Download CCP4 6.1.3: FAQ

• My operating system isn't listed
• My Linux executables are a mixture of those for my selected platform and Red Hat 8
• What are the available packages and their dependencies?
• Some packages don't have executables for my system
• How do I check my system for the dependencies?
• What are the licensing conditions for the packages?
• What do the filesizes refer to for each package?
• My download file is missing some components
• The pages complain that "No packages were selected" even though I selected at least one package
• While my download archive is being packed, I am asked to download archive2.php
• The install.sh script stops after creating ccp4.setup file
• I'd rather use FTP than the automated download pages
• I downloaded the latest version of CCP4, but it doesn't contain program X
• I do not know which installer to choose on windows
• When installing rampage i see this:

  cat: .../ccp4-6.0.2/./Makefile.in: No such file or directory

• I don't see my question addressed here

My operating system isn't listed

The download pages explicitly list only those platforms and operating systems for which prebuilt executables are available. If your operating system doesn't appear then you still have a number of options:

• For all platforms, you can download the source code by selecting the Generic option and selecting the packages that you wish to install.
• For Linux platforms, you can try downloading and installing the binaries for Red Hat 8 Linux, as these have generally been found to work on other Linux platforms.

My Linux executables are a mixture of those for my selected platform and Red Hat 8

For Linux platforms, where executables have not been built on the specific target platform we have provided the nearest compatible binaries, which are those for Red Hat 8.

What are the available packages and their dependencies?

The software has been divided into a number of separate downloads:

• CCP4 Program Suite: this is the minimal CCP4 suite which contains the core CCP4 libraries plus the standard programs and the user interface CCP4i. It includes iMosflm, the Clipper software, and MrBUMP.
  You will need the Tcl/Tk and associated packages in order to run CCP4i and iMosflm. You will need Python, Fasta and Clustalw to run MrBUMP.
• Phaser and CCTBX: Phaser is a powerful package for phasing macromolecular crystal structures with maximum likelihood techniques. Phaser also requires the CCTBX libraries, so the source code download for Phaser includes these libraries (downloading executables provides the phaser binary alone).
  You will need the Python scripting language if you wish to build Phaser and CCTBX from the source code.
• CHOOCH: performs calculation of anomalous scattering factors from X-ray fluorescence data.
• Balbes database: is an annotated database of structures designed for use in Molecular Replacement. The Balbes program itself is included in the main CCP4 package.
• CCP4mg: CCP4 molecular graphics package, with emphasis on structure analysis and publication-quality presentation graphics. CCP4mg is currently only available from us as precompiled binaries.
• Coot: provides model-building tools for molecular graphics. Coot is currently only available from us as precompiled binaries.

Some packages don't have executables for my system

Where possible we have provided executables built on the specific target platforms. Unfortunately for various reasons, we are unable to provide binaries for every package on every platform. If the option to download executables for a particular package is not presented for your system then this is not an error - it simply means that you will have to download the source code and build the package yourself.

How do I check my system for the dependencies?

For Unix and Linux systems:

• Tcl/Tk/BLT: type bltwish at the command prompt; if these packages are already installed on your path then a prompt will appear and you can find the versions by typing the following commands:

  % puts $tcl_version
  % puts $tk_version
  % puts $blt_version
      

• Python: type python at the command prompt; if Python is installed on your path then it will report its version when it starts, e.g.

  > python
  Python 2.3.4 (#1, Nov 30 2004, 12:32:43)
      

What are the licensing conditions for the packages?

Users of the software packages must hold a valid licence that is appropriate for their usage of that package.

The following packages are covered by the CCP4 licence, and users must agree to observe the conditions of the CCP4 licence when downloading, installing and using this software:

• CCP4 Program Suite: see the CCP4 Licence Page.
• CCP4mg: see the CCP4 Licence Page.

The following packages have a mixture of CCP4 and other licensing:

• Phaser and CCTBX: Phaser is covered by the CCP4 licence, see the CCP4 Licence Page. CCTBX is covered by its Open Source License which can be found via http://cctbx.sourceforge.net/

The following packages are not covered by the CCP4 licence conditions and instead have their own licensing. Users are not bound by the CCP4 licence when downloading, installing or using this software:

• CHOOCH: is covered by the GNU General Public License (GPL), see http://www.gnu.org/licenses/licenses.html
• Coot: is covered by the GNU General Public License (GPL), see http://www.gnu.org/licenses/licenses.html
• Tcl/Tk and BLT: Tcl/Tk is free for use by both commercial and non-commercial applications, its licensing conditions can be found here: http://www.tcl.tk/software/tcltk/license_terms.txt. BLT is covered by the BSD License which means it is also freely available for download and use, for more information on BSD see http://www.opensource.org/licenses/bsd-license.php
• Python: is covered by the Python Software License (PSF), see http://www.python.org/psf/license.html, and is freely available for (most) applications.
• Fasta: please see the Fasta COPYRIGHT statement.
• ClustalW: please see the ClustalW LICENSE statement.
• Graphviz: is covered by the Common Public License Version, see http://www.graphviz.org/License.php

What do the filesizes refer to for each package?

