | yes | yes | - |
| Coot-1 | updated to version 1.1.08 | yes | yes | yes | - |
| WinCoot | updated to version 0.9.8.95 | - | - | - | yes |
| WinCoot-1 | updated to version 1.1.07 | - | - | - | yes |
| ccp4cloud | updated to version 1.7.022 | yes | yes | yes | yes |
Update 9.0.002
Date: 24.07.24
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| servalcat | fixes for strict NCS and metadata, version 0.4.77 | yes | yes | yes | yes |
| refmac | fixes for isses with ncs cif output | yes | yes | yes | yes |
| libccif | change in default warning message level | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.000 | yes | yes | yes | yes |
Update 9.0.003
Date: 13.09.24
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| ccp4i2 | version 2.20.2, fixes | yes | yes | yes | yes |
| coot | version 1.1.10 | yes | yes | yes | yes |
| mosflm | fix mosaicity calculation issues | yes | yes | yes | yes |
| jscofe | update to 1.8.001 | yes | yes | yes | yes |
| servalcat | update to 0.4.82 | yes | yes | yes | yes |
| arcimboldo | update | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.001 | yes | yes | yes | yes |
Update 9.0.004
Date: 18.10.24
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| ccp4cloud | update to version 1.8.002 | yes | yes | yes | yes |
| jligand | fixes for metals | yes | yes | yes | yes |
| follow changes in monomers in 9.0.002 | yes | yes | yes | yes | |
| simbad | update to 0.2.8.2 | yes | yes | yes | yes |
| gemmi | update to 0.6.7 | yes | yes | yes | yes |
| servalcat | update to 0.4.88 | yes | yes | yes | yes |
| dials | update to 3.20 | yes | yes | yes | yes |
| h5py | update to 3.9 to support dui2 | yes | yes | yes | yes |
| acedrg | bug fixes in bond order and charge routines | yes | yes | yes | yes |
| Using LIG instead of UNL for monomer names if users not provide one | yes | yes | yes | yes | |
| cootapi | update to 1.10 | yes | yes | yes | yes |
| iris | update to 0.3.0 | yes | yes | yes | yes |
| ccp4i2 | update | yes | yes | yes | yes |
| ccp4i | fix for imosflm launch | - | - | - | yes |
| mrbump | update to 2.3.0. mrparse search option | yes | yes | yes | yes |
| fix | - | - | - | yes |
Update 9.0.005
Date: 27.11.24
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| dials | update to 3.21.1 | yes | yes | yes | yes |
| xia2 | update to 3.21.1 | yes | yes | yes | yes |
| ccp4cloud | update to 1.8.003 | yes | yes | yes | yes |
| acedrg | fix for covalent links | yes | yes | yes | yes |
| modelcraft | update to 4.0.2 | yes | yes | yes | yes |
| morda | slurm queueing | yes | yes | yes | - |
| tortoize/pdb-redo | fix for pdb file reading | yes | yes | yes | yes |
Update 9.0.006
Date: 13.02.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| WinCoot-1 | updated to version 1.1.11 | - | - | - | yes |
| Coot-1 | updated to version 1.1.11 | yes | yes | yes | - |
| ccp4cloud | updated to version 1.8.005 | yes | yes | yes | yes |
| ccp4i2 | updated to version 2.1.0. | yes | yes | yes | yes |
| updated to version 2.1.1 | yes | yes | yes | yes | |
| updated to version 2.2.1 | yes | yes | yes | yes | |
| updated to version 2.2.2 | yes | yes | yes | - | |
| updated to version 2.2.3 | yes | yes | yes | yes | |
| cootapi | update to Release 1.1.11 | yes | yes | yes | yes |
| findmysquence | updated to version 1.0.12. | yes | yes | yes | yes |
| dui2 | updated to version 2024.12.17 | yes | yes | yes | yes |
| pairef | updated to version 1.4.2 | yes | yes | yes | yes |
| monomers | updated for metals | yes | yes | yes | yes |
| acedrg | fixes for Hs | yes | yes | yes | yes |
| gemmi | update to 0.7 | yes | yes | yes | yes |
| servalcat | update to 0.4.100 | yes | yes | yes | yes |
