This page is not intended as a substitute for the official CCP4 updates page. It only covers problems we found during installation and running of CCP4 within the context of our programs (SHARP/autoSHARP, BUSTER and autoPROC).

In the listings below, we give a timestamp (YYYYMMDD) to specify the date a specific issue was diagnosed and described. This might make it easier to check if it has been fixed or described on the official CCP4 site.

We always recommend to use the latest version of CCP4 our software supports (see release notes of our software for details). When installing CCP4, you want to keep the previous version(s) available before making a complete switch.

CCP4 6.5

  • the autoSHARP interface can fail with an error message like can't read "autoSHARP_cel1(2)": no such element in array or can't read "autoSHARP_cel1(1)": no such variable. The fix is to remove (or comment) lines 222-224 of file $CCP4/share/ccp4i/scripts/autoSHARP.script (as of CCP4 6.5.007). This fix is submitted to CCP4 for incorporation in an upcoming update release.
  • For using the latest CCP4i interface to autoSHARP, please update to CCP 6.5 (update 006). This includes support for an input partial model (initial MR solution or such) as part of heavy-atom detection, parameter refinement, phase improvement and density-modification.
  • AIMLESS versions prior to 0.5.4 created wrong records in SCALEPACK-formatted output files for incomplete anomalous data. Please keep your CCP4 6.5 installation up-to-date with the official update mechanism (6.5.004 at time of writing).

CCP4 6.4.0

Several issues are described on the known problems page.

CCP4 6.3.0

Several issues related to the build system - these are fixed as part of the build script below.

  • to use this version with our programs, you need to edit the files $BDG_home/machines/*/ccp4.setup, $autoPROC_home/machines/*/ccp4.setup and/or $SHARP_home//*/ccp4.setup and change not only the CCP4 assignement, but also:

CCP4 6.2.0

CCP4 6.2.0 was officially released on 22 July 2011. The complete packages for downloading can be found here.

Note 1: be aware that those packages might have changed at different times after that release without notice. So if you installed the precompiled binaries from CCP4, check that you still have the latest version of those!

Note 2: updates to the software are often given as patches or updated source code. It might therefore be easier to maintain a version of CCP4 compiled from source - which allows quick application of those patches (precompiled binaries are not always updated).

Note 3: a more technical listing is provided here.

Installation (20110801)

The script(s) coming with the automatic download tarball are using some non-standard sh-syntax, especially when creating the various setup files for sh-like shells (bash, ksh, dash, zsh). A suggested patch is

Compilation (20110803)

The 'configure' step sometimes hangs on OsX (Darwin or Darwin64) systems when running on a NFS filesystem:

checking for working non-fixed mmap... 

A simple workaround is the following patch to $CCP4/configure:

--- configure.orig      2011-05-05 16:07:55.000000000 +0100
+++ configure   2011-07-21 16:05:57.000000000 +0100
@@ -3206,6 +3206,9 @@
   if test "$system" = sunos64; then
     xopts="$xopts --enable-64-bit=yes"
+  case `uname` in
+    Darwin*) xopts="$xopts --disable-mmap";;
+  esac
   if test "$with_rxdispencer" = yes; then

This should only be necessary for NFS mounted filesystems: configuring on a local filesystem seems to be fine.

Setup files (20110801)

The file


contains a bug that could create confusing settings for LD_LIBRARY_PATH and/or DYLD_LIBRARY_PATH. The suggested patch is:

< if test "LD_LIBRARY_PATH"; then
> if test "$LD_LIBRARY_PATH"; then
< if test "DYLD_LIBRARY_PATH"; then
> if test "$DYLD_LIBRARY_PATH"; then

Update : it seems this has been fixed in the latest source tarball from

ccp4-6.2.0-core-src.tar.gz 	295109 KB 	01/08/11  17:20:00

CAD (20110801)

CAD is used to combine several MTZ files e.g. in autoSHARP. It has a parameter to describe the maximum number of files it can have as input (currently set to 9). However, this parameter also seems to be used to allocate arrays related to the maximum number of datasetgs the MTZ header can hold.

After running CAD several times to add data from another MTZ file, the list of datasets can easily become larger than 9. After that, memory corruption can lead to weird effects - e.g. autoSHARP suddenly 'loosing' columns from earlier datasets.

There is currently no fix available.

POINTLESS (20110801)

There is a serious bug in pointless versions 1.5.X. Updated precompield binaries are available either from CCP4 for Linux and OsX, or from Phil Evan's FTP site. These should be copied into $CBIN/pointless.

Warning: the CCP4 binaries have been compiled differently (statically instead of shared) and on a different Linux system (2.6.9 kernel instead of 2.2.5) than all other precompield binaries!

The updated binaries also fix a bug where POINTLESS would create corrupted MTZ files when converting XDS_ASCII.HKL files into MTZ format.

Updated sources can be found at the CCP4 or LMB site. You should be able to substitute your existing sources and binaries using something like:

% cd $CCP4/src
% wget
% tar -xzvf pointless.tgz
% make pointless
% make install

or (untested)

% cd $CCP4/src/pointless
% wget
% tar -xzvf pointless-1.6.2.tar.gz
% cd ../
% make pointless
% make install

POINTLESS (20110921)

Some additional problems have been encountered (memory corruption) that should be fixed in the latest version 1.6.5 from the LMB site.

PDB_EXTRACT (20110802)

The file


will not work correctly during configuration and installation on systems that use dash as /bin/sh: some lines are not standard sh-syntax. The fix:

% cp -pi src/harvest_app_/pdb_extract/etc/ src/harvest_app_/pdb_extract/etc/
% sed -e "s/\[\[/[/g" -e "s/]]/]/g" src/harvest_app_/pdb_extract/etc/ > src/harvest_app_/pdb_extract/etc/
% chmod +x src/harvest_app_/pdb_extract/etc/

Update : the problem has been described on the CCP4 problems page, including an updated file.

Compiling yourself

Compiling CCP4 yourself will give the most control and simplifies applying known patches and big fixes. But it can be a daunting task: see also

CCP4 6.3.0 (20120717)

Similar to the above:

  • download the file into an empty directory
  • make sure all required development tools are installed (gfortran, gcc, m4, flex, ... etc)
  • execute the script
    % chmod +x
    % ./

Tested on:

  • Linux (run cat /etc/*elease to determine distribution) with gcc/gfortran from distribution:
    • Ubuntu 10.04.4 LTS (64bit)
    • CentOS 5.8 (64bit)
    • SUSE Linux Enterprise Server10 (64bit)
    • openSUSE 11.4 (32bit)
    • openSUSE 11.4 (64bit)
    • openSUSE 12.1 (64bit)
  • OsX (run sw_vers to figure out which version you have):
    • 10.7.4 with GCC 4.7.1

CCP4 6.2.0 (20111018)

If you want to compile your own copy of CCP4 6.2.0 (as of 18th October 2011) on a Linux machine:

  • download the file into an empty directory
  • make sure all required development tools are installed (gfortran, gcc, m4, flex, ... etc)
  • execute the script
    % chmod +x
    % ./

This should compile and install most of the distributed programs and generate adequate setup scripts.