The filesizes given when choosing your packages refer to the estimated sizes of each package when unpacked on your system, i.e. the amount of diskspace that the package will occupy.

The total size given when checking the dependencies is thus an estimate of the total disk space that the files will occupy after download and unpacking. (Because some files are duplicated between different packages, in practice this is likely to be a slight overestimate.)

However as the files are compressed prior to downloading to your system, these sizes do not represent the size of the downloaded file, which is typically 50-70% smaller than the uncompressed version.

(Please note also that some browsers e.g. Firefox may also incorrectly report the size of the compressed file in their download managers!)

My download file is missing some components

The final download file for each combination of options is cached to speed things up for subsequent downloads. Sometimes the download file can get corrupted, and subsequent downloads will pick up the same corrupted file. The symptoms are usually a smaller-than-expected filesize, or missing components. If this happens, please contact us at ccp4@ccp4.ac.uk and we will remove the corrupted file.

The pages complain that "No packages were selected" even though I selected at least one package

Users of older browsers may experience problems with the package selection in the pages: even if one or more packages are selected for download at step 2 ("Choose Packages"), after clicking "Continue" step 3 ("Check dependencies") always gives the message:

This behaviour has been observed when using Netscape 4.76 running on a UNIX platform, as well other older browsers. The solution in this situation is to use an alternative route to download, either:

• Use a newer browser on a different system (it is possible to download archives for one system using another) and then transfer the downloaded files manually between machines, or
• Use the CCP4 FTP area - see below.

If you are using a relatively modern browser and are experiencing this problem then please contact us at ccp4@ccp4.ac.uk.

While my download archive is being packed, I am asked to download archive2.php

The downloads process generates a customised file for download, and this can occasionally take some time and result in a timeout. One symptom of this is a query on the download of "archive2.php". If this occurs, click Cancel and reload the page in the browser. It may be possible to adjust the timeout in your browser, but it may also be due the configuration of your proxy server (if you have one).

The install.sh script stops after creating ccp4.setup file

On some platforms the install.sh script has failed with the following output:

...
unpacking program packages...
######################
# CCP4 Installation  #
######################

Creating ccp4.setup file...
./install.sh:
CCP4_MASTER=/amd/srfs2/user/pxfs5/ccp4/ccpstaff/ccp4/pjx/SAFE/CCP4L: is
not an identifier

This appears to be a result of a general problem with the Bourne shell implementation on the platforms that exhibit this behaviour. There is currently no fix, instead you will have to perform the installation manually - see the CCP4 Installation Manual for how to do this.

I'd rather use FTP than the automated download pages

Users that for their own reasons prefer to use FTP rather than the automated pages, can still download the packages the various archives for the different packages via the CCP4 FTP site:

• ftp://ftp.ccp4.ac.uk/ccp4/current/README.html

The various packages are held in the appropriate subdirectories. Note that if you obtain the packages from the FTP then there is no automated install script and you will have to perform the installations manually - see the CCP4 Installation Manual for how to do this.

I downloaded the latest version of CCP4, but it doesn't contain program X

Because of the long preparation time for an official release, some very recent software doesn't make it into the official release. Pending the next official release, such software is made available on the CCP4 Prerelease Software page. We believe this software to be ready for use. However the level of support, in terms of binaries and installation, may be limited.

I do not know which installer to choose on windows

There are two different installers. There is the single user environment set up or the all user environment set up. If you are the only user of the machine then the first option is better. If there is more than one user of the machine that will be using CCP4 then choose the second option. This will install the CCP4 environment settings so that all user accounts can access them.

When downloading one of the update packages, you should use the same kind of installer as for the original installation. If you don't, you may experience problems, in which case try again with a different installer.

When installing rampage i see this:

cat: .../ccp4-6.0.2/./Makefile.in: No such file or directory

This is happening if you installed rampage on top of a binary installation only of ccp4. This is harmless message, you can ignore it.

I don't see my question addressed here

Please contact us at ccp4@ccp4.ac.uk.