| modelcraft | update to 5.0.2 | yes | yes | yes | yes |
| slicendice | update to 0.1.2 | yes | yes | yes | yes |
| simbad | update to 0.2.8.5 | yes | yes | yes | yes |
Update 9.0.007
Date: 28.03.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| pisa | Incorporated changes from the PDBe/CCP4 "pisa-lite" project by Grisell Diaz Leines | yes | yes | yes | yes |
| mmdb2 | Extension of cif handling in MMDB2 to read/write modern mmcif files from the PDB by Grisell Diaz Leines, PDBe | yes | yes | yes | yes |
| ccp4srs | Bug fix | yes | yes | yes | yes |
| Coot | Updated to version 0.9.8.96 | yes | yes | yes | yes |
| Coot-1 | Updated to version 1.1.13 | yes | yes | yes | - |
| WinCoot-1 | Updated to version 1.1.13 | - | - | - | yes |
| cootapi | Updated to version 1.1.12. | yes | yes | yes | yes |
| dui2 | Updated to version v2025.1.12 | yes | yes | yes | yes |
| ccp4cloud | Updated to version 1.8.006 | yes | yes | yes | yes |
| morda | Fixes for slurm. | yes | yes | yes | yes |
| findmysequence | Updated to version 1.0.014 | yes | yes | yes | yes |
| pyrvapi | Added mmcif download. | yes | yes | yes | yes |
| hdf5plugin | Disabled OpenMP for hdf5plugin, providing considerably better performance for dials.find_spots and dials.integrate. | yes | yes | yes | yes |
| rabdam | Uodated to version 2.0.1: Introduces minor changes to make mmcif file parsing of unit cell parameters more robust | yes | yes | yes | yes |
| slicendice | Updated to version 0.1.3: change for EM usage | yes | yes | yes | yes |
Update 9.0.008
Date: 10.04.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| Coot-1 | updated to version 1.1.15 | yes | yes | yes | - |
| WinCoot-1 | updated to version 1.1.14 | - | - | - | yes |
| ccp4mg | recompiled libraries | yes | yes | yes | yes |
Update 9.0.009
Date: 27.05.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| ccp4cloud | updated to version 1.8.007 | yes | yes | yes | yes |
| phaser | updates for compatibility with the current version of cctbx | yes | yes | yes | yes |
| metalCoord | a new metal coordination analysis tool | yes | yes | yes | yes |
| servalcat | update to version 0.4.105 | yes | yes | yes | yes |
| gemmi | update to version 0.7.1 | yes | yes | yes | yes |
| pointless | update for gemmi 0.7.1 | yes | yes | yes | yes |
| doublehelix | update to version 5.6.3 | yes | yes | yes | yes |
| fixes a bug that may pop up with the new checkMySequence gui in CCP4 Cloud | yes | yes | yes | yes | |
| findmysequence | updated for the hmmer API at EBI | yes | yes | yes | yes |
| mrparse | updated to version 0.4.3 | yes | yes | yes | yes |
| parallel Phmmer support for searching AFDB on CCP4 servers | yes | yes | yes | yes | |
| mrbump | update for running Phmmer in parallel on CCP4 servers | yes | yes | yes | yes |
| simbad | update to version 0.2.8.7 | yes | yes | yes | yes |
| various bug fixes | yes | yes | yes | yes | |
| slicendice | updated to version 0.1.8 | yes | yes | yes | yes |
| dimple | updated | yes | yes | yes | yes |
| modelcraft | updated to version 5.0.3 | yes | yes | yes | yes |
| ccp4i2 | update to version 2.3.1 | yes | yes | yes | - |
| ModelCraft used by default in the DR/MR/MB pipeline | yes | yes | yes | yes | |
| added a Coot 1 task | yes | yes | yes | - | |
| added a MetalCoord task | yes | yes | yes | - | |
| observation type selection from CIF files in the import merged task | yes | yes | yes | yes | |
| changing Buccaneer to ModelCraft in the Phaser EP task | yes | yes | yes | yes | |
| increased maximum Coot files saved from 10 to 250 | yes | yes | yes | yes | |
| a few bug fixes | yes | yes | yes | yes | |
| update to version 2.2.5 | - | - | - | yes | |
| added an i2run script | - | - | - | yes | |
| updated to version 2.3.1 | - | - | - | yes | |
| dials | update email address | yes | yes | yes | yes |
| privateer | update to version MkV.I | yes | yes | yes | yes |
Update 9.0.010
Date: 21.06.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| ccp4cloud | updated to version 1.8.007 | yes | yes | yes | yes |
| fixed some issues with RNA import | yes | yes | yes | yes | |
| monomers library | updated | yes | yes | yes | yes |
| dui2 | updated to version 2025.5.28 | yes | yes | yes | yes |
| new feature: threshold mask for previews of spot finding algorithm | yes | yes | yes | yes | |
| pointless | 1.13.6 improved detection of centred lattices, automatic removal of extra reflections by default (see KEEPLATTICE and LATTICE options) | yes | yes | yes | yes |
| acedrg | updated to version 320 | yes | yes | yes | yes |
| metalcoord | updated to version 0.2.1 | yes | yes | yes | yes |
| findmysequence | updated to version 1.0.20 | yes | yes | yes | yes |
| ccp4i2 | updated to version 2.3.3 | yes | yes | yes | yes |
| avoid reimporting files with the same checksum | yes | yes | yes | yes | |
| fixed collections, iterable import | yes | yes | yes | yes | |
| fix for the Coot RSR Morph task | yes | yes | yes | yes |
Update 9.0.011
Date: 12.09.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| ccp4cloud | updated to version 1.8.008 | yes | yes | yes | yes |
| ccp4i2 | updated to version 2.4.0 | yes | yes | yes | yes |
| acedrg | bug fixes | yes | yes | yes | yes |
| monomers | monomers library updated | yes | yes | yes | yes |
| pointless | update to version 1.14.2 | yes | yes | yes | yes |
| refmac | bug fix in neutron refinement | yes | yes | yes | yes |
| iris | update to version 0.3.3 | yes | yes | yes | yes |
| Moorhen | updated to version 0.21.1 | yes | yes | yes | yes |
| WinCoot-1 | updated to version 1.1.18 | - | - | - | yes |
| Coot-1 | updated to version 1.1.18 | yes | yes | yes | - |
Update 9.0.012
Date: 12.12.25
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| ccp4i2 | Updated to version 2.4.3 | yes | yes | yes | yes |
| gemmi | update to version 0.7.3 | yes | yes | yes | yes |
| servalcat | update to version 0.4.126 | yes | yes | yes | yes |
| nanobind | update to version 2.7.0 | yes | yes | yes | yes |
| omegaconf | new dependency of servalcat, version 2.3.0 | yes | yes | yes | yes |
| libccp4 | fix in error handling when reading a corrupted mtz file | yes | yes | yes | yes |
| Moorhen | updated to version 0.22.3 | yes | yes | yes | yes |
| Coot-1 | updated to version 1.1.19 | yes | yes | yes | - |
| monomers | fix 180-degree ideal angles | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.010 | yes | yes | yes | yes |
| dui2 | updated to version v2025.9.24 | yes | yes | yes | yes |
| ccp4mg | now downloads the .cif version of PDB-REDO coordinate files, rather than .pdb | yes | yes | yes | yes |
| metalCoord | updated to version 0.2.5 | yes | yes | yes | yes |
| cootapi | updated to version 1.1.19 | yes | yes | yes | yes |
| pairef | updated to version 1.4.3 | yes | yes | yes | yes |
Update 9.0.013
Date: 20.01.26
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| metalcoord | update to version 0.2.7 | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.011 | yes | yes | yes | yes |
Update 9.0.014
Date: 20.02.26
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| metalCoord | update to version 0.2.11 | yes | yes | yes | yes |
| cad | change VRSET_MAGIC | yes | yes | yes | yes |
| dui2 | update to v2026.2.6 | yes | yes | yes | yes |
| fix on macos | yes | yes | - | - | |
| cootapi | fix python import | - | - | - | yes |
| add docstrings | yes | yes | yes | yes | |
| iris | update to v0.3.3 | - | - | - | yes |
| WinCoot-1 | updated to version 1.1.20 | - | - | - | yes |
| ccp4cloud | updated to version 1.8.012 | yes | yes | yes | yes |
| ccp4i2 | updated to version 2.5.2 | yes | yes | yes | yes |
| acedrg | updated to version 330 | yes | yes | yes | yes |
Update 9.0.015
Date: 16.04.26
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| gemmi | update to version 0.7.4 | yes | yes | yes | yes |
| servalcat | update to version 0.4.128 | yes | yes | yes | yes |
| dimple | update to version 0.7 | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.013 | yes | yes | yes | yes |
| monomers library | add TRP-MAN link and modifications | yes | yes | yes | yes |
| delete SS link | yes | yes | yes | yes | |
| p link: set phosphate bond angle sigmas to 1.5 | yes | yes | yes | yes | |
| metalcoord | updated to version 0.2.13 | yes | yes | yes | yes |
| cootapi | updated to version 1.1.20 | yes | yes | yes | yes |
| modelcraft | updated to version 6.1.0 | yes | yes | yes | yes |
| nucleofind | new program | yes | yes | yes | yes |
| version 1.3.2 | yes | yes | yes | yes | |
| Coot-1 | updated to version 1.1.20 | yes | yes | yes | - |
| ccp4i2 | updated to version 2.6.0 | yes | yes | yes | yes |
| New NucleoFind task for predicting locations of nucleic acid features in maps | yes | yes | yes | yes | |
| New AREAIMOL task for calculating solvent accessible surface area | yes | yes | yes | yes | |
| other fixes and improvements | yes | yes | yes | yes | |
| updated to version 2.6.1 | yes | yes | yes | yes | |
| dui2 | update to v2026.3.20 | yes | yes | yes | yes |
| pointless | update to version 1.15.2 | yes | yes | yes | yes |
| fix when reindexing merged files with anomalous | yes | yes | yes | yes | |
| aimless | update to version 0.8.3 | yes | yes | yes | yes |
| jligand | fix for standard monomers | yes | yes | yes | yes |
| relaxed requirements on covalent links | yes | yes | yes | yes | |
| lorestr | uses refmacat instead of refmac5 | yes | yes | yes | - |
| mrbump | updates for afdb version check | yes | yes | yes | yes |
| libcifpp | components.cif file updated | yes | yes | yes | - |
Update 9.0.016
Date: 02.07.26
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| servalcat | updated to version 0.4.142 | yes | yes | yes | yes |
| refmacat fixes | yes | yes | yes | yes | |
| gemmi | updated to version 0.7.5 | yes | yes | yes | yes |
| a new drg subcommand: aiming at reproducing acedrg -c | yes | yes | yes | yes | |
| gemmi-convert: added option --pysel=SEL | yes | yes | yes | yes | |
| bindings for FlatStructure | yes | yes | yes | yes | |
| acedrg | updated to version 331 | yes | yes | yes | yes |
| enabled non-geo_opt module | yes | yes | yes | yes | |
| findmysequence | updated to version 1.0.28 | yes | yes | yes | yes |
| updated handling of remote services errors and provides easier parsing of error msgs from log files | yes | yes | yes | yes | |
| metalcoord | updated to version 0.2.14 | yes | yes | yes | yes |
| NCS and SCALE cases handling added | yes | yes | yes | yes | |
| libcifpp | components.cif file updated | yes | yes | yes | - |
| Coot-1 | updated to version 1.2 | yes | yes | yes | - |
| WinCoot-1 | updated to version 1.2 | - | - | - | yes |
| Moorhen | updated to version 0.22.4 | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.014 | yes | yes | yes | yes |
| ccp4i2 | updated to version 2.6.3 | yes | yes | yes | yes |
Update 9.0.017
Date: 05.08.26
| Component | Description | macOS Intel | macOS ARM | Linux | MS Windows |
|---|---|---|---|---|---|
| gemmi | fix for mmCIF output | yes | yes | yes | yes |
| ccp4cloud | updated to version 1.8.015 | yes | yes | yes | yes |